title: GENETIC CORRECTION OF HUNTINGTON'S DISEASE PHENOTYPES IN INDUCED PLURIPOTENT STEM CELLS

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Huntington's Disease (HD) is caused by a CAG expansion in the huntingtin gene. Expansion of the polyglutamine tract in the huntingtin protein results in massive cell death in the striatum of HD patients. We report that human induced pluripotent stem cells (iPSCs) derived from HD patient fibroblasts can be corrected by replacing the expanded CAG repeat with a normal repeat using homologous recombination, and that the correction persists in iPSC differentiation into DARPP-32 positive neurons in vitro and vivo. Further, correction of the HD-iPSCs normalized pathogenic HD signaling pathways (cadherin, TGF-β, BNDF, caspase activation), and reversed disease phenotypes such as susceptibility to cell death and altered mitochondrial bioenergetics in neural stem cells. The ability to make patient-specific, genetically corrected iPSCs from HD patients will provide relevant disease models in identical genetic backgrounds and is a critical step for the eventual use of these cells in cell replacement therapy.

overall_design: 16 experimental samples were used overall. There were 8 replicates per group, with one group being the control, and the other being the experimental. Comparison was carried out on the Nimblegen platform.

first: Mahru

last: An

first: Ningzhe

last: Zhang

first: Gary

last: Scott

first: Daniel

last: Montoro

first: Tobias

last: Wittkop

first: Sean

last: Mooney

first: Lisa

last: Ellerby


title: Host Gene Expression Signatures Discriminate between Ferrets Infected with Genetically Similar H1N1 Strains.

status: Public on Jun 16 2012

city: Birmingham

first: Carl

middle: E

last: Bruder

state: AL

address: 2000 9th Ave South

department: Viral Biochemistry

country: USA

institute: Southern Research Institute

summary: Different respiratory viruses induce virus-specific gene expression in the host. Recent evidence, including those presented here, suggests that genetically related isolates of influenza virus induce strain specific host gene regulation in several animal models. Here, we identified systemic strain-specific gene expression signatures in ferrets infected with pandemic influenza A/California/07/2009, A/Mexico/4482/2009 or seasonal influenza A/Brisbane/59/2007. Using uncorrelated shrunken centroid classification, we were able to accurately identify the infecting influenza strain with a combined gene expression profile of 10 selected genes, independent of the severity of disease. Another gene signature, consisting of 7 genes, could classify samples based on lung pathology. Furthermore, we identified a gene expression profile consisting of 31 probes that could classify samples based on both strain and severity of disease. Thus, we show that expression-based analysis of non-infected tissue enables distinction between genetically related influenza viruses as well as lung pathology. These results open for development of alternative tools for influenza diagnostics.

overall_design: Blood derived total RNA from 63 ferrets. 30 ferrets were infected with A/California/07/2009 (15 with 10E6 TCID50/ml and 15 with 10E4 TCID50/ml, 15 with A/Mexico/4482/2009 and 12 with A/BN/2007. 6 animals were mock infected with PBS and used as controls. Three animals per group were euthanized at days 1, 2, 3, 5 and 7.

first: Karl

last: Ljungberg

first: Alexis

last: McBrayer

first: Jeremy

middle: V

last: Camp

first: Ronald

last: Tapp

first: Diana

middle: L

last: Noah

first: Sheila

last: Grimes

first: Mary

last: Proctor

first: Peter

last: Liljeström

first: Colleen

middle: B

last: Jonsson


title: Correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP)

status: Public on Jun 15 2012

city: Menlo Park

first: Denise

last: Nishita

state: CA

address: 333 Ravenswood Ave.

department: Molecular Genetics

institute: SRI International

summary:
Background: We seek to understand correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP).

Methodology: We evaluated clinical features, salivary RNA metrics and differential expression of candidate genes in unfractionated saliva samples from 48 individuals (31% female, 55% ever-smoking) randomly selected from two groups stratified by high versus low severe negative life events and difficulties within the last year as as measured by the Life Events and Difficulties Schedule (LEDS, Brown & Harris, 1978). We used multiple analytical platforms, multiple reference genes and 18 replicates of all gene expression assays (assays). We chose 38 candidate genes previously identified as differentially expressed in a genome-wide scan of monocyte RNA in 11 familial caregivers of glioblastoma multiforme patients and 10 control subjects matched on age (middle-aged), gender (57% female), ethnicity and marital status and free of major stressors during the previous year.

Principal Findings: We observed significant differences in smoking prevalence (Pearson’s χ22d.f.=4.5, P=0.035) and RNA integrity score (t=2.12, P=0.039) between stress strata. We analyzed quantitative PCR data using both the comparative standard curve (CSC) and relative standard curve (RSC) methods because 34% of assays had efficiency estimates <90%. Assay data exhibited excellent linearity and low variability. We observed significant under expression of five assays in the high stress stratum using both methods, four of which interrogate glucocorticoid receptor regulated genes. Post-hoc analyses identified significant associations of RNA yield, integrity score, gender, ever-smoking and/or stress with results of normalized gene expression in 22/37 assays. IL8 expression remained significantly associated with chronic stress after adjustment for clinical and salivary RNA variables. Salivary IL8 expression has been previously associated with oropharyngeal squamous cell cancer.

Conclusions: A gene expression signature of chronic stress previously observed in adult hematopoietic samples is observed in the unfractionated saliva of young adults. Future investigation will need to analyze associated clinical, metabolic, meta-genomic, and proteomic components of unfractionated saliva to elucidate factors influencing the salivary transcriptome.

overall_design: Gene expression was performed on a Fluidigm 48 x 48 array on 48 individuals for 38 target genes and 6 possible reference genes (represented by 9 reference assays) in triplicate. Quantitative Q-PCR datas were normalized according to relative levels of four reference genes (CDKN1B, YWHAZ, RPL13A, and UBC).

first: Andrew

middle: W

last: Bergen

first: Aditi

last: Mallack

first: Xin

last: Wei

first: Martha

last: Michel

last: David

last: Swan

first: Mark

last: Reid

first: Anne

last: Simons

first: Judy

middle: A

last: Andrews


title: Co-inoculation with Dekkerea bruxellensis impacts the trancriptome of Saccharomyces cerevisiae during wine fermentation

status: Public on Jun 13 2012

city: Ljubljana

first: Janez

last: Kosel

state: Slovenia

address: Jamnikarjeva 101

country: Slovenia

institute: Biotechnical faculty

summary: The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as ‘‘medicinal’’ in white wines (due to vinyl phenols) and as ‘‘leather’’, ‘‘horse sweat’’ and ‘‘stable’’ in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as ‘smoky’, ‘spicy’ and ‘toffee’ are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (1.2 um pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 1.2 um pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation.

overall_design: Fermentations were carried out in synthetic wine must in duplicate for both the control S. cerevisiae (strain Lalvin EC1118) and mixed fermentation. Sampling of yeast S. cerevisiae for RNA extractions were performed at 22 h of fermentation, during the exponential growth phase of S. cerevisiae, at 92 h and 144 h of fermentation, during its early and late stationary growth phase and at 187 h of fermentation, during its phase of growth decline.

first: Richardo

last: Duarte

first: Neža

last: Čadež

first: Laura

last: Carretto

first: Dorit

last: Schuller

last: Raspor


title: Custom Agilent array-CGH of somatic cell hybrids targeted to 17q21.31 deletion syndrome locus

status: Public on Jun 02 2012

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

type: Genome variation profiling by genome tiling array

summary: This is array CGH data of recurrent 17q21.31 deletions used to delineate breakpoints within segmental duplications in a study by Itsara et al. Somatic cell hybrids were generated from three parent-child trios probands with 17q21.31 deletions and three 17q21.31 probands for which no parental DNA was available that isolated individual chromosome 17 homologues. In parents, this isolated the H2 from the H1 haplotypes in distinct cell lines, and in probands, isolated the deletion-bearing chromosomes from the unaffected chromosome 17. In parent-child trios, the deletion-bearing chromosomes were hybridized against the progenitor parental chromosome. In probands with no parental DNA, the deletion-bearing chromosomes were hybridized against an H2 chromosome.

sample_organism:
Homo sapiens
Mus musculus

overall_design: 6 experimental hybes of deletion-bearing proband vs H2 chromosome reference. 3 control hybes of H1 vs H2 haplotype, H2 vs H2 haplotype (different individuals), and H1 vs deletion-bearing H2 haplotype.

first: Evan

last: Eichler


title: Effects of exposure to the β-blocker propanolol on the reproductive behavior and gene expression of the fathead minnow, Pimephales promelas.

status: Public on Jun 01 2012

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

summary: Propranolol is a beta-adrenergic receptor antagonist (β-blocker) that has been detected in United States wastewater effluents at concentrations ranging from 0.026 to 1.90 µg/l. In mammals, there is evidence that β-blockers can cause sexual dysfunction, and alter serotonergic pathways which may impact reproductive behavior but little is known about the effects on fish behavior. The present study tested the effects of propranolol on fecundity and on reproductive behavior of the fathead minnow, Pimephales promelas, a fish that exhibits male parental care. Sexually mature fathead minnows were housed at a ratio of one male and two females per tank and exposed to nominal concentrations of 0, 0.1, 1, 10 µg/l for 21 days.  Measured concentrations (±SD) of propranolol were 0.05±0.02, 0.88±0.34 and 4.11±1.19 µg/l. There were no statistically significant differences in fecundity, fertilization rate, hatchability and time to hatch. Propranolol exposure was not associated with a change in nest rubbing behavior, time spent in the nest or approaching the females. There was a significant difference in the number of visits to the nest with males receiving low and medium propranolol treatments. The microarray analysis showed that there were 335 genes up-regulated and 400 genes down-regulated in the brain after exposure to the highest dose of propranolol. Among those genes, myoglobin and calsequestrin transcripts (fold change=10.84 and 5.49, respectively) were highly up-regulated. Ontological analyses indicated changes in genes involved in calcium ion transport, transcription, proteolysis and apoptosis/anti-apoptosis.  The results showed that exposure to propranolol at concentrations as high as 4.11 µg/l did not significantly impact reproductive behavior or spawning abilities of fathead minnow but did alter the regulation of genes within the brain of fish.

