title: Dam selectivity upon glass eel migration: insights from genes expression analysis.

status: Public on Nov 20 2014

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: Gene expression analyses have been performed on brain, liver and muscle of eels (Anguilla anguilla) sampled in three different segment of the Canal des Etangs ( artificial canal linking Arcachon Basin and Lacanau Lake). The present study relies on intraspecific differences of glass eels encountered below and above the water dams.  Eels were collected using electric fishing under similar climatic and hydrological conditions. Individuals were sampled below the obstacle, close to the fishway entry in segment 1 (Pas du Bouc; +44° 50' 27.95, -1° 9' 8.09) and 2 (Langouarde, +44° 51' 32.92, -1° 9' 5.03). Fish from the segment 3 (Joncru; +44° 52' 57.13, -1° 8' 11.70) were sampled on the fishway, as water depth before the obstacle, approximately 2 meters, precluded the use of electro-fishing technique. Ten individuals were selected from each site according to their body size (between 83 and 155 mm) and health status (no externally visible pathogens) criteria. Internal parasites such as Anguilicola crassus were taken into account. Sampled and selected fish were immediately sacrified by decapitation and the whole brain, liver and muscle tissue (posterior bottom body part) were dissected and stored at -80°C in separate tubes with RNAlater buffer (Quiagen) for gene expression analysis.  Microarray analysis was conducted using an European eel-specific array consisting of a total of 14,913 probes based on a large collection of high-throughput transcriptomic sequences (Pujolar et al. 2012). Probe sequences and further details on the microarray platform can be found on the GEO database under accession number GPL15124.

overall_design: A comparative analysis of gene expression was conducted between eels sampled in differents segments of Canal des Etangs. Total RNAs were extracted from the whole liver,muscle and brain using the Absolutely RNA RT-PCR Miniprep kit (Agilent) according to the manufacturer’s instructions. Three independent RNA pools, each consisting of three individuals RNA samples, were prepared for each sampling site and tissues. Due to technical problems, it was no possible to perform microarray analyses in muscle of eels sampled in forebay 3. Accordingly, DNA microarray analysis has been performed in a total of 24 pools. RNAs’ quality was evaluated by electrophoresis on a 1% agarose gel and their concentrations were determined by spectrophotometry. Total RNA was stored in RNAse free water at -80° C. Sample labelling and hybridization were conducted following the details in Pujolar et al. (2012). Hybridized slides were scanned at 5 µm resolution using an Agilent DNA microarray scanner. Slides were scanned at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%) and the two linked images generated were analysed together. Data were extracted and background subtracted using the standard procedure in Agilent Feature Extraction (FE) software v. 9.5.1. Data were normalized separately for each tissue using a quantile normalization procedure using R (http://www.r-project.org).

first: Milan

last: Massimo

first: Pujolar

last: Marti

first: Podgorniak

last: Tomasz


title: Inflammation gene profile of sc-microglia in SOD mice

status: Public on Nov 24 2014

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Amyotrophic lateral sclerosis (ALS) is a paralytic degenerative disease of the nervous system. In the SOD1 mouse model of ALS we found loss of the molecular and functional microglia signature associated with pronounced expression of miR-155 in SOD1 mice. We also found increased expression of miR-155 in the spinal cord of ALS subjects. Genetic ablation of miR-155 increased survival in SOD1 mice and reversed the abnormal microglial and monocyte molecular signature. In addition, dysregulated proteins in the spinal cord of SOD1 mice that we identified in human ALS spinal cords and CSF were restored in SOD1G93A/miR155-/- mice. Treatment of SOD1 mice with anti-miR-155 SOD1 mice injected systemically or into the cerebrospinal fluid prolonged survival and restored the microglial unique genetic and microRNA profiles. Our findings provide a new avenue for immune based therapy of ALS by targeting miR-155.

overall_design: Total RNA was isolated from FACS sorted adult FCRLS+ microglia from spinal cords and Ly6CHi splenic monocytes from Non-Tg/miR155+/-, SOD1G93A-miR155+/- and SOD1G93A-miR155–/- mice at the age of 120d. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Mouse inflammation kit was used for gene expression profile.


