title: IDH1 mutation defines methylation class and survival in human glioma

status: Public on Dec 20 2010

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary:
Astrocytoma, oligodendroglioma, oligoastrocytoma, and ependymoma are the main histologic subtypes of glioma. The molecular character of these subtypes has profound implications for understanding their causes and treatment. We describe the epigenetic landscape of these tumor types using novel DNA methylation profiling tools. There is a robust association of methylation profile with tumor histology and IDH1 mutation status. Furthermore, tumors with IDH1 mutation independently predict a tumor hypermethylator phenotype, histology, TP53 mutation status, patient age, and survival. Integrating tumor epigenetic and genetic alterations, this work provides a critical step toward better defining the somatic nature of glioma which will have  great potential to impact clinical approaches to disease.

This work provides an important step forward in classification of malignant brain tumors using DNA methylation profiling, integrating knowledge regarding IDH1 mutation in gliomas. The epigenetic homogeneity of the IDH1 mutant subclass despite histologic diversity implies that IDH1 mutation is a “driver” or functional determinant of a distinct DNA methylation phenotype, suggesting a novel role for an altered metabolic profile in the brain. This association occurs across histologic subtypes and demonstrates a clear relationship between genetic alteration and epigenetic profile.

overall_design: Fresh frozen tumor tissues were obtained from the University of California San Francisco (UCSF) Brain Tumor Research Center tissue bank with appropriate institutional review board approval. Tumors were diagnosed between 1990 and 2003.  Tumor samples were defined as secondary GBM if the patients had prior histological diagnosis of a low-grade glioma. Tumors had previously been reviewed by UCSF neuropathologists to assign histologic subtype and grade. Normal brain tissue samples were from cancer-free patients who underwent temporal lobe resection as treatment for epilepsy at UCSF.

middle: C

first: Karl

last: Kelsey

first: Johh

last: Wiencke


title: Binding targets of transcription factor E2-2 in human plasmacytoid dendritic cells

status: Public on Dec 21 2010

city: New York

first: Boris

last: Reizis

state: NY

department: Microbiology and Immunology

country: USA

institute: Columbia University Medical Center

type: Genome binding/occupancy profiling by array

summary: The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the “default” cDC fate, in part through direct regulation of lineage-specific gene expression programs.

overall_design: Cells of the human PDC lymphoma line CAL-1 (Maeda et al., Int J Hematol 2005) were crosslinked with formaldehyde, sonicated, and subjected to immunoprecipitation with anti-E2-2 mAb (Bain et al., Mol Cell Biol 1993) or mouse IgG control as described (Cisse et al., Cell 2008). After crosslink reversal, the isolated chromatin was amplified, labeled and hybridized to Human Promoter ChIP-on-chip Microarray Set (Agilent Technologies). Hybridized microarrays were scanned and analyzed using DNA Analytics software (Agilent Technologies).

first: Babacar

last: Cisse


title: Comparison of the transcriptional response to ethanol in laboratory and wild yeast strains

status: Public on Dec 17 2010

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

summary: An S288c-derived lab strain of Saccharomyces cerevisiae has lower ethanol resistance than either the vineyard strain M22 or the oak strain YPS163.  We performed a 60 minute time-course experiment in the presence of 5% ethanol and compared the transcriptional response to ethanol between strains.  We additionally analyzed the time-point of maximal response (30 min.) in wild type cells, YPS163 msn2D, and YPS163 hap1D cells.

overall_design: The genomic expression response to 5% ethanol stress was measured in 3 different strain backgrounds, and 2 different mutant backgrounds.  Basal gene expression was also compared in two non-lab strains to the S288c reference.  A single replicate was performed for the time-course experiment.  All of the single time-point experiments were performed using biological triplicates.

middle: A

first: Isaac

middle: M

last: Elkon

first: McSean

last: McGee

first: Alan

middle: J

last: Higbee

first: Audrey

middle: P

last: Gasch


title: Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence

status: Public on Dec 15 2010

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

department: Microbiology

institute: University of Iowa

summary: Vibrio parahaemolyticus senses surfaces via impeded rotation of its polar flagellum. We have exploited this surface-sensing mechanism to trick the organism into thinking it is on a surface when it is growing in liquid. This facilitated studies of global gene expression in a way that avoided many of the complications of surface-to-liquid comparisons, and illuminated ~ 70 genes that respond to surface sensing per se. Almost all are surface-induced (not repressed) and encode swarming motility proteins, virulence factors or sensory enzymes involved with chemoreception and c-di-GMP signalling. Follow-up studies were performed to place the surfaceresponsive genes in a regulatory hierarchy. Mapping the hierarchy revealed two surprises about LafK, a transcriptional activator that until now has been considered to be the master regulator for the lateral flagellar system. First, LafK controls a more diverse set of genes than previously appreciated. Second, some laf genes are not under LafK control, which means LafK is not the master regulator after all. Additional experiments motivated by the transcriptome analyses revealed that growth on a surface lowers c-di-GMP levels and enhances cytotoxicity. Thus, we demonstrate that V. parahaemolyticus can invoke a programme of gene control upon encountering a surface and the specific identities of the surfaceresponsive genes are pertinent to colonization and pathogenesis.

overall_design: The gene expression profiles of swarming and swimming cell types of Vibrio parahaemolyticus were compared using Affymetrix custom microarrays.

first: Cindy

last: Gode-Potratz

first: Ryan

last: Kustusch

first: Patrick

last: Breheny

first: David

middle: S

last: Weiss

middle: L


title: A critical role of microRNAs in human pulmonary arterial hypertension. miR-204: a novel therapeutic target (TaqMan qPCR)

status: Public on Dec 16 2010

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: Pulmonary arterial hypertension (PAH) is a vascular remodeling disease characterized by enhanced pulmonary artery smooth muscle cell (PASMC) proliferation and suppressed apoptosis. Downregulation of the BMPR2 gene along with activation of the transcription factor NFAT have been implicated in the maintenance of pro-proliferative and anti-apoptotic stages of cells. Since an increasing number of microRNAs have been implicated in the regulation of genes specifically important for cell proliferation and apoptosis, we hypothesized that microRNAs might be associated with these cellular features in the etiology of PAH. We demonstrate that downregulation of one such microRNA (miR-204) in human PAH-PASMC promotes the activation of an Src/STAT3/NFAT axis that increases PAH-PASMC proliferation and their resistance to apoptosis. Stimulation experiments using the pro-PAH factors (PDGF, endothelin-1 and angiotensin II) and time course analysis in experimental PAH show that STAT3 activation leads to miR-204 downregulation, thereby activating an Src-dependent positive feedback loop sustaining STAT3 and activating NFAT. More importantly, restoring miR-204 expression decreases proliferation and resistance to apoptosis in human and in an experimental PAH model. Taken together, our study uncovers a new STAT3-miR-204-Src/STAT3/NFAT axis that links the STAT3-dependent downregulation of BMPR2 with the NFAT-mediated pro-proliferative and anti-apoptotic phenotype observed in PAH. Our data point toward a novel potential strategy for treating patients with PAH.

overall_design: Comparative expression profiling of PAH versus healthy patients to evaluate the modulated genes in the disease. Following the demonstration of the downregulation of miR-204 in PAH we want to investigate the effect of the inhibition (using antagomir) of miR-204 expression in PASMC cells.

last: Courboulin

first: Roxane

last: Paulin

first: Nellie

last: Giguère

first: Nehmé

last: Saksouk

first: Jacques

last: Côté

first: Martin

last: Simard

first: Sébastien

last: Bonnet


title: Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish

city: Bethesda

first: Viviana

last: Gallardo

state: MD

address: 50 South Dr. Bldg 50. Room 5535

institute: NHGRI/NIH

summary: The posterior lateral line system in zebrafish involves cell migration, proliferation and differentiation into mechanosensory cells. During development, a group of cranial placodal cells delaminate and become a coherent, migratory primordium that traverses the length of the fish to form this sensory system. As they migrate, the primordium deposits groups of cells called neuromasts, the specialized organs that contain the mechanosensory hair cells. The lateral line hair cells of fish are related to inner ear hair cells; therefore the primordium provides both a model for studying collective directional cell migration and the differentiation of sensory cells from multipotent progenitor cells.   Through the combination of transgenic fish, Fluorescence Activated Cell Sorting and microarray analysis we identified a repertoire of key genes expressed in the migrating primordium and in differentiated neuromasts. We validated the specific expression in the primordium of a subset of the identified sequences by quantitative RT-PCR, and by in situ hybridization. We also show that interfering with the function of f11r and cd9b induces defects in its migratory behavior. Finally, pathway construction revealed functional relationships among the genes enriched in the migrating cell population. Our results demonstrate that this is a robust approach to globally analyze specific expression and we predict that many of the genes identified in this study will show critical functions in developmental and tumor progression process relating to posterior lateral line development.