overall_design: Effects of propanolol exposure were investigated in the brain of adult male fathead minnow exposed to 10 µg/L of propanolol or a solvent control solution (0.01% ethanol). For each treatment, the brain of four different fish were analyzed.

first: Varenka

last: Lorenzi

first: Alvina

first: Nancy

middle: D

last: Denslow

first: Daniel

last: Schlenck


title: MCF7 Cells: Control siRNA -E2 vs. Control siRNA +E2, Control siRNA -E2 vs. PES1 siRNA -E2,Control siRNA -E2 vs. PES1 siRNA +E2

status: Public on Jun 10 2012

city: Beijing

first: cheng

last: long

address: 27 Tai-Ping Lu Rd

country: China

institute: Beijing Institute of Biotechnology

summary: The initiation of breast cancer is associated with increased expression of tumor-promoting estrogen receptor α (ERα) protein and decreased expression of tumor-suppressive ERβ protein. However, the mechanism underlying this process is unknown. Here we show that Pescadillo/PES1, an estrogen-inducible protein that is over-expressed in breast cancer, can regulate the balance between ERα and ERβ. PES1 enhances transcriptional activity of ERα and reduces that of ERβ, and modulates many estrogen-responsive genes. Consistent with this regulation of ERα and ERβ transcriptional activity, PES1 increases the stability of the ERα protein and decreases that of ERβ through the ubiquitin-proteasome pathway, mediated by the carboxyl terminus of Hsc70-interacting protein (CHIP). Moreover, PES1 can transform normal human mammary epithelial cells and is required for estrogen-induced breast tumor growth in nude mice. Further analysis of clinical samples showed that expression of PES1 correlates positively with ERα expression and negatively with ERβ expression, and predicts good clinical outcome in breast cancer. Our data demonstrate that PES1 contributes to breast tumor growth through regulating the balance between ERα and ERβ and may be a better target for the development of drugs that selectively regulate ERα and ERβ activities.

overall_design: Three samples: Control siRNA -E2 vs. Control siRNA +E2, Control siRNA -E2 vs. PES1 siRNA -E2,Control siRNA -E2 vs. PES1 siRNA +E2

first: Long

last: Cheng

first: Qinong

last: Ye


title: Staphylococcus aureus walKR mutants (TPS3130 and TPS3190) vs. parent strains (JKD6009 and JKD6004)

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

country: Australia

institute: Austin Health

summary:
WalKR is an essential two component regulatory system in S. aureus, thought to control cell wall metabolism. Using genome sequencing of 5 paired clinical isolates of vancomycin-susceptible and vancomycin-intermediate S. aureus we found frequent, but unique, mutations in this locus. To investigate the contribution of these mutations to vancomycin resistance allelic replacement WalK (G223D) and WalR (K208R) mutants were generated and compared to the parent strains.
Mutations in walk and walR led to increased vancomycin resistance, reduced biofilms formation and attenuation of virulence, demonstrating that minor genetic changes in this locus can lead to significant changes in bacterial resistance and virulence. Microarray transcriptional comparisons were performed to investigate the regulatory effects of the WalK (G223D) and WalR (K208R) mutations, and demonstrated that while changes in genes affecting cell wall metabolism were detected, more dramatic changes were found in regulation of cellular metabolism.

overall_design:
Transcriptional profiling of laboratory derived S. aureus walKR mutants compared to the parent isolates. TPS3130 has a single point mutation in walK, and TPS3190 has a single point mutation in walR.
Two condition experiment TPS3130 vs JKD6009 and TPS3190 vs JKD6004. 3 biological replicates per isolate pair, one replicate per slide.

middle: P

first: Wei

last: Gao


title: Gene expression profiling upon knockdown of JAK1 in IM9 cells

status: Public on Jun 28 2012

city: Essen

first: Stefan

last: Heinrichs

address: Virchowstr. 179

department: Institute of Transfusion Medicine

country: Germany

institute: University Hospital Essen

summary: Natural Killer (NK) cells are primary effectors of innate immunity directed against transformed cells. In response, tumor cells have developed mechanisms to evade NK cell-mediated lysis but the molecular basis for target cell resistance is not well understood. In the present study, we used a lentiviral shRNA library targeting more than 1000 human genes to identify 83 genes that promote target cell resistance to human NK cells. Many of the genes identified in this genetic screen belong to common signaling pathways, however, none of these genes have previously been known to modulate susceptibility of human tumor cells to immunologic destruction. In particular, gene silencing of two members of the JAK family (JAK1 and JAK2) in a variety of tumor cell targets increased their susceptibility to NK-mediated lysis and induced increased secretion of interferon gamma (IFN-gamma by NK cells.  Treatment of tumor cells with JAK inhibitors also induced increased susceptibility to NK cell activity. These findings may have important clinical implications and suggest that small molecule inhibitors of tyrosine kinases being developed as therapeutic anti-tumor agents may also have significant immunologic effects in vivo.

overall_design: IM9 cells were transduced with shRNA-encoding vectors and selected with Puromycin. Two vectors were specifically targeting JAK1 (JAK1-1 and JAK1-3) and one vector encoded an irrelevant control shRNA (CTRL-2). Total RNA was obtained from the parental IM9 cell line, the control-shRNA expressing IM9 cells, the JAK1-1-shRNA and JAK1-3-shRNA expressing IM9 cells in 2 separate experiments (Exp1 and Exp2).

first: Roberto

last: Bellucci

first: Hong-Nam

last: Nguyen

first: Allison

last: Martin

first: Anna

last: Schinzel

first: William

last: Hahn

first: Jerome

last: Ritz


title: Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v2]

status: Public on May 31 2012

first: Constance

middle: Regina

last: Baer

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary: Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of   aberrant epigenetic regulation at the respective regions.

overall_design: 5 samples total: 1 primary CLL sample, 1 CLL related cell line -/+ 5-aza-2’-deoxycytidine (DAC) treatment (Granta-519), myeloid cell line Kasumi-1 (-/+ 5-aza-2’-deoxycytidine treatment); H3K4me3 enriched vs. Input

first: Rainer

last: Claus


title: Avian 12th motor neuron

city: Durham

first: Miriam

middle: Virtudes

last: Rivas

state: NC

address: 451 Bryan Research Building

department: Neurobiology

institute: Duke University Medical Center

summary: To determine what kind of genes are involved in vocal learning ability, we performed microarray experiments using 3 vocal learning species (zebra finch, budgerigar, Anna's hummingbird) and 2 non-vocal learning species(ring dive, and Japanese quail) from the bird group. All of the animals are male adults. They were isolated over night and had 1hour light exposure at morning. Birds who did not sing were used in this experiment.

sample_organism:
Calypte anna
Melopsittacus undulatus
Taeniopygia guttata
Coturnix japonica
Streptopelia risoria

overall_design: We used 2-3 animals each species. We used the 12th motor neuron for both vocal learners and non-vocal learners. We used the Supra Spinal motor neuron (ssp) as control area for both groups.

first: Erich

last: Jarvis

first: James

middle: M

last: Ward

first: Erina

last: Hara

first: Andreas

last: Pfenning


title: Epigenetic regulation of miRNA in CLL [MCIp_hsa_miRNA_v3b]

type: Methylation profiling by genome tiling array

summary: Genome-wide profiling of DNA methylation 35 kb upstream and 5 kb downstream of  microRNAs in 24 CLL patients and B cells of 2 healthy donors versus a pool of 10 healthy donors.

overall_design: 26 samples total (24 CLL B cell samples and 2 healthy donor B cell samples) were hybridized against a pool of 10 healthy donor B cell samples.

first: C

first: R


title: Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v3b]

overall_design: 11 samples total: 3 primary B-cell samples (1 chronic lymphocytic leukemia [CLL] and 2 healthy controls), 2 CLL related cell lines -/+ 5-aza-2’-deoxycytidine (DAC) treatment (Mec-1, EHEB), T-lymphoid cell line JURKAT, myeloid cell line HL-60,  colon cancer cell line HCT-116 wild type and double knock out; H3K4me3 enriched vs. input


title: The role of yeast IME2 in early meiotic gene expression

city: Detroit

first: George

last: Brush

state: MI

address: 110 E. Warren Ave.

department: School of Medicine

institute: Wayne State University

summary: We examined global RNA expression in S. cerevisiae wild type cells and ime2D cells (lacking the IME2 gene) that were induced to enter meiosis. These data have provided evidence that the Ime2 protein kinase is required for normal transcription of many genes that contain cell cycle box promoter elements.

overall_design: Cells populations were induced to enter meiosis synchronously and gene expression was analyzed at 0, 2, 4, and 6 hours. Two independent experiments were performed.