title: MG447 profile of lumbar spinal cord homogenate from healthy controls and ALS

overall_design: Total RNA was isolated from whole spinal cord homogenate - post mortem obtained from healthy donors without known neurologic diseases and from sALS and fALS donors. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nanostring custom MG447 human microglia chip was used for gene expression profile


title: MG400 profile of spinal cord microglia during disease progression in SOD mice

overall_design: Total RNA was isolated from FACS sorted adult FCRLS+ microglia from spinal cords of Non-Tg and SOD1G93A mice from 30d, 60d, 90d, 120d and 140d of age. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring custom-made MG400 chip was used for gene expression profile


title: Transcriptome profiling of RNAi-trasgenic Solanum lycopersicum plants resistant to Tomato yellow leaf curl virus

status: Public on Nov 29 2014

city: Zurich

first: Maria Rita

last: Lecca

department: FGCZ

country: Switzerland

institute: University of Zurich

summary: RNA interference (RNAi) is a widely-used approach to generate virus-resistant transgenic crops. However, durability of RNAi-mediated resistance under extreme field conditions and side-effects of stable RNAi expression have not been thoroughly investigated.  Here we performed field trials and molecular characterization of two RNAi-transgenic Solanum lycopersicum lines resistant to Tomato yellow leaf curl virus (TYLCV) disease, the major constraint for tomato cultivation in Cuba and worldwide. In order to determine potential impact of the hairpin RNA transgene expression on tomato genome expression and development, differences in the phenotypes and the transcriptome profiles between the transgenic and non-transgenic plants were examined. Transcriptome profiling revealed a common set of up- and down-regulated tomato genes, which correlated with slight developmental abnormalities in both transgenic lines.

overall_design: Two RNAi transgenic TYLCV-resistant tomato (Solanum lycopersicum cv. Campbell) lines  have been generated and were designed as Kanamicin-resistant (KmR) line 126 (designated as T1) and Basta-resistant (BaR) line B1 (designated as T2).  A non-transgenic tomato line (Solanum lycopersicum cv. Campbell), designed as C line, was also taken to perform comparative gene expression analysis with the transgenic lines T1 and T2. Total RNA from control (line C) and transgenic (T1 and T2) lines (two biological replicates from each line) was extracted using standard protocols and linearly amplified to obtain Cy-3 labeled complementary RNA (cRNA) which was hybridized on commercial 4 x 44 K tomato arrays. Hybridization intensities generated after scanning of the arrays were computed to generate the raw intensity data.  Statistical analysis was performed to characterize differences in gene expression profiles, by performing two-group comparative analysis between control and transgenic tomato lines.

first: Alejandro

last: Fuentes

first: Natacha

last: Carlos

first: Yoslaine

last: Ruíz

first: Danay

last: Callard

first: Yadira

last: Sánchez

first: Vivian

last: Doreste

first: María

last: Ochagavía

first: Jonathan

last: Seguin

first: Nachelli

last: Malpica Lopez

first: Thomas

last: Hohn

first: Maria

first: Hubert

last: Rehrauer

first: Mayte

last: Piñón

first: Laurent

last: Farinelli

first: Merardo

last: Pujol

first: Mikhail

middle: M

last: Pooggin


title: miRNA profile in lumbar spinal cord homogenate from healthy controls and ALS

first: Oleg

last: Butovsky

overall_design: Total RNA was isolated from whole spinal cord homogenate - post mortem obtained from healthy donors without known neurologic diseases and from sALS and fALS donors. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring human miRNA assay kit was used for miRNA expression profile


title: Differentially Expressed Genes in Bordetella pertussis Strains Belonging to a Lineage Which Recently Spread Globally

status: Public on Nov 21 2014

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Pertussis is a highly contagious, acute respiratory disease in humans caused by the Gram-negative pathogen Bordetella pertussis. Pertussis has resurged in the face of intensive vaccination and this has coincided with the emergence of strains carrying a particular allele for the pertussis toxin promoter, ptxP3, which is associated with higher levels of pertussis toxin (Ptx) production. Within 10 to 20 years, ptxP3 strains have nearly completely replaced the previously dominant ptxP1 strains resulting in a worldwide selective sweep. In order to identify B. pertussis genes associated with the selective sweep, we compared the expression of genes in ptxP1 and ptxP3 strains that are under control of the Bordetella master virulence regulatory locus (bvgASR). The BvgAS proteins comprise a two component sensory transduction system which is regulated by temperature, nicotinic acid and sulfate. By increasing the sulfate concentration, it is possible to change the phase of B. pertussis from virulent to avirulent. Until recently, the only distinctive phenotype of ptxP3 strains was a higher Ptx production. Here we identify additional phenotypic differences between ptxP1 and ptxP3 strains which may have contributed to its global spread by comparing global transcriptional responses under sulfate-modulating conditions. We show that ptxP3 strains are less sensitive to sulfate-mediated gene suppression, resulting in an increased production of the vaccine antigens pertactin (Prn) and Ptx and a number of other virulence genes, including a type III secretion toxin, Vag8, a protein involved in complement resistance, and lpxE involved in lipid A modification. Furthermore, enhanced expression of the vaccine antigens Ptx and Prn by ptxP3 strains was confirmed at the protein level. Identification of genes differentially expressed between ptxP1 and ptxP3 strains may elucidate how B. pertussis has adapted to vaccination and allow the improvement of pertussis vaccines by identifying novel vaccine candidates.