overall_design: The experiment was performed in two developmental stages, 36 and 48 hours post-fertilization. Two-condition experiment, GFP- (negative control) and GFP+ cells. Two biological repeats by stage, each by quadruplicate including a dye swap.

middle: E

first: Jin

last: Liang

first: Martine

last: Behra

first: Abdel

last: Elkahloun

first: Eduardo

last: Villablanca

first: Vincenzo

last: Russo

first: Miguel

last: Allende

first: Shawn

last: Burgess


title: Molecular prediction of gastrulation stages with small extra-embryonic gene-set

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

summary: Axis specification in mouse is determined by a sequence of reciprocal interactions between embryonic and extra-embryonic tissues so that a few extra-embryonic genes appear as ‘patterning’ the embryo. Considering these interactions as essential, but lacking in most mammals the genetically driven approaches used in mouse and the corresponding patterning mutants, we examined whether a molecular signature originating from extra-embryonic tissues could relate to the developmental stage of the embryo proper and predict it. To this end, we have profiled bovine extra-embryonic tissues at peri-implantation stages, when gastrulation and early neurulation occur, and analysed the subsequent expression profiles through the use of predictive methods as previously reported for tumour classification. A set of six genes (CALM1, CPA3, CITED1, DLD, HNRNPDL, and TGFB3), half of which had not been previously associated with any extra-embryonic feature, appeared significantly discriminative and mainly dependent on embryonic tissues for its faithful expression. The predictive value of this set of genes for gastrulation and early neurulation stages, as assessed on naive samples, was remarkably high (93%). In silico connected to the bovine orthologues of the mouse patterning genes, this gene set is proposed as a new trait for embryo staging. As such, this will allow saving the bovine embryo proper for molecular or cellular studies. To us, it offers as well new perspectives for developmental phenotyping and modelling of embryonic/extra-embryonic co-differentiation.

overall_design: 20 samples  - Amplified material from each embryo (stage 2, stage3, stage4, stage5+) was indirectly labelled using "random" hexamers. One independent target per embryo was generated and hybridised onto one array. 5 measurements per embryonic stage were generated.

first: Severine

last: Degrelle

first: Kim-Anh

last: Le Cao

first: Christele

last: Robert-Granie


title: Host intelligence in response to bacteriophage c2 infection in Lactococcus lactis IL1403

city: Fermoy

last: Fallico

address: Moorepark

country: Ireland

institute: Teagasc Food Research Centre

summary: Bacteriophage infection of Lactococcus lactis strains used in the manufacture of fermented milk products is a major threat for the dairy industry. A greater understanding of the global molecular response of the bacterial host following phage infection has the potential to identify new targets for the design of phage control measures for biotechnological processes. In this study, we have used whole-genome oligonucleotide microarrays to gain insights into the genomic intelligence driving the instinctive response of L. lactis subsp. lactis IL1403 to the onset of a challenge with the lytic prolate-headed phage c2. Following phage adsorption, the bacterium differentially regulated the expression of 61 genes belonging to 14 functional categories, and mostly to cell envelope (12 genes), regulatory functions (11 genes), and carbohydrate metabolism (7 genes). The nature of the differentially regulated genes suggests the orchestration of a complex response involving induction of cell envelope stress proteins, D-alanylation of cell-wall lipoteichoic acids (LTAs), restoration of the proton motive force (PMF), and energy conservation. Increased D-alanylation of LTAs would act as an adsorption blocking mechanism, which we speculate may allow the survival of a small percent of the cell population when facing more realistic in vivo low titer-phage attacks. The modification of LTAs decoration in response to phage c2 adsorption also suggests these cell wall structures as possible primary receptors for this phage. Restoration of a physiological PMF is achieved by regulating the expression of genes affecting the two main components of the PMF, and serves to reverse a drastic depolarization of the host membrane caused by phage adsorption. Down-regulation of energy-consuming metabolic activities and a switch to anaerobic respiration helps the bacterium to save energy in order to sustain the PMF and the overall response to phage. We finally propose that the overall transcriptional response of L. lactis IL1403 to the phage stimuli is orchestrated by the concerted action of Phage Shock Proteins and of the bivalent transcriptional regulator SpxB following activation by the two-component system CesSR. To our knowledge, this represents the first detailed description in L. lactis, and probably in Gram-positive bacteria, of the molecular mechanisms involved in the host response to the membrane perturbation mediated by phage adsorption.

sample_organism:
Lactococcus lactis
Ceduovirus c2

platform_organism:
Ceduovirus c2
Lactococcus lactis subsp. lactis Il1403

overall_design: Two-condition experiment: IL1403 vs. Bacteriophage c2-infected IL1403 cells. Biological replicates: 2 controls, 2 infected, independently grown and harvested. Two technical replicates per array.

first: Gerald

middle: F

last: Fitzgerald

first: Olivia

last: McAuliffe

first: R

last: Ross


title: Helicobacter pylori induce miR-155 in T cells in a cAMP-Foxp3 dependant manner

status: Public on Dec 22 2010

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: The human pathogen Helicobacter pylori (Hp) colonizes the gastric epithelium as a unique niche in the stomach. Infections commonly occur in childhood and persist lifelong, leading in some cases to adenocarcinoma and MALT lymphoma. Several studies define mammalian microRNAs as key regulators of the immune system and of carcinogenesis processes. Here, we show Hp infection induces miR-155 expression in epithelial and hematopoietic cells in vitro and in vivo. This induction is mediated by at least two main bacterial virulence factors, the vacuolating toxin (VacA) and the gamma-glutamyl transpeptidase (GGT) in an LPS independent manner. Using adenylate cyclases agonists and inhibitor, we demonstrated that the miR-155 microRNA regulatory cascade in Hp infection involves the second messenger cyclic adenosine monophosphate (cAMP). Furthermore, the study showed that a knock-down of the Foxp3 transcription factor in T cells abolishes miR-155 expression. Together, these findings are the first demonstration of a direct interconnection between the regulatory T cell development factor Foxp3 and a microRNA. This study supports the link between Hp infection, regulation of cellular immunity, inflammation and cancer development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: A color-swap dye reversal experimental setting was applied. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A two-fold change expression cut off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.01), robust and reproducible.

first: Lina

last: Fassi Fehri

first: Manuel

last: Koch

first: Thomas

last: Meyer


title: Genome-wide analysis of alternative splicing in Caenorhabditis elegans

status: Public on Dec 14 2010

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

summary: Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provides the most comprehensive set of annotated splice variants in C. elegans to date, and is therefore expected to faciliate focused, high resolution in vivo functional assays of AS function.

overall_design:
Alternative splicing events were identified from alignments of C. elegans mRNA/EST sequences (UniGene Build #26) to C. elegans genomic sequence (NCBI timestamp: Sept. 25, 2006), essentially as previously described (Pan et al. 2005; Pan et al. 2004). In total, 499 cassette type AS events were identified. For each AS event, 3 exon probes and 3 exon junction probes were designed to profile the AS event on the microarray, essentially as previously described (Pan et al. 2004).