middle: S

first: Alan

last: Dombkowski


title: Arrays of time course experiment (2-28 d) laser microdissected samples of H. pylori -infected mice

status: Public on May 12 2012

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Mice were infected with Helicobacter pylori strain SS1 for 2, 7, 14 or 28 days or left uninfected. They were sacrificed at the appropriate times, the stomachs were removed and one half was plated for colony counts. The other half was embedded in OCT and cryosections were produced for 6-7 animals per timepoint. The sections were stained using the Histogene dye and roughly 500-1000 cells per gastric epithelial cell type were harvested by laser microdissection. RNA was prepared from these samples, subjected to two rounds of amplification, labelled and hybridized to 40.000 element murine cDNA arrays. The array names are composed as follows: "LCM" stands for laser capture microdissection; "mock" or "SS" stands for mock-infected or SS1-infected, respectively; "2,7,14 and 28" refers to the length of infection; "1-4" corresponds to the numbers given to every animal.The cellular origin of the RNA is represented by "mucus producing" or pit cell, "parietal" or acid-producing cell and "chief" or zymogenic cell. Between 5 and 7 samples were harvested per timepoint and cell type. Where the first labelling reaction and hybridization did not produce sufficiently good data (less than half of all spots made a regression correlation cutoff of >0.6), both were repeated (indicated by the addition of "relabeled" to the array name).  The differential regulation of genes can be analyzed in both a time and cell type specific manner using publicly available software.
Cell Type: "mucus producing" or pit cell (pit), acid-producing cell (parietal) and zymogenic cell (chief)

first: Anne

last: Mueller


title: Epigenetic regulation of miRNA in CLL

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

overall_design: Refer to individual Series


title: Bovine Embryonic Developmental Competence Is Predicted By Expression Levels Of Genes Related To Oxidative Stress Response

status: Public on May 16 2012

city: Bonn

first: Eva

last: Held

address: Endenicher Allee 15

department: Animal Science

institute: University of Bonn

summary: The aberrant gene expression of early bovine embryos are a major cause for developemtal arrest. Therefore our aim was to detect transcriptomic fingerprints which correlate with the subsequent developmental competence of a two cell stage embryo.

overall_design: 2-cell stage embryos were bisected; one blastomere was cultured individually, its sister-blastomere was snap-frozen. According to the development of individual cultured blastomeres, the corresponding frozen samples were pooled into three groups for global gene expression analyses. We defined three groups: I. embryos which did not cleave after separation (2CB), II. embryos which  stopped cleaving at four cell stage (8CB) and III. embryos reaching blastocyst stage (BL).

first: Dessie

last: Salilew-Wondim

first: Dawit

last: Tesfaye

first: Karl

last: Schellander

first: Michael

last: Hoelker


title: The effects of knockdown of PML by different individual siRNAs in HUVEC cells

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 2123 Adelbert Road, RT400-L

department: Biochemistry

institute: Case Western Reserve University

summary: To study the potential target genes regulated by PML in endothelial cells, we carried out siRNA-mediated knockdown of PML in HUVEC cells. To eliminate the off-target effects of siRNAs, we utilized two different siRNAs. Only the genes changed in the same pattern following both siRNAs transfection are considered as potential PML-knockdown responsive genes.

overall_design: The experiment is one-factor (siRNA) with three ranks (siCtrl, siPML-1, siPML-2). We included technical duplicates for each sample. To minimize systemic errors assoicated with technique, we distributed the duplicates on two different microarray chips.

first: Xiwen

last: Cheng


title: Rif1 regulates the replication timing domains on the human genome

status: Public on May 15 2012

city: Setagaya-ku

first: Satoshi

last: Yamazaki

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Genome Dynamics Project

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

summary: DNA replication is spatially and temporally regulated during S-phase. DNA replication timing is established in early G1-phase at a point referred to as TDP (timing decision point). We show that Rif1 (Rap1-interacting-factor1), originally identified as a telomere binding factor in yeast, is a critical determinant of the replication timing program in human cells. Depletion of Rif1 results in specific loss of mid-S replication foci profiles, stimulation of initiation events in early S-phase and changes in long-range replication timing domain structures. Overall replication timing is shifted toward mid-S in both directions, suggesting that replication timing regulation is abrogated in the absence of Rif1. Rif1 tightly binds to nuclear insoluble structures at late-M to early-G1 and regulates the chromatin-loop sizes. Furthermore, Rif1 colocalizes specifically with the mid-S replication foci. Thus, Rif1 establishes the mid-S replication domains that are restrained from being activated at early S-phase. Our results indicate that Rif1 plays crucial roles in determining the replication timing domain structures through regulating higher-order chromatin architecture.

overall_design: HeLa cells (ATCC), with a total of 4 individual replicates

first: Ai

last: Ishii

first: Yutaka

last: Kanoh

first: Masako

last: Oda

first: Yasumasa

last: Nishito

first: Hisao

last: Masai


title: The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression

status: Public on May 18 2012

city: San Francisco

first: Laurie

last: Littlepage

address: 513 Parnassus Avenue, Box 0452

department: Anatomy

institute: University of California, San Francisco

summary: The transcription factor ZNF217 is a candidate oncogene in the amplicon on chromosome 20q13 that occurs in 20-30% of primary human breast cancers and that correlates with poor prognosis. We show Znf217 overexpression drives aberrant differentiation and signaling events, promotes increased self-renewal capacity, mesenchymal marker expression, motility and metastasis, and represses an adult tissue stem cell gene signature downregulated in cancers. By in silico screening, we identified candidate therapeutics that at low concentrations inhibit growth of cancer cells expressing high ZNF217. We demonstrate that the nucleoside analog triciribine inhibits ZNF217-induced tumor growth and chemotherapy resistance, and inhibits signaling events (e.g., P-AKT, P-MAPK) in vivo. Our data suggest ZNF217 is a biomarker of poor prognosis and a therapeutic target in breast cancer patients, and triciribine may be part of a personalized treatment strategy in patients overexpressing ZNF217. Since ZNF217 is amplified in numerous cancers, these results have implications for other cancers.

overall_design: Total RNA was isolated from samples overexpressing ZNF217 (3 Primary and 5 SCp2). RNA was also harvested from each cell line expressing a vector control to use as a reference for each microarray sample analyzed. Total RNA was hybridized to mouse MEEBO arrays as described (http://www.microarray.org/sfgf/meebo.do). Samples were verified to have strong overexpression of ZNF217 by qRT-PCR or Western analysis.

first: Adam

last: Adler


title: Jasmonate-responsive genes in rice

status: Public on May 30 2012

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

summary: The plant hormone jasmonate (JA) plays important roles in the regulation of defense responses in many plants. To clarify the response to JA in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, treatment of JA caused high upregulation of many defense-related genes including pathogenesis-related (PR) genes in rice. However, many of these defense-related genes were not upregulated in JA-insensitive transgenic rice plant overexpressing JAZ8deltaC.

overall_design: An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies,　Redwood City, CA, USA) was used for the microarray analysis. Total RNA was extracted from leaf blades of four-leaf stage rice plants that had been treated with 100 μM JA for 1 day. For each biological replicate, material from at least three rice plants was pooled to provide a single sample for RNA extraction. We performed 4 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (100 ng) was labeled with Cy-3 using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2565CA; Agilent Technologies). Feature extraction software (Agilent Feature Extraction; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

first: Kenji

last: Gomi

first: Shoko

last: Yamada

first: Akihito

last: Kano

first: Ayumi

last: Miyamoto

first: Kazuya

last: Akimitsu


title: Transcriptional profiling of human white blood cells at the different stages of NYHA classification

status: Public on May 03 2012

city: Toulouse

first: Philippe

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

summary: Human white blood cells from healthy, heart failure risk patients, asymptomatic left ventricular dysfunction patients, chronic heart failure, acute heart failure patients

overall_design: Common reference experiment, 9 replicates per group.

first: Fatima

last: Smih


title: Diurnal Variation of Melatonin Receptors in Danio rerio (Zebrafish)

status: Public on May 10 2012

city: San Marcos

first: Dana

last: Garcia

state: TX

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

summary: To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation.

overall_design:
Wild-type ZDR zebrafish (Danio rerio) were obtained from Animal Wonders, San Marcos, TX, and Aquatica Tropicals, Plant City, FL. Fish were conditioned on a 12 hour light/dark cycle for a minimum of 14 days before use. The design of this analysis compared the experimental to the control: midnight samples were used as experimental and midday as control. Samples were collected in triplicate per time point with each replicate representing total RNA pooled from 9 fish. Dual-color microarray was used to compare the midnight and midday samples. A statistically significant (p-value ≤ 0.05) and 2-fold or more change in an experimental sample as compared to a control indicated an up- or down-regulation in gene expression.