sample_organism:
Bordetella pertussis B1917
Bordetella pertussis B1920

platform_organism:
Bordetella bronchiseptica
Bordetella pertussis

overall_design: This study was designed to investigate gene expression differences between the Bordetella pertussis strains ptxP1 and the ptxP3 in rich medium with different sulfate concentrations. Both the ptxP1 strain under low (<0.02 mM) , intermediate (5 mM) and high sulfate (50 mM) conditions and the ptxP3 strain under low, intermediate and high sulfate conditions. Culturing and gene expression analysis of B. pertussis was performed 4 times and analyzed using custom microarrays. Gene expression values were log2-transformed and differentially expressed genes were identified based on log2 fold changes. P values were calculated with a Bayes-regularized one-way ANOVA.

first: Daan

last: de Gouw

first: Dimitri

last: Diavatopoulos

first: Frits

last: Mooi


title: Genetic interactions between SUPPRESSOR OF GENE SILENCING3 and ABSCISIC ACID HYPERSENSITIVE1/CAP-BINDING PROTEIN80 affecting fertilization, embryogenesis, germination, flowering time, and powdery mildew resistance

status: Public on Nov 19 2014

city: Lubbock

first: Christopher

middle: Dale

last: Rock

state: TX

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

summary: Arabidopsis ABA HYPERSENSITIVE1 (ABH1) / CAP-BINDING-PROTEIN80 functions in cap-binding, splicing, ABA and stress response signaling and in the biogenesis of microRNAs (miRNAs).  SUPPRESSOR OF GENE SILENCING3 (SGS3) plays a crucial role in post transcriptional gene silencing (PTGS).  We show that abh1 sgs3 double mutant manifests pleiotropic phenotypes including altered ABA sensitivity in seed germination, fused cotyledons, delayed growth in root initiation and leaf production, accelerated juvenile-to-adult phase transition and flowering time, short and bent siliques with ectopic carpelloid tissues, reduced seed set due to altered carpel structure and pollen tube growth, and increased resistance to powdery mildew infection. A systems approach using meta-analysis of whole genome tiling microarray datasets for mutants of PTGS, RNA processing, and responses to environmental stress was taken to design a 135k feature custom microarray to probe the molecular bases of these phenotypes.  Results confirmed documented effects of ABA or abh1 on precursor MIRNA expression (pre-MIR159, pre-MIR168) and identified novel miRNAs and their targets regulated by ABA (pre-MIR408, LACCASE12 and -13; pre-MIR824) or elevated in abh1 sgs3 double mutant (pre-MIR156A,C; pre-MIR164B, pre-MIR167A, pre-MIR408, At5g15845/CONSTANS-LIKE1-cis-NAT-RNA). miR156 targets SQUAMOSA-PROMOTER-BINDING-PROTEIN-LIKE genes that spawn siRNAs and control phase change; miR164 targets CUP-SHAPED-COTYLEDON1 and -2 genes; miR166 methylates target PHABULOSA genomic DNA in trans; miR167 targets AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 which regulate both female and male reproduction; miR408 targets a plantacyanin which is expressed predominantly in the transmitting tract of the pistil and affects pollen tube guidance on the stigma. We also identified sgs3 by ABA interactions on gene expression which reveal potential nodes in regulatory networks linking ABA, mRNA processing and PTGS with development.

overall_design: 24 RNA samples; four genotypes (control Col-0; sgs3; abh1, sgs3 abh1 double mutant) each with and without 30 micromolar ABA treatment for 3 hr.  Three biological replicates per genotype and treatment.  Two color strand-specific labeling of cRNA, hybridized in 'round robin' factorial hybridization scheme to 12 arrays on technical duplicate slides for a total of 48 datasets.