This submission represents the expression microarray component of the study.

first: John

last: Calarco

first: Arun

middle: K

last: Ramani

first: Sepand

last: Mavandadi

first: Ying

last: Wang

first: Andrew

last: Nelson

first: Leo

last: Lee

first: Quaid

last: Morris

first: Benjamin

last: Blencowe

first: Mei

last: Zhen

middle: G

last: Fraser


title: Effects of the Fnr homologue AadR on global gene expression

status: Public on Dec 13 2010

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

summary: In order to define the AadR regulon we did transcriptome analysis of an aadR in frame-deletion mutant and compared to that of wild type. We found that AadR positively modulated expression of 43 genes, most of which are involved in degradation of aromatic acids under anaerobic conditions. It also activated expression of four genes encoding for unknown proteins and a possible DNA-binding stress protein. Furthermore, AadR repressed the expression of 100 genes, including fixK and many genes controlled by FixK, mainly those involved in a microaerobic lifestyle

overall_design: R. palustris strains were grown in defined medium anaerobically in light (photosynthetically) in sealed tubes with nitrogen gas in the headspace. Succinate and p-coumarate were provided as carbon sources.

first: Federico

last: Rey

first: Caroline

last: Harwood


title: Corneal epithelial cells

status: Public on Dec 11 2010

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Dr. Panjwani's laboratory is focusing on the mechanism by which galectins-3 and 7 mediate corneal epithelial cell migration.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We are currently performing studies to: (i) identify and characterize the corneal epithelial cell surface and extracellular matrix (ECM) molecules which serve as counterreceptors of galectin-3 and -7, to establish whether the lectins modulate corneal epithelial cell migration by binding to well known integrins, growth factor receptors, and/or ECM molecules and (ii) determine whether galectin-3 mediates corneal epithelial cell migration indirectly by modulating the expression of key adhesion and/or signal transduction molecules by using small interfering RNA, cDNA microarrays and glycogene arrays.
We have prepared three independent preparations of total RNA of corneal epithelial cells from WT mice (total six samples) for analysis of glycogene expression. Samples are Normal Cornea (Left eye) and Laser ablation + 16-18 hours healing (right eye)

first: Noorjahan

last: Panjwani


title: Gene expression responses of mouse neural cells to heparin-binding growth factors

summary:
The general area of research interests of my lab is the glycobiology of HSPGs in cell-cell/cell-matrix interactions and growth factor signalling.
Heparan sulfate binding proteins in neural development and differentiation. We used the Glyco-gene Chips to study the gene expression responses of mouse neural cells to heparin-binding growth factors. The experimental systems studied is in vivo (developing mouse brain). The goal is to examine the global responses of neural cells to particular growth factors during differentiation in terms of effects on HS biosynthetic enzymes and proteoglycan core proteins, as well as growth factors and their receptors.

overall_design: Analysis of A) P1 mouse brain wild type for Heparan sulfate 2-O sulfotransferase (HS2ST) and B) heterozygous for Heparan sulfate 2-O sulfotransferase (HS2ST) loss of function mutation.

first: Jeremy

last: Turnbull


title: Glycosylation change in mouse CD8 T cells during development

summary: Dr. Jameson's research focus is on development and regulation of lymphocytes, especially T cells. Recent work has suggested that differential glycosylation effects the sensitivity of the T cell receptors and its coreceptors, suggesting that regulation of glycosylation may be a critical element in controlling T cell development, survival and functional activity.

overall_design:
Determination of how glycosylation enzymes/substrates change in gene expression during development of mouse CD8 T cells. Highly purified pre-selection CD4+8+ thymocytes (using transgenic/knockout mice in our colony) are compared to mature CD8 T cells from the lymph node. The goal is to build on data suggesting that this developmental step involves regulated expression of sialyltransferases (and/or neuraminidases).
Highly purified pre-selection CD4+8+ thymocytes (using transgenic/knockout mice in our colony) are compared to mature CD8 T cells from the lymph node. Pre-selection  CD4+8+ (DP) thymocytes were sorted from TCRa-/- thymi.  Post-selection (post-positive selection) DP thymocytes came from an OT-I TCR transgenic mouse.  Naïve (CD44lo) CD8 T cells from  lymph node of OT-I mice were used as naïve CD8 T cells. For activated cells,  naïve OT-I T cells were activated for 48 hours in vitro with cognate antigen (SIINFEKL peptide/Kb) (displayed on cell sized latex beads) in the presence of IL-2 and IL-12.


title: H3K9K14ac ChIP-chip in lung cancer cells treated with histone deacetylase inhibitor

city: Tainan

first: Yi-Ching

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

type: Genome binding/occupancy profiling by genome tiling array

summary: Lung cancer is the leading cause of cancer mortality worldwide, yet the therapeutic strategy for advanced non-small cell lung cancer (NSCLC) is limitedly effective. In addition, validated histone deacetylase (HDAC) inhibitors for the treatment of solid tumors remain to be developed. Here, we propose a novel HDAC inhibitor, OSU-HDAC-44, as a chemotherapeutic drug for NSCLC. OSU-HDAC-44 was a pan-HDAC inhibitor and exhibits 3-4 times more effectiveness than suberoylanilide hydroxamic acid (SAHA) in suppressing cell viability in various NSCLC cell lines. Upon OSU-HDAC-44 treatment, mitosis and cytokinesis were inhibited and subsequently led to mitochondria-mediated apoptosis. The cytokinesis inhibition resulted from OSU-HDAC-44-mediated degradation of mitosis and cytokinesis regulators Auroroa B and survivin. The deregulation of F-actin dynamics induced by OSU-HDAC-44 was associated with reduction in RhoA activity resulting from srGAP1 induction. Chromatin-immunoprecipitation-on-chip analysis revealed that OSU-HDAC-44 induced chromatin loosening and facilitated transcription of genes involved in crucial signaling pathways such as apoptosis, axon guidance and protein ubiquitination. Finally, OSU-HDAC-44 efficiently inhibited A549 xenograft tumor growth and induced acetylation of histone and non-histone proteins and apoptosis in vivo. Collectively, our data provide compelling evidence that OSU-HDAC-44 is a potent HDAC targeted inhibitor and can be tested for NSCLC chemotherapy.

overall_design: ChIP-chip analysis for H3K9K14ac in A549, H1299 and CL1-1 lung cancer cells treated with 2.5 uM histone deacetylase inhibitor, OSU-HDAC-44, for 2 hours.

first: Yen-An

last: Tang

first: Wei-Ling

last: Wen

first: Jer-Wei

last: Chang

first: Tzi-Tang

last: Wei

first: Yi-Hung

last: Tan

first: Chien-Tien

last: Chen

first: Ching-Shih


title: The composition and origins of intravarietal genomic heterogeneity in soybean

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

type: Genome variation profiling by genome tiling array

summary: Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species.  Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists.  There is even evidence for heritable phenotypic variation among individuals within some varieties.  ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’  To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals.  Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci.  In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes.  Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity.  Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals.  Collectively, these findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process.  We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intravarietal genetic heterogeneity may be much greater than previously assumed.  This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are utilizing or working towards developing a reference genome sequence.

overall_design: Soybean variety Williams 82 (Wm82) was derived from a Williams x Kingwa BC6F3 population.  CGH was performed to detect regions of Kingwa genomic introgression in Wm82; Williams was hybridized as a common reference against Kingwa and four different Wm82 individuals.  Two different Wm82 individuals (SGC and ISU) were also hybridized with one another.  The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.

first: William

last: Haun

first: Carroll

last: Vance


title: Genes regulated by HoxA3 in endothelial and hematopoietic progenitors

city: Minneapolis

first: Michael

last: Kyba

address: 312 Church St. SE

summary: We used a murine ES cell line in which HoxA3 expression is under control of a tetracycline-responsive element and differentiated these cells as embryoid bodies (EBs). Endothelial (Flk-1 VE-cadherin double positive, FV) and hematopoieitc progenitors (c-Kit CD41 double positive, K41) were isolated from differentiated EBs that had been induced for 6 hours by doxycycline (Dox) treatment.

overall_design: Here we show genes regulated upon HoxA3 upregulation (6 hours doxycycline treatment) in hematopoietic and endothelial progenitors.

first: Michelina

last: Iacovino


title: Eighteen hours monoclonal antibody C7 exposure

city: San Sebastian

first: Iñigo

last: Fernandez de Larrinoa

state: Guipuzcoa

address: Pº Manuel de Lardizabal #3

department: Química Aplicada

country: Spain

institute: Universidad del País Vasco (UPV/EHU)

summary: We have developed a monoclonal antibody (mAb) C7 that reacts with Als3p and enolase present in Candida albicans cell wall and exerts three anti-Candida activities: candidacidal activity and inhibition of both adhesion and filamentation. To investigate the mode of action of mAb C7 on fungal viability, we examined changes in the genome-wide gene expression profile of C. albicans grown in presence of a subinhibitory concentration of mAb C7 (12.5 µg/ml) by using microarrays. A total of 49 genes were found to be differentially expressed upon treatment with mAb C7. Of these, 28 were found to be up-regulated and 21 down-regulated. The categories of up-regulated genes with the largest number of variations were those involved in iron uptake or related to iron homeostasis (42.86%), while the energy-related group accounted for 38.10% of the down-regulated genes (8/21). Results were validated by real time PCR. Since these effects resembled those found under iron-limited conditions, the activity of mAb C7 on C. albicans mutants with deletions in key genes implicated in the three iron acquisition systems described in this yeast was also assessed. Only mutants lacking TPK1  gene, and TPK2 to a lesser extent were less sensitive to the candidacidal effect of mAb C7. FeCl3 or hemin at concentrations ≥ 7.8µM reversed the candidacidal effect of mAb C7 on C. albicans, on a concentration dependent manner. The results presented in this study provide evidence that the candidacidal effect of mAb C7 is related to the blockage of the reductive iron uptake pathway of C. albicans.