Supplementary files:
In Complete processed data file, "x" marked spots show intensities of less than 1000.
In Intensity trimmed data file, all genes with signal intensities of less than 1000 in all triplicate time points were removed from the analysis.

first: Shobhit

last: Sharma


title: Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species

status: Public on May 01 2012

city: Berkeley

first: Thomas

last: Poorten

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

summary: Amphibian populations around the world are threatened by an emerging infectious pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). How can a fungal skin infection kill such a broad range of amphibian hosts? And why are certain species particularly susceptible to the impacts of Bd? Here we use a genomics approach to understand the genetic response of multiple susceptible frog species to Bd infection. We characterize the transcriptomes of two closely-related endangered frog species (Rana muscosa and Rana sierrae) and analyze whole genome expression profiles from frogs in controlled Bd-infection experiments. We integrate the Rana results with a comparable dataset from a more distantly-related susceptible species (Silurana tropicalis). We demonstrate that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response. The genetic response to infection is shared across the focal susceptible species, suggesting a common effect of Bd on susceptible frogs.

sample_organism:
Rana muscosa
Rana sierrae

platform_organism:
Rana muscosa
Rana sierrae

overall_design: A total of five (12-plex) chips were analyzed from 60 samples comprising 2 conditions (control and infected), 3 tissues (skin, liver and spleen) and 2 timepoints (early and late). Three biological replicates were used for each condition and tissue at each time point.  Twentyfour arrays were analyzed for skin samples, 24 for liver, and 12 for spleen.  The same dye, Cy5, was used for all samples.

first: T

middle: J

first: E

last: Rosenblum

first: M

last: Settles

first: G

middle: K

last: Murdoch


title: Comparison of DNA methylation profiles in diploid and transformed tetraploid MEF cells

status: Public on Apr 30 2012

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: We propose that tetraploidy induces epigentic changes including DNA methylation due to the abnormal chromatin in the cells. To test our hypothesis, we employed methylated CpG island recovery assay (MIRA) assisted microarray to determine the DNA methylation profiles in both diploid and tetraploid cells.

overall_design: First, we conducted a methylated-CpG island recovery assay (MIRA). Briefly, we enriched for methylated CpG islands with methylated DNA binding proteins, MBD2/MBD3L1. The pulled down DNA fragments containing CpG islands and input DNA fragments were amplified with real-time PCR. After labeling, they were hybridized to CpG island promoter array. Data were collected and analyzed.

first: Li

last: Zheng

first: Binghui

last: Shen


title: Comparison of Trabecular Meshwork-Derived Cells (TMDCs) with other somatic Cell Types

city: Singapore

first: Cheryl

last: Tay

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Microarray study comparing trabecular meshwork-derived cells (TMDCs) from the iridocorneal angle of the human eye, with other human cell types such as scleral fibroblasts, corneal fibroblasts, retinal pigmented epithelial (RPE) cells, corneal stroma, human embryonic stem cells (hESC), neural precursors differentiated from hESC, human umbilical vein endothelial (HUVEC) cells and human adipose-tissue-derived mesenchymal stromal cells (MSC)

overall_design: 19 samples were analysed, including 6 biological replicates of TMDC, 2 biological replicates of scleral fibroblasts, 3 biological replicates of hAd-MSC

first: Lawrence

last: Stanton


title: plant genotype x rhizobium genotype interaction

city: Urbana

first: Katy

last: Heath

state: IL

address: 1201 W. Gregory Dr

department: Plant Biology

institute: University of Illinois

summary:
Coevolutionary change requires reciprocal selection between interacting species, i.e., that the partner genotypes that are favored in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype ´ genotype (G ´ G) interactions for fitness from interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G ´ G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G ´ G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation is the largest influence on nodule gene expression, and that plant genotype and the plant genotype ´ rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome, and illuminates potential molecular routes of coevolutionary change.
We assayed gene expression using three biological replicates for each plant genotype × rhizobium genotype combination (4 combinations) for a total of 12 chips.

sample_organism:
Sinorhizobium meliloti
Medicago truncatula

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: We compared gene expression in each of four combinations of Medicago truncatula families and Sinorhizobium meliloti strains using Affymetrix Medicago GeneChips to study how the entire transcriptome and individual genes responded to differences between plant families, between rhizobium strains, and due to the plant family × rhizobium strain (G × G) interaction.


title: RIP-Chip analysis of Musashi (Msi1) in the U251, a human glioma cell line

status: Public on Apr 12 2012

city: san antonio

first: raquel

last: abreu

address: 8403 Floyd Curl Drive

institute: CCRI

summary: Musashi1 (Msi1) is a highly conserved RNA binding protein that is required during the development of the nervous system.  Msi1 has a role in neural stem cells, controlling the balance between self-renewal and differentiation. Msi1 has also been implicated in cancer, being highly expressed in multiple tumor types. In this study, we analyzed Msi1 expression in a large cohort of medulloblastoma samples and showed that Msi1 is highly expressed in tumor tissue compared to normal cerebellum and that high Msi1 expression is associated with a poor prognosis.  Using a nude mouse xenograft model, we demonstrate that Msi1 is important for tumor growth.  We then used RIP-chip (ribonucleoprotein immunoprecipitation followed by microarray analysis) to identify mRNA targets of Msi1 in medulloblastoma.  In conclusion, our results suggest that Msi1 functions as a regulator of multiple processes in medulloblastoma formation and could become an important therapeutic target.

overall_design:
RIP-Chip analysis to identify mRNA preferentially associated with Msi1 protein.
RIP-Chip experiments were performed on two biologically replicated samples. A total of 8 microarrays were carried on using technical replicates of Msi1 antibody vs. prebleed serum for each dye orientation. We prepared two biological replicates for two different arrays. Each array consisted of 4 microarrays with 2 replicates for each dye orientation.

first: Dat

middle: T

last: Vo

first: Dharmalingam

last: Subramaniam

first: Shrikant

last: Anant

first: Philip

last: Uren

first: Raquel

last: Abreu

first: Uthra

last: Suresh

first: Mei

last: Qiao

first: Suzanne

last: Burns

first: Kaushal

last: Joshi

first: Andrew

last: Smith

first: Ichiro

last: Nakano

first: Robert

last: Bachoo

first: Luiz

middle: F

last: Penalva


title: Molecular mechanism underline immune cell type population shift upon anti-DLL4 treatment

city: Tarrytown

first: Wen

last: Zhang

address: 777 Old Saw Mill River Road

institute: Regeneron Pharma.

overall_design: C57BL/6 mice were injected with anti-DLL4, or an isotype control antibody as controls. Two weeks later mice were sacrificed, and thymi was harvested from 4 anti-DLL4 and 4 control animals. Total thymocytes, DN cells (CD4-CD8-) and DN1(CD4-CD8- CD44+CD25-) cells were isolated. Samples included in this data set are: 3 Thymocytes-anti-DLL4; 3 Thymocytes-isotype control; 3 DN1-anti-DLL4; 2 DN1-isotype controls; 3 DN-anti-DLL4; 3 DN-isotyoe control.

first: Dimitris

last: Skokos


title: Zeus RNAi expression profiling

city: Cambridge

first: Sidi

last: Chen

state: MA

institute: MIT

summary: Constitutive knockdown of Zeus gene and expression profiling of male wholebody and reproductive organs

overall_design: two-color, hybridize Zeus-RNAi and Caf40-RNAi against wildtype with male wholebody or reproductive organ samples

first: Manyuan

last: Long

first: Kevin

last: White

first: Xiaochun

last: Ni


title: Effect of urban effluents on fathead minnow gene expression: linkages between pollutants and physiological processes.

status: Public on Apr 25 2012

city: Gainesville

first: Ignacio

middle: Alejandro

last: Rodriguez-Jorquera

state: Florida

address: Mowry Drive 471

department: Soil and Water Science

institute: University of Florida

summary: Three surface waters in Gainesville, Florida were used in a 48 hour whole effluents exposure to assess gene expression profiles of male fathead minnow liver. Microarray analysis was used to determine changes in gene expression of exposed fish to waters from a site downstream of a wastewater treatment plant (streamwater), a wastewater treatment plant (wastewater), and a lake (stormwater). Differences in gene expression between fish exposed to collected waters and controls were observed.  Number of altered genes and biological processes were 1028 and 18 for stormwater; 787 and 19 for streamwater; and: 575 and 12 for wastewater. In general, the effects observed in all exposed fish were related with fatty acid metabolism, DNA repair, oxidation-reduction process, cell wall catabolic process and apoptosis. All exposed fish showed altered expression of genes related with DNA damage repair. In particular fish exposed to stormwater and streamwater showed downregulation of several key intermediates transcripts of cholesterol. The presence and environmental persistence of perfluorinated chemicals (PFCs) in these waters, the resemblance in known effects on transcripts with those found in this study, suggest that the set of genes differentially regulated in fathead minnows after 48 hours of exposure may be attributed to exposure to PFCs.

overall_design: Three surface water sites were chosen for effluent collection in Gainesville, Florida: A lake (stormwater), surface water downstream of a wastewater treatment plant (streamwater), and a wastewater treatment plant effluent used for landscaping irrigation (wastewater). Water from each site was collected two days prior to the fish exposure experiment using Chemfluor ® tubing and a 120 liters  steel barrels coated with polyester resin (gel coat) to avoid cross-contamination. Three barrels for each effluent were collected during day 1. Water from the barrel was transported to the laboratory and pumped into four fiberglass cylinders in the aquatic toxicology facility.  Water from each cylinder was then pumped into four replicate aquariums per treatment  and kept for 1 day without fish (pre-treatment).  On day 2, four male fathead minnows from a common tank were transferred to each replicate aquarium and kept for 48 hours, with one 75% water change after first 24 hours. The exposure system consisted of 40 L glass aquaria. Each exposure was conducted in quadruplicate and each aquarium contained the four male fish in 25 L of treatment water . The water used in the control treatment was carbon filtered, dechlorinated tap water. The positions of the treatment tanks were randomized  and test initiation times were staggered to ensure an exposure/sampling interval of 48 h. The fish were not fed during the experiment.  The temperature range of the water was 24-26 °C with a photoperiod of 16 h light: 8 h dark. Liver was isolate from 4 males indviduals for each treatment except for control group (3 individuals).