middle: D


title: Gene expression comparision in the developing striatum between transgenic rats expressing full-length human mutant huntingtin and time-matching controls

status: Public on Nov 30 2014

city: Freiburg im Breisgau

first: Julian

last: Jaeger

address: Breisacher Straße 64

country: Germany

institute: Medical Center Freiburg

summary: The mechanisms involved in the pathogenesis of HD that result in late, and fatal, neurodegeneration are still not fully understood. The monogenic nature of HD is in contradiction with the complexity of the cellular alterations found in patients with HD. Huntingtin interacts with a broad range of proteins within the cell, and it is altered by the expanded polyglutamine tract. Transcriptional dysregulation is a common finding in genetic models and in human HD patients, and it is thought to play an important role in the disease. Although the onset of the disease is late in life, growing lines of evidence suggest that mHtt causes alterations in development. In this microarray study, the effects of mHtt on the transcriptome were investigated with a full-length  human huntingtin (96 CAG repeats) expressing transgenic rat model of HD at an early stage of development (E14).

overall_design: Aiming to reveal early transcriptional changes in transgenic embryos, we used Affymetrix GeneChip Rat Gene 1.0 ST Arrays to determine genome-wide expression profiles of transgenic and WT E14 ganglionic eminences. For this purpose, the cycles were synchronized, and time-bred transgenic rats were sacrificed on E14 in order to obtain time-matched transgenic and WT ganglionic eminences. Six BACHD+/+ and six WT transgenic ganglionic eminences were used, derived from three time-bred transgenic dams dissected on the same day. Genotyping was performed at both the genomic and transcriptional levels, in order to ensure accurate genotype determination.

first: Marie-Christin

last: Pauly

first: Lesley

last: Jones

first: Hoa

last: Nguyen

first: Guido

last: Nikkhah

first: Máté

last: Döbrössy


title: Transcriptomic change of Legionella pneumophila in water.

status: Public on Nov 26 2014

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary:
Legionella pneumophila (Lp) is an opportunistic pathogen and its survival in water is critical for human infection. Therefore, identifying the genes of Lp that are required for survival in water may help devise strategies to prevent Legionella outbreaks. In this study, we exposed Lp in rich medium and in an artificial freshwater medium (Fraquil) for 2, 6 and 24 hours to uncover the global transcriptomic changes of Lp in water. The repression of major metabolic pathways, such as division, transcription and translation, suggests that Lp enters a dormant state in water. The induction of the flagellar associated genes (flg, fli and mot), enhance entry genes (enh) and some Icm/Dot effectors suggests that Lp may be waiting to establish intracellular replication in suitable host.
Moreover, many genes involved in resistance to antibiotic and oxidative stress were induced, suggesting that Lp may be more tolerant to environmental stresses in water. Indeed, Lp exposed to water is more resistant to erythromycin, gentamycin and kanamycin than those cultured in rich medium. Apart from this, the gene bdhA involved in the degradation of the intracellular energy storage compound poly-hydroxybutyrate is highly expressed in water. Further characterization shows that bdhA is positively regulated by RpoS during short-term exposure to water. The deletion mutant of bdhA had a survival defect in water at 37°C, demonstrating that this gene is important for maintaining the long-term survivorship of Lp in water. Other identified genes highly induced upon exposure to water could also be necessary for Lp to survive in water.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila Philadelphia-1 strain JR32 was grown in AYE broth at 25°C shaking to OD600 of 1 in triplicate. Samples were taken for analysis; this is the control. Then the cultures were washed three times in Fraquil and resuspended in Fraquil to an OD600 of 1 and transfered to vessels of bioreactior (Biostat Q-plus). Samples were taken after 2h, 6h and 24h.