overall_design: A saturated culture of C. albicans grown overnight was diluted to an optical density at 600 nm of approximately 0.1 and divided in two aliquots. One of them was used untreated as control and the second one was treated with a subinhibitory concentration (12.5 µg/ml) of monoclonal antibody C7 . Both cultures were incubated for 18 h at 37ºC before harvesting cells. Antibody added and control samples were obtained each time. The experiment was repeated once. Dye-swap technique was used for hybridization and four arrays were analyzed to compare the expresion of over six thousands genes in response to antibody C7.

first: Sonia

last: Brena

first: Jonathan

last: Cabezas-Olcoz

last: Moragues

first: Angel

last: Dominguez

first: Guillermo

last: Quindós

first: Jose

last: Pontón


title: Identification of new markers of cutaneous melanoma invasion

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

summary:
T1C3 is a clonal cell line from a human melanoma tumor, expressing PNA lectin, and characterized by a high capacity of dermal invasion.
IC8 is a clonal cell line from a human melanoma tumor, negative for PNA lectin, and non-invasive.
To identify new gene markers involved in the mechanisms of early invasion, oligonuclotide microarrays were used to assess transcriptional chnages between the two cell lines.

overall_design: Dye-swap hybridization were performed. Slides were scanned with a Genepix 4000 microarray scanner (Axon Instruments, Molecular devices, Sunnyvale, CA). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained by using Genepix Pro 4.0 software (Axon Instruments) and were saved as a result file.

first: Odile

last: Berthier

first: Manale

last: El Kharbili

first: Léa

last: Casu

first: Xavier

last: Gidrol

first: Franck

last: Amiot


title: Pancreatic tumor cell lines

first: Steven

last: Head

summary:
Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids.
RNA samples from two human pancreatic cell lines. The relevance of the variable expression levels of isoforms belonging to the polypeptide GalNAc-transferase gene-family is still a puzzle to us. The polypeptide GalNAc-transferase gene family is estimated to contain 24 gene-members all participating in the initiation of mucin-type O-glycosylation. It has become apparent that each of these individual isoforms have different tissue distribution profiles and kinetic capabilities. Mucin-type O-glycosylation is thus controlled, and dependent upon the repetoir of expressed GalNAc-transferases in any given organ and cell type at any given time. We have been trying to contribute to the understanding of the ordered process controlling mucin-type O-glycosylation in both normal and malignant models, and are currently investigating a pancreatic cell line model in the lab. The pancreatic tumor cell line ASPC-1 has been found to possess low metastatic potential in mouse models, in contrast to the pancreatic tumor cell line Suit-T2 possessing high metastatic potential. Immunohistochemical analysis of both cell lines, ASPC-1 and Suit-T2, using our monoclonal antibodies to 7 isoforms has revealed great differences in the expression profile of these 7 isoforms in theses two cell lines, and for instance GalNAc-T3 has been found to be highly expressed in Suit-T2 but completely lacking in ASPC-1.

overall_design: Two cell lines: ASPC-1 and Suit-T2 are analyzed with 3 independent replicate prepared for each cell line.

first: Henrik

last: Clausen


title: Maltose utilization by Lactobacillus reuteri 100-23

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

summary: Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model.

sample_organism: Limosilactobacillus reuteri subsp. rodentium

overall_design: Analysis of the microarray data was obtained from two independent biological replicates. A dye swap was included in the analysis

first: Gerald

middle: W

last: Tannock

first: Gregory

last: Cook

first: Jocelyn

last: Eason

first: Paul

last: O'Toole

first: Blair

last: Lawley


title: Non-Biological Variability Study

summary: Assessment of sources of non-biological (technical) variability in the processing of RNA samples and gene chips during microarray analysis. The purpose of this experiment was to measure technical variability in microarray data introduced by various steps in preparation of the RNA, amplification/labeling of the RNA and hybridization of the sample to the arrays on separate days. The experimental design utilized a single tissue source - homogenized brain tissue pooled from 3 eight week old male C57/Bl mice.

overall_design:
Variables examined include: I) Technician extracting RNA (technician #1 prepared Pools 1 and 2; technician #2 prepared pools 3 and 4). II) RNA extraction (Pools 1-4 represent four independent RNA extractions from 3 homogenized pooled whole mouse brains from 8 week old male C57/B6 mice) III) Independent RNA labeling/amplification reactions - three performed from each RNA pool labeled A, B and C) and IV) Day of hybridization to GLYCOv1 arrays (labeled samples were hybridized to arrays over 3 days - 11/14/02, 11/15/02 and 11/18/02). 32 samples made it through to completion generating a high quality .CEL file for analysis. Four samples failed at various steps in the preparation/hybridiztion.
All samples were male 8 week old C57/Bl mouse brain total RNA.


title: SAGE analysis of A. thaliana leaf tissue

status: Public on Dec 10 2010

city: Saskatoon

first: Dustin

last: Cram

institute: Agriculture and Agri-Food Canada - Saskatoon Research Centre

summary: Arabidopsis thaliana (Col-4) aerial tissue collected from 14-day old plants. Grown under sterile conditions at 22 degrees Celsius and 125 uE light on 0.5xMS media.

overall_design: This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.


title: Chicken retina LD2 vs LD18

city: College Station

first: Phillip

middle: D.

last: Beremand

state: TX

department: Biology

institute: Texas A&M University

summary: Chickens were kept under a regimen of 12 hours of light and 12 hours of dark for 7 days. At LD2, 2 hours into the light cycle on the 8th day, 3 chickens were sacrificed by decapitation and their retinas dissected and pooled. Similarly, at LD18, 6 hours into the dark cycle on the 8th day, retinas were harvested from 3 chickens. Total RNA was extracted from each set of retinas using Trizol Reagent (Invitrogen). The total RNA samples were amplified to produce aRNA using the Message Amp Kit (Ambion). Randomly primed fluorescent probes were produced from the aRNA samples using a Genisphere 3DNA Array 900MPX expression array detection kit. The fluorescent dye on the probe derived from the experimental aRNA (LD2) was Cy5 while the dye on the control probe (LD18) was Cy3. Hybridizations and washes were as suggested by Genisphere. Labeled arrays were scanned in an Affymetrix 428 array scanner. The images obtained were subsequently analyzed by GenePixPro software (Axon Instruments). The GenePix results (.gpr) file was further analyzed by GeneSpring 5 (Silicon Genetics) which applied intensity dependent LOWESS normalization to the results and calculated normalized Cy5 to Cy3 ratios.


title: RL-SAGE analysis of Zea mays leaf transcriptome

city: Columbus

first: Guo-Liang

last: Wang

state: OH

address: 2021 Coffey Road

department: Plant Pathology

institute: Ohio State University

summary: Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library.


title: Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

summary: The cell wall is essential for viability of fungi and is an effective drug target in pathogens such as Candida albicans. The contribution of posttranscriptional gene regulators to cell wall integrity in C. albicans is unknown. We show that the C. albicans Ccr4-Pop2 mRNA deadenylase, a regulator of mRNA stability and translation, is required for cell wall integrity. The ccr4/pop2 mutants display reduced wall β-glucans and sensitivity to the echinocandin caspofungin. Moreover, the deadenylase mutants are compromised for filamentation and virulence. We demonstrate that defective cell walls in the ccr4/pop2 mutants are linked to dysfunctional mitochondria and phospholipid imbalance. To further understand mitochondrial function in cell wall integrity, we screened a Saccharomyces cerevisiae collection of mitochondrial mutants. We identify several mitochondrial proteins required for caspofungin tolerance and find a connection between mitochondrial phospholipid homeostasis and caspofungin sensitivity. We focus on the mitochondrial outer membrane SAM complex subunit Sam37, demonstrating it is required for both trafficking of phospholipids between the ER and mitochondria and cell wall integrity. Moreover, in C. albicans also Sam37 is essential for caspofungin tolerance. Our study provides the basis for an integrative view of mitochondrial function in fungal cell wall biogenesis and resistance to echinocandin antifungal drugs.