last: Kroll

first: Nancy

last: Denslow


title: The connexin43-dependent transcriptome during brain development: importance of genetic background

status: Public on Apr 14 2012

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Use of null mutant mice is a powerful way to evaluate the role of specific proteins in brain function. Studies performed on knockout mice have revealed some unexpected roles of the gap junction proteins (the connexins). Thus, analyses of gene expression in connexin43 (Cx43) null brains indicated that deletion of a single gene (Gja1) induced expression level change of numerous other genes located on all chromosomes and involved in a wide diversity of functional pathways. The significant overlap between alterations in gene expression level, control and coordination in Cx43 knockout and knockdown astrocytes raised the possibility that Gja1 represents a transcriptomic node of gene regulatory networks. However, conditional deletion of Gja1 in astrocytes of two mouse strains resulted in remarkably different phenotypes. In order to evaluate the influence of the genetic background on the transcriptome, we performed microarray studies on brains of GFAP-Cre:Cx43f/f C57Bl/6 and 129/SVEV mice. The surprisingly low number of Cx43 core genes (regulated in all Cx43 nulls regardless of strain) and the high number of differently regulated genes in the two Cx43 CKOs indicate high influence of mouse strain on brain transcriptome.

overall_design: The transcriptomes of WT and Cx43 null brains from both C57Bl/6 and SVEV strains were profiled and compared at perinatal and adult time points to learn more about the strain dependence of the Cx43-null phenotype. For this purpose, differently labeled cDNAs from biological replicas (4 of each genotype) were co-hybridized with Duke MO36K mouse oligonucleotide array spotted with 36k Operon oligonucleotides V4.0.

first: Sanda

first: David

last: Spray

first: Eliana

last: Scemes


title: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in tumor and non-tumor samples from chronically infected woodchucks

status: Public on Apr 11 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

summary:
The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis.
Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB.

overall_design: Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine non-tumor vs. tumor gene expression in liver samples obtained from animals chronically infected with WHV (n=13). Multiple technical replicates per woodchuck sample are included.

first: Simon

last: Fletcher

first: Daniel

last: Chin

first: Yongmei

last: Ji

first: A

middle: L

last: Iniguez

first: Bruce

last: Taillon

last: Swinney

first: Palanikumar

last: Ravindran

first: Hans

last: Bitter

first: Uri

last: Lopatin

first: Han

last: Ma

first: Klaus

last: Klumpp

first: Stephan

last: Menne


title: Prevention of acute liver failure

status: Public on Apr 13 2012

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

summary:
Aim of this project was the evaluation of the effect of flushing (intraportal and intraoperative) hepatic allografts with tacrolimus before transplantation. Group A was administered tacrolimus, 20ng/ml in 1500ml albumin solution; and Group B was administered only albumin solution. Wedge biopsie of the allograft were harvested after 15 min flushing time and the gene expression profile were determined.
The primary study objective  was to determine on a genome-wide basis whether intraoperative and intraportal treatment of the allograft with tacrolimus reduces inflammatory signature in the liver. The secondary objective was the causally test, whether suppression of genes belongong to the ontologies of inflammation and immune response by tacrolimus will lead to a better initial function of the liver.

overall_design: randomized double-blind, placebo-controlled trial

first: Ivan

last: Kristo


title: MAPK Signaling Determines Anxiety in the Juvenile Mouse Brain but Depression-like Behavior in Adults

status: Public on Apr 19 2012

city: Neuherberg/Munich

first: Benedikt

last: Wefers

address: Ingolstaedter Landstr. 1

department: Institute of Developmental Genetics

institute: Helmholtz Zentrum Muenchen

summary: MAP kinase signaling has been implicated in brain development, long-term memory, and the response to antidepressants. Inducible Braf knockout mice enabled us to unravel a new role of neuronal MAPK signaling for emotional behavior. Braf mice that were induced during adulthood showed normal anxiety but increased depression-like behavior, in accordance with pharmacological findings. In contrast, the inactivation of Braf in the juvenile brain leads to normal depression-like behavior but decreased anxiety in adults. In these mutants we found no alteration of GABAergic neurotransmission but reduced neuronal arborization in the dentate gyrus. Analysis of gene expression in the hippocampus revealed nine downregulated MAPK target genes that represent candidates to cause the mutant phenotype.   Our results reveal the differential function of MAPK signaling in juvenile and adult life phases and emphasize the early postnatal period as critical for the determination of anxiety in adults. Moreover, these results validate inducible gene inactivation as new valuable approach, allowing to discriminate between gene function in the adult and the developing postnatal brain.

overall_design: Five male Braf-cko, six male homozygous Braf-flox littermates, six male heterozygous CamkII-Cre, and six male wildtype littermates were killed with CO2, the complete hippocampal tissue was prepared, and total RNA was extracted with the Trizol protocol. The integrity and quality of the RNA samples were analyzed with an RNA electrophoresis chip (RNA 6000 Nano Kit, Agilent, Boeblingen, Germany). RNA samples of high integrity and quality (RIN ≥ 7.5) were further processed with the TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA) and hybridized onto MouseWG-6 v1.1 Expression Bead-Chips (Illumina, San Diego, CA, USA) following manufacturer’s instructions. Data were analyzed using the software R (used packages: beadarray, limma, and vsn).

first: Christiane

last: Hitz

first: Sabine

last: Hölter

first: Dietrich

last: Trümbach

first: Jens

last: Hansen

first: Peter

last: Weber

first: Benno

last: Pütz

first: Jan

last: Deussing

first: Martin

last: Hrabe de Angelis

first: Till

last: Roenneberg

first: Fang

last: Zheng

first: Christian

last: Alzheimer

first: Alcino

last: Silva

first: Wolfgang

last: Wurst

first: Ralf

last: Kühn


title: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Spleen gene expression in uninfected, resolved and chronically infected woodchucks

first: Donavan

last: Cheng

overall_design: Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine spleen gene expression in animals chronically infected with WHV (n=4), animals that had resolved WHV infection at least 12 months prior (R; n=4; range 12-18 months), and uninfected animals (U; n=2). Multiple technical replicates per woodchuck sample are included.

first: Simon

last: Fletcher

first: Daniel

last: Chin

first: Yongmei

last: Ji

first: A

last: Iniguez

first: Bruce

last: Taillon

first: David

last: Swinney

first: Palanikumar

last: Ravindran

first: Hans

last: Bitter

first: Uri

last: Lopatin

first: Han

last: Ma

first: Klaus

last: Klumpp

first: Stephan

last: Menne


title: DNA methylation analysis of Colon Cancer cell line SW48

status: Public on Apr 04 2012

city: Philadelphia

first: Noel

middle: J-M

last: Raynal

state: Pennsylvania

address: 3307 N. Broad Street

department: Fels Institute for Cancer and Molecular Biology

institute: Temple University

summary: We combined gene expression experiments in response to HDAC inhibitor Depsipeptide with DNA methylation level to assess gene reactivation arising from hypermethylated promoters.

overall_design: We did one experiment with 1 untreated and 1 treated batch of cells

first: Marcos

last: Estecio


title: Reshaping of the maize transcriptome by domestication

status: Public on Apr 01 2012

city: Saint Paul

first: Nathan

last: Springer

state: MN

address: 1445 Gortner Ave

institute: University of Minnesota

summary: Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize.  A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits.  We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings.  We detected evidence for more than 600 genes having significantly different expression levels in maize compared to teosinte as well as 800 genes with significantly altered co-expression profiles reflective of substantial rewiring of the transcriptome since domestication.  These genes likely include loci with altered expression due to domestication.  The genes with altered expression show a significant enrichment for genes located in regions that previous population genetic analyses have identified as having undergone a selective sweep during maize domestication; thirty-two genes previously identified as putative targets of selection also exhibit altered expression levels and co-expression relationships.    We also identified 45 genes with altered, primarily higher, expression in inbred relative to out-crossed teosinte.  These genes are over-represented for genes that function in response to biotic stress and may reflect responses to the effects of inbreeding.  This study not only documents alterations in the maize transcriptome following domestication and identifies several genes that may have contributed to the evolution of maize but also highlights the complementary information that can be gained by combining gene expression with population genetic analyses.

sample_organism:
Zea mays
Zea mays subsp. parviglumis

overall_design: A 135,000 feature array was used to profile gene expression levels in above-ground seedling tissue of 38 maize genotypes and 24 teosinte genotypes.


title: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Kidney gene expression in uninfected, resolved and chronically infected woodchucks

overall_design: Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine kidney gene expression in animals chronically infected with WHV (n=5), animals that had resolved WHV infection at least 12 months prior (R; n=4; range 12-18 months), and uninfected animals (U; n=3). Multiple technical replicates per woodchuck sample are included.


title: Transcriptome analysis of isolated Escherichia coli mutants using VERT for the study of n-butanol tolerance

status: Public on Mar 31 2012

city: College Station

first: Luis

middle: Humberto

last: Reyes

state: Texas

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

summary: Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance.  The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT.  Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent.

overall_design: Three biological replicas. Each sample represents an isolated mutant. The reference for each mutant corresponds to wild-type, both exposed to the same concentration of n-butanol (0.8% (v/v)).

middle: H

first: Katy

last: Kao


title: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in uninfected, resolved and chronically infected woodchucks

first: Donavan

last: Cheng

overall_design: Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine liver gene expression in animals chronically infected with WHV (n=13), animals that had resolved WHV infection at least 12 months prior (R; n=11; range 12-18 months), and uninfected animals (U; n=10). Multiple technical replicates per woodchuck sample are included.