first: Laam

last: Li

first: Nilmini

last: Mendis

first: Hana

last: Trigui

middle: P


title: Gene expression analysis of canine osteosarcoma tissue from patients with normal and increased serum alkaline phosphatase concentration

city: Madison

first: Timothy

last: Stein

state: WI

address: 2015 Linden Drive

department: Medical Sciences

institute: University of Wisconsin-Madison

summary: Serum alkaline phosphatase (ALP) concentration is a prognostic factor for osteosarcoma in multiple studies, though its biological significance remains incompletely understood.  To determine whether gene expression patterns differed in osteosarcoma from patients with differing serum ALP concentrations, microarray analysis was performed on 18 primary osteosarcoma samples and six osteosarcoma cell lines from dogs with normal and increased serum ALP concentration.  No differences in gene expression patterns were noted between tumors or cell lines with differing serum ALP concentration using a gene-specific two-sample t-test. Using a more sensitive empirical Bayes procedure, DCUN1D1 was increased in both the tissue and cell lines of the normal ALP group.  Using QPCR, differences in DCUN1D1 expression between the two groups failed to reach significance.  The homogeneity of gene expression patterns of osteosarcoma associated differing serum ALP concentrations are consistent with previous studies suggesting serum ALP concentration is not associated with intrinsic differences of osteosarcoma cells.

overall_design: A total of 18 canine primary osteosarcoma tumor samples were used in this study.  9 tumor samples were from patients having a normal serum alkaline phosphatase concentration.  9 tumor samples were from patients having an increased serum alkaline phosphatase concentration.  There were no reference tissues or controls used in this study.

middle: J

first: Lucas

middle: C

last: Rodrigues

first: Michael

middle: A

last: Newton


title: Functional analysis of the uropathogenic Escherichia coli R049 gene

city: Tianjin

first: Dongjing

last: Yang

address: 6, Huayue Road

department: Tianjin Institute for Preventive Medicine

country: China

institute: Tianjin Centers for Disease Control and Prevention

summary: The objective was to determine the function of the novel uropathogenic Escherichia coli (UPEC) gene R049 during host infection. We infected the urinary tracts of mice with E. coli UPEC132 or the R049 deletion mutant UPEC132ΔR049.The mouse kidneys were harvested at 4 and 8 h post-infection and screened for differentially expressed genes by microarray analysis. We identified 379 and 515 differentially expressed genes at 4 and 8 h post-infection, respectively. Thirty-four of these genes were associated with inflammatory and immune signaling pathways, including those related to mitogen-activated protein kinase signaling, leukocyte transendothelial migration, cytokine-cytokine receptor interaction, Toll-like receptor signaling, and apoptosis. Protein binding (GO 0005515) was the most prevalent molecular function in the Gene Ontology terms related to differentially expressed genes. In conclusion, R049 expression in UPEC132 is related to the early innate immune and inflammatory responses in UPEC-infected hosts. This work lays the foundation for further research on anti-infective immunity against UPEC.

overall_design: A ten chip study using total RNA recovered from 10 separate mouse kidneys of five experimental groups. The five experimental groups respectively were the UPEC132_4h group, UPEC132_8h group, UPEC132ΔR049_4h group, UPEC132ΔR049_8h group and Phosphate Buffered Saline (PBS) groups. Two separate mouse kidneys in every group were tested with two chips. Each chip measures the expression level of 44,170 genes from BALB/c mouse with three 60-mer probe pairs per gene.

first: Jie

last: Dong


title: Genome-wide RNA polymerase II recruitment study during the intraerythrocytic life cycle of Plasmodium falciparum.

city: Singapore

first: Mark

middle: Stephen

last: Featherstone

state: Singapore

address: 60, Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

type: Genome binding/occupancy profiling by array

summary: We exploited the phosphorylation state of the RNAPII CTD to assess the transcriptional status of most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide recruitment and activity of RNAPII.

overall_design: We raised and used 3 different anti-RNAPII antibodies in ChIP-on-chip analysis to map the position and status of RNAPII across the entire P. falciparum genome over the 48 h of the IDC at 8 h intervals resulting in TP1-6. Total 4 antibodies were used for ChIP-chip analysis for six time points each done in triplicates, except one antibody 8WG16 which was done in duplicate. We also used 8WG16, commercial RNAPII antibody in similar study done in duplicates.

first: Ragini

last: Rai

first: Zbynek

last: Bozdech

first: Lei

last: Zhu

first: Haifen

last: Chen

first: Archana

last: Gupta

last: Zheng

first: Christiane

last: Ruedl


title: Host cell gene and pathway changes associated with high baculovirus in vitro production yields