overall_design: Two-color experimental design comparing cells with a double-knockout of the CCR4 genes to cells with a reintegrated CCR4 gene.

first: Michael

last: Dagley

first: Cecile

last: Beaurepaire

first: Ana

last: Traven


title: Genome wide screen reveals WNT11, a noncanonical WNT gene, as a target of ETS transcription factor ERG

first: Liliana

middle: H.

last: Mochmann

state: Berlin

address: Hindenburgdamm 30

department: Hematology and Oncology

institute: Charite

summary: ERG is a transcription factor that is involved in leukomogenesis and its mRNA overexpression has been associated with poor prognosis in a subset of patients with T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Herein, a genome-wide screen of ERG target genes was conducted by chromatin immunoprecipitation-on-chip (ChIP-chip) in Jurkat cells. 342 significant annotated regions were derived from ChIP-chip experiments. Seventeen candidate promoter regions resulted in at least two-fold enrichment by quantitative PCR. Notably, ERG potential targets included WNT signaling genes: WNT2, WNT9A, WNT11, CCND1, and FZD7. Functionally, expression of WNT11 was downregulated with siRNA ERG knockdown and substantially upregulated in a tet-on ERG-inducible assay in K562 cells. To investigate a role for ERG in WNT signaling, a WNT agonist was used to inhibit glycogen synthase kinase (GSK-3). This treatment resulted in an ERG-dependent proliferative growth advantage in the tet-on ERG-inducible system. Lastly, chromatin immunoprecipitation assays of primary leukemia blasts confirmed WNT11 promoter enrichment dependent on ERG mRNA expression. In conclusion, ERG transcriptional networks in leukemia are revealed. Specifically, WNT11 emerged as a target of ERG. We propose that overexpression of ERG in acute leukemia may lead to a proliferative advantage upon activation of WNT signals.

overall_design: ChIP-chip with ERG antibody C20 and combined C17/20 and nonspecificic IgG in Jurkat

middle: H

first: Juliane

last: Bock

first: Jutta

last: Ortiz-Tanchez

first: Cornelia

last: Schlee

first: Arend

last: Bohne

first: Konrad

last: Neumann

first: Wolf

last: Hofmann

first: Eckhard

last: Thiel

first: Claudia

middle: D

last: Baldus


title: Classification of diet modified gene signatures at the colon cancer initiation and progression stages

status: Public on Dec 09 2010

first: Jennifer

last: Goldsby

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

summary:
We used DNA microarrays to identify discriminative gene signatures for the purpose of classifying n-3 PUFA-fed, carcinogen injected Sprague Dawley rats at the initiation and progression stages.  Animals were assigned to three dietary treatments differeing only in the type of fat (corn oi/n-6 PUFA, fish oil/n-3 PUFA, or olive oli/n-9 monounsaturated fatty acid).  The effects of diet on colonic mucosal gene expression signatures during tumor initiation with the progression of colon cancer.  Each dietary lipid source exhibited its own unique transcriptional profile, as assessed by linear discriminant analysis.  Applying this novel approach we identified the single genes and the two- to three-gene combinations that best distinguished the dietary treatment groups.  For the chemoprotective fish oil diet, mediators of stem cell homeostasis, e.g., ephrin B1 and bone morphogenic protein 4, were the top-permorming gene classifiers.

keywords: diet analysis

overall_design: 29 samples were analyzed.  10 samples had repeat arrays.  No control or reference samples were included.

first: Priyanka

last: Kachroo

first: Ivan

last: Ivanov

first: Laurie

last: Davidson

first: Bhanu

last: Chowdhary

first: Joanne

last: Lupton

first: Robert

last: Chapkin


title: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (expression)

first: Qun

last: Pan

summary: The rate of RNA polymerase II (pol II) elongation can influence splice site selection in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing is not well understood. We performed experiments to perturb pol II elongation and then globally compared alternative splicing patterns with genome-wide pol II occupancy. RNA binding and RNA processing functions were significantly enriched among the genes with pol II elongation inhibition-dependent changes in alternative splicing. Under conditions that interfere with pol II elongation, including cell stress, increased pol II occupancy was detected in the intronic regions flanking the alternative exons in these genes, and these exons generally became more included. A disproportionately high fraction of these exons introduced premature termination codons that elicited nonsense-mediated mRNA decay (NMD), thereby further reducing transcript levels. Our results provide evidence that kinetic coupling between transcription, alternative splicing and NMD affords a rapid mechanism by which cells can respond to changes in growth conditions, including cell stress, to coordinate the levels of RNA processing factors with mRNA levels.

overall_design: In order to identify alternative splicing events influenced by changes in pol II elongation, we performed quantitative alternative splicing microarray profiling (Pan et al., 2004 (PMID 15610736); Shai et al., 2006 (PMID 16403798)) of RNA isolated from stimulated Jurkat T lymphoma cells, cultured separately in the presence or absence of two different drugs that can inhibit pol II elongation: 5,6-dichloro-1-β-D-ribofuranosyl-benzimidazole (DRB) and camptothecin.

first: Joanna

middle: Y

last: Ip

first: Dominic

last: Schmidt

first: Arun

last: Ramani

first: Jonathan

last: Ellis

first: Andrew

last: Fraser

first: Duncan

middle: T

last: Odom

first: Benjamin

last: Blencowe


title: Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

status: Public on Dec 08 2010

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

summary: We have constructed and validated human origin libraries to near homogeneity from early-S- and log-phase HeLa cells, as well as from log-phase GM06990, a karyotypically-normal lymphoblastoid cell line.  Hybridization to Affymetrix ENCODE tiling arrays suggests that the three origin libraries correspond to 15.3, 16.4, and 21.8% of the human genome, respectively.  Approximately half the origin fragments cluster into zones, and their signals are generally higher than those of isolated fragments.  Interestingly, initiation events are distributed about equally between genic and intergenic template sequences.  Furthermore, while only 13.2% and 14.0% of genes within the ENCODE regions are transcribed in HeLa and GM06990 cells, 54.5% and 25.6% of zonal origin fragments overlap transcribed genes, most with activating chromatin marks in their promoters. Comparison between early-S- and log-phase HeLa origin maps shows that cell synchronization activates a significant number of inchoate origins. In addition, HeLa and GM06990 cells activate remarkably different origin populations.

overall_design: 5 samples, 5 controls; no replicates or reference samples included

first: Larry

last: Mesner

first: Veena

last: Valsakumar

first: Neerja

last: Karnani

first: Anindya

last: Dutta

first: Joyce

last: Hamlin


title: Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis

status: Public on Dec 07 2010

city: Dallas

first: Todd

middle: C.

last: Hoopman

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

summary: Series of DNA microarrays (4) comparing the M. catarrhalis strain 035E response to 50 mM hydrogen peroxide relative to a water-only control.

overall_design: Wild-type cells were exposed to either 50 mM hydrogen peroxide or a water-only control for 15 minutes.  RNA was extracted and DNA microarray analysis performed.  4 biologic replicates were studied.  One dye swap was included in this series analysis.

middle: C

first: Eric

last: Hansen

first: Wei

middle: Z

last: Liu


title: Definition of Salmonella rpoN regulon

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: comparison of total RNA profiles obtained from wt and rpoN mutant strains in presence of the dctDAAA peptide and chIP/chip experiments to define rpoN targeted DNA segments

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: chIP/chip using rabbit anti-RpoN under various conditions and transcriptional profiling in rich medium with dctDAAA peptide

first: Steffen

last: Porwollik

first: Tim

last: Hoover

last: Frye

first: Anna

last: Karls


title: Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis: Evaluation of OxyR dependent Genes

summary: Series of DNA microarrays (4) comparing the M. catarrhalis strain 035E and M. catarrhalis oxyR mutant response to 50 mM hydrogen peroxide.

overall_design: Wild-type cells and oxyR mutant cells were exposed to 50 mM hydrogen peroxide for 15 minutes. RNA was extracted and DNA microarray analysis performed. 4 biologic replicates were studied. One dye swap was included in this series analysis. Control oxyR mutant cells exposed to water

middle: J


title: Understanding the Diversity of Maize Cell Wall (affy_cellwall_maize)