first: Simon

last: Fletcher

middle: C


title: Expression of intergenic regions of Synechococcus WH 7803 under environmentally relevant stresses

city: Freiburg

first: Gregor

middle: Josef

last: Gierga

department: Institut of Biology III -Genetics

institute: University of Freiburg

type: Expression profiling by genome tiling array

summary: We constructed a tiling microarray, covering nearly all of the intergenic regions larger than 50 bp on both strands of the genome of the marine picocyanobacterium Synechococcus WH7803. We analyzed transcript levels from cultures grown under ecologically relevant stress conditions. The investigated stress conditions were cold stress, high light stress, phosphate depletion and iron depletion. We identified several previously unknown small RNAs, partially differentially expressed. The detected RNAs provide a starting point for further investigations on the acclimatisation to different stresses for Synechococcus WH7803.

overall_design: For every applied growth condition the cultures were grown in triplicates as were the respective controls. Respective controls were treated the same as the stressed bacterial cultures in terms of centrifugation and / or dilution. Bacteria were harvested by rapid filtering and directly freezed by liquid nitrogen.

first: Björn

last: Voss

first: Wolfgang

middle: R

last: Hess


title: Dynamic gene expression of two Caenorhabditis elegans wild type strains (N2 and CB4856)

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

summary: We analyzed the consequences of recombination in gene expression. For this, we measured expression patterns in two C. elegans wild types, N2 and CB4856 (CB). We compare these profiles with gene expression values from a Recombinant Inbred Population (RIL) derived from the same wild types. Expression values of the RILs (GSE17071) were obtained from Viñuela et al. (Genome Research, 2010). N2 and CB strain nematodes were cultured in identical conditions. Likewise, mRNA was extracted at three different ages (juveniles, reproductive and old worms) to investigate the transcriptional consequences of recombination in aging worms. Then, we explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in natural isolates. Moreover, we investigated the progression of those parameters with age.

overall_design: In total, 14 dual-color microarrays were done on two wild type strains (N2 and CB4856) and three age groups (40, 96, and 214 hours). 5 replicates of t1 (juvenile) and t3 (senescent) samples, and 4 replicates of t2 (reproductive) samples, in a dye-swap design.

first: Jan

middle: E

last: Kammenga

first: L

middle: B

last: Snoek


title: Calibration of a custom designed microarray

status: Public on Mar 27 2012

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

institute: MPI for Evolutionary Biology

summary: We designed a custom expression 8x15 k microarray for Cottus fishes based on transcriptome sequencing. It is a known fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet) for more information.

overall_design: Labeled cRNA was prepared from 3 Cottus fish. These 3 fish were representative of species (C.rhenanus, C.perifretum, invasive hybrid species) used in another experiment. An calibration pool was prepared from equimolar amounts of this cRNA. Increasing amounts of labeled cRNA (75 ng, 150 ng, 300 ng, 600 ng, 1200 ng, 2400 ng, 4800 ng), corresponding to (1/8, 1/4, 1/2, 1, 2, 4 and 8 times the recommended amount of 600 ng) were hybridized to 7 microarrays (one microarray per dilution-step). The change in observed signal intensity in relation to the change in amount of labeled cRNA was used to infer the target-binding behavior of the individual probes. This information was extracted, to be used for a normalization procedure in another experiment with the same microarray (see Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet)

first: Jie

first: Alexander

last: Pozhitkov

first: Arne

middle: W

last: Nolte


summary: European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. See the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology no doi yet) for more information.

sample_organism:
Cottus
Cottus perifretum
Cottus rhenanus

overall_design: The transcriptome was compared between an invasive hybrid species of Cottus (Sieg population n = 8) and its parent species C.rhenanus and C.perifretum. Expression profiles of both parental populations were assessed by two independent replicate population (C.rhenanus: Broel and Naaf; C.perifretum Laarse Beek and Witte Nete; each population n = 8). The transcriptomes of F2 crosses between the populations of C.rhenanus and C.perifretum were assessed with for independent crosses with 4 biological replicates for each cross (n = 4 x 4 = 16).   We used a custom design microarray with probes designed based on transcriptome sequencing. We used a newly developed calibration method to account for differences in individual probe binding behavior and to detect and remove probes unfit for analysis. Data stored as “normalized data” are normalized and quality filtered based on this new calibration method and normalized for interarray comparability by division by the 75%tile signal intensity for each array. Please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet) for more information.


title: Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68

status: Public on Mar 24 2012

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. This therapy relies on efficient replication of virus in tumor cells in vivo with minimal or no replication in normal tissues. We recently described GLV-1h68 as a modified Vaccinia Virus (VACV) construct with exclusive in vivo tropism for tumor cells in experimental animal models. Moreover, we had previously observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro during the first 20 hours following infection and the in vivo ability to colonize and eliminate the corresponding tumor implant. Thus, we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines, extensively characterized and used for the assessment of novel therapeutic modalities. All cell lines were cultured and infected in identical conditions. Pre-infection transcriptional profiling was obtained to search for correlates of permissivity to viral infection. Selected cell lines were also tested for permissivity to another VACV and a vesicular stomatitis virus (VSV) strain. We observed that permissivity to VACV infection during the first 20 hours is quite heterogeneous among cell lines but highly reproducible within each cell line. The tissue of origin of each cell line does not influence permissivity to infection with the exception of B cell derivation. Permissivity correlates between two VACV constructs and between them and VSV suggesting a common permissive phenotype. No clear transcriptional pattern predictive of permissivity to infection could be identified though weak associations were observed that suggest a multifactorial control of viral replication. This study adds to the current characterization of the NCI-60 panel to guide the design and interpretation of experimental models testing oncolytic therapies.

overall_design: Seventy-four microarray samples were obtained from 8 renal cancer cell lines (786-0, A498, ACHN, CAKI-I, RXF-393, SN12C, TK-10, UO-31); 12 melanoma cell lines (888-MEL, 1858-MEL, 1936-MEL, 397, A375-MEL, LOX IMVI, M14, SK-MEL-2, SK-MEL-5, SK-MEL-28, UACC 62, UACC 257 ); 11 lung cancer cell lines (A549 p7, A549 p107, EKVX, HOP-62, HOP-92, NCI-H23, NCI-H226, NCI-H322M, NCI-H460, NCI-H522, NCI-H1299); 13 colon cancer cell lines (HCT-15, HCT-116, HT-29 p155, HT-29 p9, KM-12, SW-620, Colo 205, HCC 2998, NCI-ADR-RES, OVCAR 3 p7, OVCAR 3 p42, OVCAR 5, SK-OV-3); 3 ovarian cancer cell lines (OVCAR 4, OVCAR 8, IGROV); 1 cervical cancer cell line (Siha); 6 brain cancer cell lines (SNB 19, SF 295, SF 298, SNB 75, U251, SF 539); 7 breast cancer cell lines (BT-549, GI101A, HS-578T, MCF 7, MDA-MB-231 p41, MDA-MB-435, MDA-MB-231 p6); 7 hematopoietic cancer cell lines (CCFR-CEM, HL-60, K-562, MOLT-4, RPMI 8226, SR, T-47D); 3 prostatic cancer cell lines (Du-145, PC 3 p7, PC 3 p35); 1 hepatic cancer cell lines (Huh 7.5.1); and 2 pancreatic cancer cell lines (MIA PACA 2, Panc 1). Two technical repeats were performed (cell lines Siha and SNB-19). Reference T-RNA was obtained from 6 normal donor PBMCs.


title: Gene Expression Changes Associated with Respiratory Muscle Hypertrophy after Intermittent Transient Tracheal Occlusions

status: Public on Mar 26 2012

first: Vipa

last: Bernhardt

state: FL

address: 1600 Archer Rd

summary: The effect of intermittent transient tracheal occlusion (ITTO) on gene expression was compared in the diaphragm and parasternal intercostals. We hypothesized that genes responsible for protein metabolism, myogenic activation, neuromuscular transmission, and inflammatory modulation would be altered in animals exposed to this rodent model of respiratory load compensation rehabilitation. Eight adult male Sprague-Dawley rats underwent placement of a tracheal occluder cuff and were divided into ITTO (n=4) or SHAM (n=4) treatment groups. Animals received 10 days of their assigned treatments. The day following the last treatment session, the animals were euthanized and the diaphragm and parasternals extracted.  Messenger RNA was profiled with microarray analysis (Amadid: 028279, Agilent Technologies, Palo Alto, CA). Results were further analyzed with immunofluorescent examination of cross-sectional area and with quantitative reverse transcriptase polymerase chain reaction on a subset of genes exhibiting differential expression. The cross-sectional area of type IIx/b fibers was larger in the muscles of ITTO-trained animals. Microarray analysis identified 650 genes in the diaphragm and 1,181 genes in the intercostals that were differentially expressed between the groups (p<.01). In both muscles, biological processes for cell adhesion and chemical stimulus for the detection of olfaction biological processes were over-expressed. Additionally, we found significant differential expression of the g-protein signaling pathway and protein-amino acid phosphorylation in the intercostals.  The results provide insight into neuromuscular plasticity associated with respiratory load compensation rehabilitation.

overall_design: Four experimental animals that received tracheal occlusions and four surgical control animals were used. Intercostal and diaphragm muscles were excised and analyzed separately.

first: Barbara

last: Smith

first: Alvina

last: Mehinto

first: Nancy

last: Denslow

first: Paul

last: Davenport


title: Systematic Analysis of Tissue-Restricted miRISCs Reveals a Broad Role for microRNAs in Suppressing Basal Activation of the C. elegans Pathogen Response

status: Public on Mar 23 2012

city: Boulder

first: Min

last: Han

state: CO

address: Campus Box 347

department: Molecular Cellular and Developmental Biology

institute: Univeristy of Colardo, Boulder/HHMI

summary: Gene regulation by microRNAs (miRNAs) under specific physiological conditions often involves complex interactions between multiple miRNAs and a large number of their targets, as well as coordination with other regulatory mechanisms, limiting the effectiveness of classical genetic methods to identify miRNA functions.  We took a systematic approach to analyze the miRNA-induced silencing complex (miRISC) in individual tissues of C. elegans and found that mRNAs encoded by pathogen-responsive genes were dramatically over-represented in the intestinal miRISC, and that multiple miRNAs accumulated in the intestinal miRISCs upon infection.  Inactivation of the miRISC or ablation of miRNAs from different families, resulted in over-expression of several pathogen-responsive genes under basal conditions and, surprisingly, enhanced worm survival on pathogenic Pseudomonas aeruginosa.  These results indicate that much of the miRNA activity in the gut is dedicated to attenuating the activity of the pathogen response system, uncovering a novel and complex physiological function of the miRNA network.

overall_design: Each array was used for one biological replicate of a given experiment.  One channel was used to probe Total RNA, the other was for IP RNA.  Channels were swapped between biological replicates.  4 biological replicates for each asynchronous intestine IPs, 4 biological replicates for asynchronous muscle IP, 5 biolgoical replicates for L4 intestine IP, and two new biological replicates for the GFP control IP (previous biological replicates can be found in GSE9073: GSM230865-GSM2308657 and GSM230873-GSM230875).

first: Brian

middle: A

last: Kudlow


title: Differences in gene expression patterns in mouse embryonic fibroblast Flp-In-3T3 cell lines stably expressing Pax6 or Pax6(5a).

status: Public on Mar 22 2012

city: Tromso

first: Ingvild

last: Mikkola

address: 9037 Tromso

department: Department of Pharmacy

country: Norway

institute: University of Tromso

summary: Novel target genes for the two transcription factor isoforms Pax6 and Pax6(5a) were identified by generating mouse embryonic fibroblast cell lines stably expressing either Pax6 or Pax6(5a), and comparing their gene expression pattern with the original mouse embryonic fibroblast cell line.

overall_design: Flp-In-3T3 cell lines were generated according to the manufacturers instruction (Invitrogen), using the mouse Pax6 and Pax6(5a) cDNA as insert. Correct inserts were verified by PCR, sequencing and Westernblot.

first: Tonje

last: Eriksen


title: Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents

city: Lyngby

first: Nicolai

middle: Juul

last: Birkbak

address: Kemitorvet, Build. 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

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

summary: DNA repair competency is one determinant of sensitivity to certain chemotherapy drugs, such as cisplatin. Cancer cells with intact DNA repair can avoid the accumulation of genome damage during growth and also can repair platinum-induced DNA damage. We sought genomic signatures indicative of defective DNA repair in cell lines and tumors and correlated these signatures to platinum sensitivity. The number of subchromosomal regions with allelic imbalance extending to the telomere (NtAI) predicted cisplatin sensitivity in vitro and pathologic response to preoperative cisplatin treatment in patients with triple-negative breast cancer (TNBC). In serous ovarian cancer treated with platinum-based chemotherapy, higher levels of NtAI forecast a better initial response. We found an inverse relationship between BRCA1 expression and NtAI in sporadic TNBC and serous ovarian cancers without BRCA1 or BRCA2 mutation. Thus, accumulation of telomeric allelic imbalance is a marker of platinum sensitivity and suggests impaired DNA repair.

overall_design: SNP data from 27 and 40 primary triple negative breast cancer tumor samples from two clinical trials treated with cisplatin and cisplatin + bevacizumab. Labeling, hybridization and data processing was performed by Affymetrix using 70k MIP arrays and 330k MIP arrays. In the cisplatin trial, matched normal samples based on blood from all patients and an additional three samples based on FFPE negative lymph nodes were used as references (30 normal references in total). In the cisplatin+bevacizumab trial, mathed normal samples based on blood from 10 patients were used as references.

middle: J

first: Zhigang

last: Wang

first: Ji-Young

last: Kim

first: Aron

last: Eklund

first: Qiyuan

last: Li

first: Ruiyang

last: Tian

first: Christian

last: Bowman-Colin

first: Yang

first: April

last: Greene-Colozzi

last: Iglehart

first: Nadine

last: Tung

first: Paula

middle: D

last: Ryan

first: Judy

last: Garber

first: Daniel

middle: P

last: Silver

first: Zoltan

last: Szallasi

first: Andrea

last: Richardson


title: Temporal analyses of the effect of arachidonic acid on transcriptional responses of Candida albicans biofilms

status: Public on Mar 14 2012

city: Bloemfontein

first: Carolina

middle: Henrietta

last: Pohl-Albertyn

state: Free State

address: Swot Road, University of the Free State, 205 Nelson Mandela Drive

department: Microbial Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

summary:
Identification of Candida albicans genes differentially expressed in the presence of arachidonic acid

Although Candida species, more specifically C. albicans, are the most common pathogenic yeasts, little is known about the mechanism involved in eicosanoid production, a virulence factor in these organisms. This is an important area of research which may aid in the understanding of the complex interactions between host and pathogen and may possibly lead to the identification of novel antifungals or drug targets. In this study, genomic hybridization studies using C. albicans DNA microarrays were used to evaluate the regulation of C. albicans biofilm genes during incubation in the presence of arachidonic acid, the major precursor for prostaglandin E2 production. The results obtained indicated that the genes differentially expressed had diverse functions not normally required for cell growth.

overall_design: Two-condition experiment, Control biofilms vs. Arachidonic acid treated biofilms at different time intervals. Biological replicates: 3 Control, 3 Arachidonic acid treated, independently grown and harvested. Technical replicate: dye swap included. Triplicate per array.

first: Ruan

last: Ells

first: Jacobus

last: Albertyn

first: Johan

last: Kock

first: Nicky

last: Olivier

first: Dave

last: Berger

last: Pohl


title: Tiling ChIP-CHIP Ssn6-GFP, Tp11-GFP, Tup12-GFP; Hst4 vs WT Expression

status: Public on Mar 13 2012

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

summary: Tiling ChIP-CHIP Ssn6-GFP, Tp11-GFP, Tup12-GFP and Hst4 vs WT Expression

overall_design: 6 Samples


title: miR-148b modulates the C1GALT1 expression explaining the abnormal glycosylation process in IgA Nephropathy

status: Public on Mar 12 2012

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

summary: Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide characterized by aberrant O-glycosylation in the hinge region of IgA1. The basis for the abnormal glycosylation in IgAN is still unknown, but an important involvement of the enzyme core 1, beta 1,3-galactosyltransferase 1 (C1GALT1) is known. However, the role of microRNAs (miRNAs), a new family of key mRNA regulatory molecules, in the IgAN pathogenesis has not yet been reported. In this study, by high-throughput microRNA profiling, we identified 37 miRNAs differentially expressed in peripheral blood mononuclear cells (PBMCs) from IgAN patients compared to healthy subjects. Among them, upregulated miR-148b potentially targeted C1GALT1, INVS and PTEN, three genes notably downregulated in IgAN patients. C1GALT1 expression levels in IgAN patients were reduced and negatively correlated with the upregulated miR-148b expression. We demonstrated the biological relationship between miR-148b and C1GALT1 by transient transfection experiments ex vivo. When we reduced the upregulated miR-148b function in PBMCs of IgAN patients an increase of the C1GALT1 mRNA and protein levels was observed. We validated biologically also the miR-148b targeting of INVS , involved in the altered modulation of the WNT–β-catenin and PI3K/Akt pathways in IgAN patients. All together our data evidence an important role of miR-148b in the pathogenesis of IgAN, which could explain the aberrant glycosylation of IgA1 in the pathogenesis and should light on a potential target for the theraphy of the disease.

overall_design: The role of miRNAs expression in the pathogenesis of IgAN has not been well explored. To identify miRNAs differentially expressed in IgAN respect to healthy subjects (HS), we analyzed the global miRNA expression profile in PBMCs from IgAN patients and HS using the miRNA microarray approach. Among 723 human miRNAs represented on the microarrays, 147 were expressed in each sample. Unsupervised hierarchical clustering analysis generated a tree with IgAN and HS clearly separated into two group (Fig. 1). This separation was further confirmed by displaying the relationships among miRNAs expression patterns using principal component analysis (PCA) (Fig. S1). Applying a fold change threshold > 2 (false discovery rate < 0.01), 35 miRNAs were found to be significantly up-regulated and 2 were significantly down-regulated in IgAN. Complete list of differentially expressed miRNAs is shown in Table S1. To validate the microarray results we performed real-time PCR (q-RT-PCR) for miR-148b, miR-188-5p, miR-361-3p, miR-886-3p, let-7b, let-7d on miRNAs isolated from PBMCs of an independent set of 10 IgAN patients and 10 HS with the same clinical and demographic characteristics of the population used for microarray experiments. The expression of all analyzed miRNAs was significantly higher in IgAN patients confirming microarray results

first: Grazia

last: Serino

first: Fabio

last: Sallustio

middle: N

first: Francesco

last: Pesce

last: Schena


title: Identification of Copy Number Variants in Dogs

status: Public on Mar 08 2012

first: Ryan

last: Doan

address: 4467 TAMU

summary: Custom exome aCGH analysis of copy number across the genomes of 16 canine breeds

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: Two-condition experiment, All breed samples were compared to a single Boxer reference, Seizure samples were compared to breed and sex matched controls, and German Shepherds were compared to the Boxer reference

first: R

first: J

last: Levine

first: L

last: Carr

first: K

last: Rector

first: S

last: Dindot


title: Gene expression analysis for Oregon R embryos at different developmental stages.