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_cellwall_maize - affy_cellwall_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription.-Comparison of internodes from 5 maize lines grown in field conditions

overall_design: 10 arrays - maize; organ comparison

first: Magalie

last: Pichon

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

institute: The Forsyth Institute

type: Expression profiling by genome tiling array

summary:
Background:
With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes the development of this method and its application to mapping transcriptome profiles.
Results:
RNA extracted from laboratory cultures of Porphyromonas gingivalis was fluorescently labeled with an alkylation reagent and hybridized directly to probes on genomic tiling microarrays specifically designed for this periodontal pathogen. The generated transcriptome profile was strand-specific and produced signals close to background level in most antisense regions of the genome. In contrast, high levels of signal were detected in the antisense regions when the hybridization was done with cDNA.  In addition, five antisense areas were tested with independent strand-specific RT-PCR and none to negligible amplification was detected, indicating that the strong antisense cDNA signals were artifacts.
Conclusions:
An efficient method was developed for mapping transcriptome profiles specific to both coding strands of a bacterial genome. This method chemically labels and uses extracted RNA directly in microarray hybridization. The generated transcriptome profile was free of cDNA artifactual signals. In addition, this method requires fewer processing steps and is more sensitive in detecting small amount of RNA compared to end-labeling methods due to the incorporation of more fluorescent molecules per RNA fragment.

overall_design: This serial of experiments were performed to compare the transcriptome profiles revealed between the use of cDNA (converted from RNA) and RNA. Three samples of cDNA-based method were provided and two samples of RNA-based method were included. The signal intensities of these arrays were normalized based on both the in-between array method and the genomic DNA reference arrays (included) using the R 'tilingarray' package and these experiments were referred in the paper.

first: Wen-Han

last: Yu

first: Hedda

last: Høvik

first: Ingar

last: Olsen


title: Genome-wide binding of replication initiation proteins in Bacillus subtilis

first: Alan

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

institute: MIT

summary: Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC.  The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The genome-wide binding profiles of DnaA, DnaD, DnaB and DnaC were determined. Binding profiles were determined in exponentially growing cells with and without HPUra treatment. Three biological replicates were analyzed per protein/treatment (one per array). Enrichment in immunoprecipitated samples versus total genomic DNA were determined.

first: Wiep

last: Smits

first: Houra

last: Merrikh

first: Carla

last: Bonilla


title: MicroRNA expression during murine fetal liver megakaryocyte differentiation

city: Philadelphia

first: Mitchell

last: Weiss

state: PA

address: 3615 Civic Center Blvd

institute: The Children's Hospital of Philadelphia

summary: MicroRNAs are small non-coding RNAs that regulate cellular development by interfering with mRNA stability and translation.  We defined the kinetics of global microRNA expression during the differentiation of murine hematopoietic progenitors into megakaryocytes.  Of 435 miRNAs analyzed, 13 were upregulated and 81 were downregulated.  Many of these changes are consistent with miRNA profiling studies of human megakaryocytes and platelets, although new patterns also emerged.  Among 7 conserved miRNAs that were upregulated most strongly in megakaryocytes, 6 were also induced in the related erythroid lineage.  MiR-146a was strongly upregulated during mouse and human megakaryopoiesis, but not erythropoiesis.  However, overexpression of miR-146a in mouse bone marrow hematopoietic progenitor populations produced no detectable alterations in megakaryocyte development or platelet production in vivo or in colony assays.  Our findings extend the repertoire of differentially regulated miRNAs during murine megakaryopoiesis and provide a useful new dataset for hematopoiesis research.  In addition, we show that enforced hematopoietic expression of miR-146a has minimal effects on megakaryopoiesis.  These results are compatible with prior studies indicating that miR-146a inhibits megakaryocyte production indirectly by suppressing cytokine production from innate immune cells, but cast doubt on a different study, which suggests that this miRNA inhibits megakaryopoiesis cell-autonomously.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Exiqon locked nucleic acid (LNA) microarrays were used to compare microRNA expression in starting populations (ter 119- progenitors) and purified megakaryocytes.

Day13.5-14.5 murine fetal livers (strain CD1) were depleted of erythroid cells and cultured with thrombopoietin to generate megakaryocytes.  Each total RNA sample (0.5 μg per reaction) was labeled with Hy3 and Hy5 dyes using the Exiqon Power Labeling Kit and automated microarray hybridizations and washes were performed on a Tecan HS4800 station with 20 hr hybridization at 56ºC.  Dye-swap pairs of three replicate experiments comparing Ter119- fetal liver cells vs. BSA-purified megakaryocytes were co-hybridized to six arrays. The geometric average of the 532 and 635 measurements after normalization was determined for each sample.

first: Joanna

last: Opalinska


title: Novel gene discovery in up to 10 ETEC strains and production of species microarray. Discovery of conserved and unique ETEC genes by comparative genome hybridization studies.

city: Rockville

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary:
PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships.

Infectious diarrhea is a leading worldwide cause of infant mortality and secondary malnutrition. Enterotoxigenic E. coli (ETEC) is a principal etiology of travelers?diarrhea and a major endemic health threat, especially among children in developing nations where it is estimated to cause hundreds of thousands of deaths each year. Vaccine development for ETEC has been significantly hampered by the remarkable genetic plasticity of E. coli, a comparatively modest understanding of the basic pathogenesis of these organisms, and an uncertainty regarding the degree to which any given antigenic target might be conserved. While experimental and epidemiologic data suggest that a broadly protective vaccine can be achieved, this will most effectively be accomplished in a research environment that fosters sharing of vital resources and open, collaborative interactions among multiple investigators. The proposed project is aimed at providing critical leverage to ongoing international investigative efforts pertaining to ETEC pathogenesis and vaccinology.

The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a species DNA microarray to better understand the ancestral relationships among its members. Based on preliminary MLST genotyping, 11 diverse ETEC strains were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for ETEC group members. The availability of the ETEC species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of ETEC group.

overall_design: Two hundread sixteen query strains were investigated in this study, with each query strain hybridized against the reference strain, B7A.  Each strain has a single dye experiment.  Each oligo is spotted on the Etec species microarray once.  Positive controls on the array consist of oligos designed from the sequenced reference genome, B7A, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.

first: L

last: Papazisi

first: E

last: Snesrud

first: S

last: Akkoush

last: Wester

first: C

last: Sun

last: Ratnayake

last: Appalla

first: J

last: Liu

first: T

last: Dracheva

last: Wan

last: Li

last: Wei

first: A

last: Saeed

first: M

last: Belland

first: R

last: Curtiss III

last: Francis

first: O

last: Gomez-Duarte

middle: P

last: Gormley

middle: A

last: Moxley

first: G

last: Munson

first: F

last: Qadri

last: Savarino

last: Fleckenstein

first: P

last: Hardwidge

last: Fleischmann

middle: N

last: Peterson


title: RNA-affinity isolations 13 RBPs

status: Public on Dec 06 2010

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

institute: Swiss Federal Institute of Technology

summary:
To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase  in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.; see protocol). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). from the extract (input) and from the affinity isolates was purified with the RNeasy Mini/ Micro Kit (Qiagen). RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.
Antigenic peptide used in IP: TAP-tag

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Tanja

last: Scherrer


title: Gene expression profiling of flower and leaf of Cold-tolerant rice variety Stejaree45

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

summary: To stabilize crop yield under low temperature stress conditions, it is important to improve stress tolerance in crops. Upon exposure to low temperature stress, many genes are induced and their products are thought to function as cellular protectants of stress-induced damages Therefore, responses of global gene expression profiles to cold stress was analyzed at the booting stage using the 60K Rice Whole Genome Microarray.

overall_design: The cold-tolerant rice variety, Stejaree45 was transplanted in 1/5000 pot at 20 days after seeding. Fertilizers were applied at the rate of 11, 7.7 and 9.3 kg/10a in N, P2O5 The samples were selected at the booting stage of rice on the basis of the auricle distance (the distance between auricles of flag leaf and the previous leaf of the main culm). The plants with an auricle distance ranging from -5 ㎝ to 0 ㎝ were exposed up to the flag leaf auricle using cold water (13℃) for 3 days. Glumous flowers and flag leaves of the cold-resistant variety, Stejaree45, were used to examine gene expression profiles.

first: Myoung-Ryoul

first: Ki-Young

last: Kim

first: Benildo

last: Reyes

first: Song-Joong

last: Yun


title: Comparisons of transcriptome of Ciona intestinalis between eggs and 32-cell stage embryos to identify rapidly degrading maternal mRNA

status: Public on Dec 04 2010

city: Okinawa

first: Takeshi

last: Noda

address: Tancha

country: Japan

institute: Okinawa Institute of Science and Technology

summary: A genome decoded chordate Ciona intestinalis is one of the suitable animal for analyzing genetic controls in early embryogenesis and zygotically expressed genes are especially intensely studied. However maternally expressed genes are less studied than zygotic ones because of their huge numbers.  These microarray experiments were carried out to screen rapidly degrading mRNA to identify crucial maternal mRNAs for Ciona embryogenesis in relatively a short period before their degradation.

overall_design: Two samples (unfertilized eggs vs 32-cell stage embryos), two biological replicates, dye Swap design


title: Expression profiling of Stomach and  Colon of Spdef Knockout mice

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

overall_design: Gene expression profiling on stomach and colon tissue from Spdef  knockout, heterozygous and wild type mice. The experiments are performed in duplicate.

first: Xuesong

last: Gu

first: Michael

last: Verzi

first: Dongxu

last: Lin

first: Marie

last: Joseph

first: Towia

last: Libermann


title: Map1p overexpression versus control cells microarrays

summary: BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control).

overall_design: Biological Replicate


title: Geminin-regulated genes in the Xenopus laevis embryonic ectoderm

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Geminin cooperates with Polycomb to restrain multi-lineage commitment in the early embryo:   Transient maintenance of a pluripotent embryonic cell population followed by the onset of multi-lineage commitment is a fundamental aspect of development. However, molecular regulation of this transition is not well characterized in vivo.  Here we demonstrate that the nuclear protein Geminin is required to restrain commitment and spatially restrict mesoderm, endoderm, and non-neural ectoderm to their proper locations in the Xenopus embryo. We used microarray analyses to demonstrate that Geminin overexpression represses many genes associated with cell commitment and differentiation, while elevating expression levels of genes that maintain pluripotent early and immature neurectodermal cell states. We characterized Geminin’s relationship to cell signaling and found that Geminin broadly represses Activin-, FGF-, and BMP-mediated cell commitment.  Conversely, Geminin knockdown enhances commitment responses to growth factor signaling and causes ectopic mesodermal, endodermal, and epidermal fate commitment in the embryo. We also characterized Geminin’s functional relationship with transcription factors that had similar activities and found that Geminin represses commitment independent of Oct4 ortholog (Oct25/60) activities, but depends upon intact Polycomb repressor function. Consistent with this, chromatin immunoprecipitation assays directed at mesodermal genes demonstrate that Geminin promotes Polycomb binding and Polycomb-mediated repressive histone modifications, while inhibiting modifications associated with gene activation. This work defines Geminin as an essential regulator of the embryonic transition from pluripotency through early multi-lineage commitment, and demonstrates that functional cooperativity between Geminin and Polycomb contributes to this process.

overall_design: For each experiment, paired Geminin-injected versus uninjected samples were used for probe synthesis and hybridization to Affymetrix Xenopus laevis genome v1.0 arrays (Washington University Genechip facility). For each sample type (Geminin stage 10.5 and 12), the entire experiment (microinjection, RNA extraction, and microarray analysis) was repeated three times; the three microarray datasets resulting from these experiments were then compared (see Supplementary files).

first: Jong-Won

last: Lim

first: Pamela

last: Hummert

first: Jason

last: Mills


title: Global analysis of miRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

city: New York

first: Nicholas

last: Socci

state: NY

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary:
Human prostate CWR22 OT-tumor cells were prospectively purified for expression of various stem cell markers (TRA-1-60/CD151/CD166/EpCAM/CD44/α2-Integrin). Unsorted total tumor cells or the additional marker positive cells that do not manifest stem-like characteristics were used as control. All these cells were subjected to molecular profiling of total RNA expression and the fold change data are tabulated according to S/TFE of the purified cells in relation to their control.
Notes: Low S/TFE   = Low sphere and tumor forming efficiency; Moderate S/TFE  = Moderate sphere and tumor forming efficiency;  High S/TFE   = High sphere and tumor forming efficiency; FDR*    = False Discovery Rate;  FC    = Fold Change;  Signal    = Average Expression Signal Level.

overall_design: Low-S/TFE, Moderate S/TFE, High S/TFE data sets were compared to No S/TFE control sets

first: Vinagolu

middle: K

last: Rajasekhar

first: Lorenz

last: Studer

first: William

last: Gerald

first: Howard

middle: I

last: Scher


title: Altered antisense-to-sense transcript ratios in breast cancer: Agilent

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. Many of the differentially expressed antisense transcripts likely represent long ncRNAs. A subset of genes that mainly generate antisense transcripts in normal but not cancer cells is involved in essential metabolic processes. These findings suggest fundamental differences in global RNA regulation between normal and cancer cells that might play a role in tumorigenesis.

overall_design: Global strand-specific transcriptome profilings of 4 samples in cancer from clinical breast tissue using Agilent Technologies Custom microarray.

first: Maruyama

last: Reo

first: Michail

last: Shipitsin

first: Sibgat

last: Choudhury

first: Zhenhua

last: Wu

first: Xiaole

middle: S

last: Liu


title: Time series analysis of the transition from light to dark growth of Dinoroseobacter shibae DFL12

status: Public on Dec 03 2010

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary:
Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. Second part of the study analysing the transition from photoheterotrophic light to heterotrophic dark growth.
Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes.  We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated.    This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process.

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Samples from light grown cells were used as a reference, 6 timepoints in the dark, biological replicates: 2

first: Regina

last: Gohl

first: Boyke

last: Bunk

first: Maria

last: Suarez Diez

first: Irene

last: Wagner-Döbler


title: Time series analysis of the transition from dark to light growth of Dinoroseobacter shibae DFL12

summary:
Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. First part of the study analysing the transition from heterotrophic dark to photoheterotrophic light growth.
Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes.  We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated.    This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process.

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Samples from dark grown cells were used as a reference, 6 timepoints in the light, biological replicates: 3 to 4


title: Transcription comparison of UC26 to wild type G217B

status: Public on Dec 05 2010

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The objective of this experiment is to compare gene expression levels of UC26 to wild type G217B.

overall_design: One UC26 sample and one G217B sample labeled differently were hybridized to one array. Totally three replicated arrays were used with one of them dye-flipped.

first: Meggan

last: Laskowski

first: Alan

middle: G

last: Smulian


title: CGH profiles of primary colorecal cancer: metastasis-free, liver and peritoneal metastasis

city: Hamburg

first: Simon

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides us no information about organ site of metastases.  Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases.

overall_design: Array Comparative Genomic Hybridization (aCGH) was employed to asses DNA copy number changes in primary colorectal tumors of three distinctive patient groups. This included formalin-fixed, paraffin-embedded tissue of patients who developed liver metastases (LM; n=36), who developed peritoneal metastases (PM; n=37) and a group who remained metastases-free (M0; n=25).

first: Sjoerd

last: Bruin


title: Becker_etal_SNParray_BSA

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

summary:
Bulk segregant analysis using microarrays, and extreme array mapping have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however require the identification of single feature polymorphisms between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.

Keywords: genomic hybridization of inbred lines and bulked segregant analysis

overall_design: Hybridizations of inbred parents for feasiblity studies and simulations as well as two hybs from a Bulk Segregant analysis. we measured the elemental profile of 412F2 plants from a cross between the Sulfur and Selenium mutant 78730 (in the Col-0 background) and the Ler-1 accession (Trays 1289-1290 and trays 1321-1323), data available at www.ionomicshub.org <http://www.ionomicshub.org>). Leaves from the 31 highest and 33 lowest S+Se accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits

middle: O


title: Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide

status: Public on Dec 02 2010

city: Bethesda

first: Eun-Hee

last: Park

address: 6 Center Dr.

department: NICHD

institute: NIH

summary: Investigation of the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies, using gene expresssion microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes

overall_design: Three biological replicates were examined (designated projects I, II, and III), representing heavy polysomes (HP), light polysomes (LP), and total RNA (T) preparations from three independent pairs of WT and eIF4G degron mutant cultures. Cy3-labeled cDNAs were generated from the 3 HP, 3 LP, and 3 total RNA samples prepared for each strain and the resulting 18 sets of cDNAs were used to probe three (technical) replicate whole-genome microarrays, containing multiple 60-mer oligonucleotides for each gene. The “normalized gene expression summary values” were calculated for each gene from the data obtained from the three technical replicates and used to calculate the translational efficiency (TE) of each gene as the ratio of the intensity values for HP to total RNA (HP/T) or LP to total RNA (LP/T) for each project.