status: Public on Mar 06 2012

city: Princeton

first: Bing

last: He

address: Washington Rd

department: Molecular Biology

institute: Princeton University

summary: The transcription profiles of newly mapped Drosophila heterochromatic sequences during early embryonic stages were investigated by microarray.

overall_design: cDNA were prepared from manually staged wild type Oregon R embryos at various developmental stages (0-1 hr, 2-2.5 hr/cycle 13-early cycle 14, 2.5-3 hr/mid- to late cycle 14, 3-4 hr, 4-5 hr, 19-22 hr) and analyzed by microarray. cDNA prepared from Oregon R embryos with mixed developmental stages (0-16 hrs) were used as reference for hybridization. Each stage has two biological repeats. 100-150 embryos were collected for each experiment. All embryos were collected at room temperature.


title: Array CGH of Drosophila ChrX deficiencies_duplications on heterochromatin custom array.

summary: Mapping the Drosophila melanogaster X heterochromatin by CGH analysis of embryos lacking specific regions of the X chromosome.

overall_design: Eight ChrX deficiencies and duplications were tested: 168 (Dp(1;Y)y[2]67g), 175 (Dp(1;Y)y[2]sc), 114n (Dp(1;Y)y[+]mal[126]), 114f (Df(1)fog[114]), 186n (Dp(1;Y)y[+]mal), 186f (Df(1)mal12), B2580 (Dp(1;Y)ct y[+]), B5280 (Dp(1;Y)ct[+]y[+]). To generate embryos lacking different portions of the X heterochromatin, two types of stocks were used: (1) males carrying a deficient X chromosome missing part of the heterochromatin (generally fog-) and a duplication on the Y chromosome that complements the deficiency, and (2) males carrying a duplication of X on the Y chromosome which covers part of the X heterochromatin. In both cases males were crossed to attached X females. In the first case, one quarter of embryos lack most of the X chromosome except the duplication of X on Y. These embryos were identified according to their defects during cellularization. Another quarter of the embryos carry the deficient X chromosome as their sole X chromosome. These embryos were identified according to their defects in posterior midgut formation during early gastrulation. In the second case, one quarter of embryos that lack most of the X chromosome except the duplication of X on Y were identified according to their defects in cellularization or posterior midgut formation. All embryos were collected at room temperature.


title: Identification of LEC1 target genes

city: Gatersleben

first: Astrid

last: Junker

address: Corrensstrasse 3

department: Molecular Genetics

institute: Leibniz Institute for Plant Genetics and Crop Plant Research

type: Genome binding/occupancy profiling by array

summary:
The transcription factor (TF) LEAFY COTYLEDON1 (LEC1) acts as an essential regulator of Arabidopsis embryogenesis and seed development. It controls aspects of early embryogenesis such as cotyledon identity and suspensor morphology, as well as seed maturation processes such as storage compound accumulation, acquisition of desiccation tolerance and dormancy.
To identify downstream components of the LEC1 regulon, dexamethasone-regulated expression of LEC1 and ChIP/chip were applied and revealed the enrichment of phytohormone- as well as elongation-related genes among LEC1 target genes.

overall_design: Two weeks old 35S::LEC1::GR seedlings were treated with DEX or ethanol for 24 hours before cross-linking and chromatin isolation. Four biological replicates were performed, using an ethanol-treated sample as control (LEC1_EtOH versus LEC1_DEX). After data normalization, statistical analysis and exclusion of putative false negatives, a number of 356 target promoter regions were identified.

first: Gudrun

last: Moenke

first: Urs

last: Haehnel

first: Lothar

last: Altschmied

first: Michael

last: Seifert


title: Array CGH of Drosophila translocations on heterochromatin custom array-eu_het boundary.

summary: CGH analysis of translocations with breakpoints at the euchromatin/heterochromatin boundary.

overall_design: Three translocations with breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X, respectively, were analyzed by CGH to distinguish heterochromatic sequences from euchromatic sequences. X: 101042(T(1;Y)B91); 2L: 130186 (T(Y;2)R146); and 3L: 102004(T(2;3)H31). To obtain embryos lacking the euchromatin portion of the chromosome arms, translocation males bearing breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X were crossed to C(2)EN, C(3)EN or attached X females, respectively. All embryos were collected at room temperature.


title: EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development

status: Public on Mar 01 2012

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: EMBRYONIC FLOWER1 (EMF1) is a plant specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination.  Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment level of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying differentiated cell fates during vegetative development.  H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.

overall_design: All experiments were done using two channels per chip, comparing DNA associated with immunoprecipitated EMF1 to control genomic DNA, DNA associated with immunoprecipitated histone H3 methylated at lysine 27 to control genomic DNA, or total RNA (converted to cDNA) to control genomic DNA. Two or three replicates per experiment are included.

first: Daniel

last: Zilberman


title: Array CGH of Drosophila translocations on heterochromatin custom array-2Rhet.

summary: Mapping the Drosophila melanogaster 2R heterochromatin by CGH analysis of embryos lacking specific regions of 2R.

overall_design: Seven translocations with breakpoints in 2R heterochromatin were tested: 2219 (T(2;3)ftz[Rpl]), 130058 (T(Y;2)B[SV5]), 130093 (T(Y;2)B63), 130112 (T(Y;2)B238), 101579 (T(2;3)bxd[68]), 101988 (T(Y;2)G10), and 107387 (T(2;3)E(da)). To generate embryos deficient for smaller regions of 2R heterochromatin, T(2;Y) or T(2;3) translocation males were crossed to C(2)EN females. One eighth of the embryos that lack 2R were identified according to their failure in forming the ventral furrow during early gastrulation. All embryos were collected at room temperature.


title: Genomic characterization implicates iAMP21 as a primary genetic event in childhood B-cell precursor acute lymphoblastic leukaemia

status: Public on Mar 02 2012

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

institute: Newcastle University

summary: Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct subgroup of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) shown to have a dismal outcome on standard therapy. For improved diagnosis and prognosis of these patients, the initiating genetic events need to be elucidated. To investigate the genetic basis, the genomes of 94 iAMP21 patients were interrogated by genomic arrays, FISH and MLPA. Detailed mapping of chromosome 21 refined the common region of amplification (CRA) to 5.1 Mb; including the RUNX1 gene, miR-802 and genes mapping to the Down Syndrome Critical Region. Over a quarter  of copy number alterations targeted chromosome 21, including telomeric deletions in 88% of patients. Global analysis by genomic arrays identified recurrent abnormalities affecting genes in key pathways. The frequency of these abnormalities were determined by FISH and/or MLPA; IKZF1 (22%), CDKN2A/B (17%), PAX5 (8%), ETV6 (19%) and RB1 (37%). Study of the clonal architecture provided evidence that these abnormalities, and P2RY8-CRLF2, were secondary to chromosome 21 instability. This study provides convincing evidence that chromosome 21 instability is the only abnormality common to all iAMP21 patients and the initiating event is likely hidden within the complex structural rearrangements of this abnormal chromosome.

overall_design: DNA copy number analysis of 17 diagnostic and 1 relapse acute lymphoblastic leukaemia samples was performed using agilent 185K microarrays. These samples were hybridised against gender matched reference DNA.


title: Transcriptomic analysis of the woodchuck model of chronic hepatitis B

status: Public on Apr 11 2012

city: Nutley

first: Donavan

last: Cheng

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

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

overall_design: Refer to individual Series


title: Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

summary: The Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV) can be propagated using H. zea insect cell cultures, for use as a biopesticide against Heliothine agricultural pests.This study sequenced, assembled and functionally annotated 29,586 transcript sequences from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). From these sequences, a genome-scale microarray platform was constructed and validated for effective expression analysis of H. zea genes. This array also included probes for all HaSNPV genes, thereby allowing virus and host gene changes to be monitored simultaneously.

overall_design: A 4x180,000 SurePrint Agilent expression array (Agilent, Santa Clara, CA) was employed so that a high number of probes can be included to test all 29,586 assembled H. zea sequences and to eventually select a best probe for each transcript. Two biological replicates for uninfected H. zea cells and two other biological replicates for infected samples at 18 hours post infection were analyzed. Six Agilent 60-mer oligonucleotide probes were designed by eArray (Agilent) for each transcript, in which each orientation had three probes randomly distributed across the sequences. Probes that had potential cross-hybridization (Xhyb) were removed. The final probe set for H. zea sequences included 153,583 probes. In addition, probes for all 135 H.armigera single-capsid nucleopolyhedrovirus (HaSNPV) genes were added to investigate host-virus interaction in culture.

first: Robin

last: Palfreyman

first: Leslie

last: Chan

first: Steven

last: Reid

first: Lars

middle: K

last: Nielsen


title: Human breast cancer MCF-7 cells: SN38-selected cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human breast cancer MCF-7 cells comparing control untreated cells with cells exposed to step-wise increasing doses of SN38, an active metabolite of irinotecan.

overall_design: MCF-7 cell clones were established by a limiting dilution method. SN38-sensitive MCF-7 clone (Clone 3) was used for further analyses. MCF-7/SNR cells were established by continuously exposing this clone to SN38 with stepwise increasing concentrations ranging from 0.5 ng/mL to 50 ng/mL over a period of six months. MCF-7/SNR cells were maintained in the presence of 50 ng/mL SN38 until 24 h prior to any experiment. Total RNA was extracted from MCF-7 and MCF-7/SNR cells for cDNA microarray analysis.

first: Yasuo

last: Imai