first: Fan

last: Zhang

last: Hinnebusch

first: Jonas

last: Warringer

first: Per

last: Sunnerhagen


title: Molecular identification of genes involved in testicular steroid synthesis and characterization of the response to gonadotropic stimulation in the Senegalese sole (Solea senegalensis)

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

summary:
In male teleosts, testicular steroids are essential hormones for the regulation of spermatogenesis and their production is regulated by pituitary gonadotropins. In the Senegalese sole (Solea senegalensis), an economically important flatfish with semi-cystic and asynchronous
spermatogenesis, the endocrine mechanisms involved in the regulation of spermatogenesis, particularly regarding the production and regulation of testicular steroids, are not well understood.This study aimed at
describing the transcriptomic changes taking place in the Senegalese sole testis in response to hCG stimulation in vivo. Gene expression analysis by microarray identified 90 differentially expressed genes in the testis in response to hCG administration, including genes potentially involved in
steroidogenesis, progression of spermatogenesis and germ cell maturation and cytoskeletal organization. Our results provide evidence for the first time that key genes involved in the regulation of steroid production and spermatogenesis in the Senegalese sole testis are under gonadotropic control.

overall_design: Testes samples from saline- and hCG-injected male Senegalese sole (8 fish per group) were pooled separatedly. Pooled testicular RNAs from each group were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC. Each hybridization was performed in duplicate.

first: Rubén

last: Marín-Juez

first: Barbara

last: Castellana


title: A mesoderm-derived mesenchymal stem/stromal cells (MSC) precursor: stages of development experiment

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

summary: Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can differentiate into a variety of cell types forming connective tissue and skeleton, and are essential participants in the development of all organs. However, MSC precursors remain largely unknown. In human embryonic stem cells (hESCs) directed to mesendodermal differentiation through coculture with OP9 stromal cells, we identified a population of mesodermal cells by surface expression of apelin receptor (APLNR1). APLNR+ cells were enriched with precursors generating compact spheroid colonies in semisolid suspension culture. Being formed by single cells, these colonies consisted of a uniform population of mesenchymal cells with a transcriptional profile representative of embryonic mesenchyme originating from lateral plate/extraembryonic mesoderm. Mesenchymal colony formation required serum-free medium and FGF2 as a colony-forming factor, could be significantly enhanced by PDGF-BB, but suppressed by VEGF. When transferred to the adherent cultures in serum-free medium with FGF2, individual colonies gave rise to multipotential mesenchymal cell lines with typical phenotype (CD146+CD105+CD73+CD31-CD43-CD45-), differentiation (chondro-, osteo-, and adipogenesis) and proliferation (>80 doublings) potentials. Consistent with lineage-restricted differentiation pattern, neither endothelial nor hematopoietic cells could be produced from adherent mesenchymal cultures, however endothelial cells could be derived from mesenchymal colonies in the early days of colony-forming culture suggesting that mesenchymal cells arose from cells with primary angiogenic potential (mesangioblasts). Together these studies identified mesangioblasts as the earliest clonogenic mesenchymal precursors at this stage of their specification from mesoderm.

overall_design: This set (11 samples) of expression data is sequential stages of MSC development from hESCs (H1), namely ALPNR+ mesodermal precursors isolated on day 2 and day 3 differentiation, mesangioblast (MB) cores (Day 2 H1-derived cores), hemangioblast (HB) cores (day 3 H1-derived cores), mesangioblast (MB) and hemangioblast (HB)  colonies, and colony-derived MSC lines at passage 1 and 5.

first: M

last: Vodyanik

first: J

last: Yu

first: S

last: Tian

first: R

last: Stewart

last: Thomson

first: I


title: A mesoderm-derived mesenchymal stem/stromal cells (MSC) precursor: time course experiment

overall_design: This set (8 samples) of expression data is a time-course experiment of hESC (H1) differentiated in OP9 coculture for 1-7 days.


title: Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate

city: Bielefeld

first: Jung-Won

last: Youn

address: Universitaetsstrasse 25

department: Genetics of Prokaryotes

institute: Bielefeld University

summary: Corynebacterium glutamicum is able to grow with lactate as sole or combined carbon and energy source. Quinone-dependent L-lactate dehydrogenase LldD is known to be essential for utilization of L-lactate by C. glutamicum. D-lactate also serves as sole carbon source for C. glutamicum ATCC 13032. Here, the gene cg1027 was shown to encode the quinone-dependent D-lactate dehydrogenase (Dld) by enzymatic analysis of the protein purified from recombinant E. coli. The absorption spectrum of purified Dld indicated the presence of FAD as bound cofactor. Inactivation of dld resulted in the loss of the ability to grow with D-lactate, which could be restored by plasmid-borne expression of dld. Heterologous expression of dld from C. glutamicum ATCC 13032 in C. efficiens enabled this species to grow with D-lactate as sole carbon source. Homologs of dld of C. glutamicum ATCC 13032 are not encoded in the sequenced genomes of other corynebacteria and mycobacteria. However, the dld locus of C. glutamicum ATCC 13032 shares 2367 bp of 2372 bp identical nucleotides with the dld locus of Propionibacterium freudenreichii subsp. shermanii, a bacterium used in Swiss-type cheese making. Both loci are flanked by insertion sequences of the same family suggesting a possible event of horizontal gene transfer.

overall_design: Three respectively two biological replicates were performed. To analyse how D-lactate influences global gene expression. DNA microarray analyses were performed. For this purpose RNA was isolated from exponentially growing cells cultivated in either complex media LB or LB+50 mM D-lactate and in CgXII medium containing a mixture of D- and L-lactate or only L-lactate as carbon source.

first: Osamu

last: Kato

first: K

last: Stansen

first: Daisuke

last: Matsui

first: Tadao

last: Oikawa

first: Volker

middle: F

last: Wendisch


title: SAGE analysis of maize root segments

status: Public on Dec 01 2010

city: Urbana

first: Mark

last: Fredricksen

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois

summary: Dark-grown maize seedlings with primary roots 12-20 mm in length were transplanted to high (-0.03 MPa) water potential vermiculite. About 1,000 roots were collected.  Each root was divided into 4 segments (distances are from the junction of the root apex and root cap): segment 1, 0-3 mm plus the root cap; segment 2, 3-7 mm; segment 3, 7-12 mm; segment 4, 12-20 mm.  Details of the conditions and nutrient modifications have been described before (Sharp et al., 1988; Spollen et al, 2000). From each segment, 250 mg of material was used and RNA was isolated form the combined sample containing all four segments. RNA was isolated using the RNeasy Maxi Kit (Qiagen). RNA integrity was verified by denaturing agarose gel electorphoresis and spectrophotometry.

overall_design: This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.


title: CGH profiles of BRCA1-mutated tumors

first: Simon

last: Joosse

summary: While new defects in BRCA1 are still being found, it is unclear whether current breast cancer diagnostics misses many BRCA1-associated cases. A reliable test that is able to indicate the involvement of BRCA1 deficiency in cancer genesis could support decision making in genetic counselling and clinical management. To find BRCA1-specific markers and explore the effectiveness of the current diagnostic strategy, we designed a classification method, validated it and examined whether we could find BRCA1-like breast tumours in a group of patients initially diagnosed as non-BRCA1/2 mutation carriers. A classifier was built based on array-CGH profiles of 18 BRCA1-related and 32 control breast tumours, and validated on independent sets of 16 BRCA1-related and 16 control breast carcinomas. Subsequently, we applied the classifier to 48 breast tumours of patients from Hereditary Breast and Ovarian Cancer (HBOC) families in whom no germ line BRCA1/BRCA2 mutations were identified. The classifier showed an accuracy of 91% when applied to the validation sets. In 48 non-BRCA1/2 patients, only two breast tumours presented a BRCA1-like CGH profile. Additional evidence for BRCA1 dysfunction was found in one of these tumours. We here describe the specific chromosomal aberrations in BRCA1-related breast carcinomas. We developed a predictive genetic test for BRCA1-association and show that BRCA1-related tumours can still be identified in HBOC families after routine DNA diagnostics.

overall_design: Chromosomal aberrations in BRCA1 samples

first: Petra

middle: M

last: Nederlof