status: Public on Nov 25 2014

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

country: Australia

institute: The University of Queensland

summary: Baculovirus-insect cell culture technology is applied for the production of veterinary and human vaccines‚ gene delivery vectors‚ and biopesticides. The current study investigated systemic cell – virus interactions under different cell culture conditions resulting in differing in virus occlusion bodies (OB)/cell yields for HearNPV infected Hzea cells. 22 microarrays were used. While mRNA levels for most genes decreased, a core set of 14 genes consistently increased in all 11 different infection conditions studied‚ suggesting a conserved up regulation pattern of these genes upon baculovirus infections. KEGG pathway analysis found strongest responses by the genes for the E3 ubiquitin-protein ligase Topors in the ubiquitin proteasome pathway‚ GAPDH in the glycolytic pathway‚ and host DNA ligase and DNA helicase in the replication process. Weighted co expression network analysis determined a module and 5 hub genes that strongly correlated to OB/cell yields. The endoplasmic reticulum functional group was particularly reduced in low producing systems. Total virus mRNA and viral genome levels had positive correlations to OB/cell yields. Virus genes were expressed in a similar temporal pattern regardless of the cell lines‚ media or infection cell densityies used. The virus Chitinase gene and Superoxide dismutase gene may be particularly important for high productivities. Overall this genome-scale expression study of different infection conditions provides insights into host insect cell responses to baculovirus infections and suggests gene expression changes that are likely important for high virus yields.

overall_design: To investigate host insect gene responses to baculovirus infection under different conditions, a set of custom microarray probes, based on de novo assembly of target sequences from deep transcriptome sequencing (SRA048534; GEO accession number: GSE34418), were used to simultaneously investigate expression of 8760 Helicoverpa zea insect genes and 134 H. armigera nucleopolyhedrovirus (HearNPV, Accession: NC_002654)) genes. In this study‚ 22 Agilent arrays (from 3 slides of 8x15,000 SurePrint Agilent format) were used to analyze samples from: 4 infections of a so called good clone generating high OB yields (duplicate cultures at 0 hour before infection (h.b.i) and at 18 h.p.i)) and 4 corresponding infections of a bad clone (poor OB yields); 6 infections of cells grown in different media (Sf900III plus FBS, IPL plus YL, and Grace's plus FBS) and 8 samples of infections conducted at low vs. high cell densities in SF900III medium, (2 replicates for each time-point‚ 0 h.p.i and 18 h.p.i‚ and for cell densities 5x10^5 and 2x10^6 cells/ml).

middle: H

first: Trinh

middle: T

last: Tran

first: Leslie

last: Chan

first: Steven

last: Reid

first: Lars

middle: K

last: Nielsen


title: Immune gene profile in lumbar spinal cord homogenate of healthy controls and ALS

first: Oleg

last: Butovsky

overall_design: Total RNA was isolated from whole spinal cord homogenate - post mortem obtained from healthy donors without known neurologic diseases and from sALS and fALS donors. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nanostring Human Immunology Kit  was used for genes expression profile


title: The S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Genome binding/occupancy profiling by genome tiling array

summary: 3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4me3, H3K9me3, H3K27me3) was mapped by ChIP-chip genome-wide promoter at post-MBT stage (5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff.

overall_design: ChIP-chip experiments were performed from  chromatin prepared by sonication after formaldehyde cross-linking, from embryos are the indicated developmental stages and ChIP DNA was hybridized onto the aforementioned Nimbegen promoter arrays.

first: O

last: Østrup

first: A

last: Reiner

first: P

last: Alestrom


title: MG400 profile of microglia from SOD miR155-KO mice

overall_design: Total RNA was isolated from FACS sorted adult FCRLS+ microglia from spinal cords of Non-Tg/miR155+/-, SOD1G93A-miR155+/- and SOD1G93A-miR155–/- mice at the age of 120d. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring custom-made MG400 chip was used for gene expression profile


title: Gene expression profiles of the Cited4-siRNA-transduced cells and the non-transduced cells.

status: Public on Nov 22 2014

city: Yonago

first: Junichiro

last: Miake

address: 36-1 Nishi-cho

department: Multidisciplinary Internal Medicine

country: Japan

institute: Tottori University Faculty of Medicine

summary: We compared the gene expression profiles of the Cited4-siRNA-transduced cells and the nontransduced cells.

overall_design: Embryoid body was formed as in vitro cardiogenesis. For comparison of gene expression profiles of  the Cited4-siRNA-transduced cells and the nontransduced cells, total RNA was extracted from  the Cited4-siRNA-transduced cells at day 6.5 and the nontransduced cells at day 6.5.


title: miRNA profile in lumbar spinal cord homogenate of SOD-miR155 Tg mice

overall_design: Total RNA was isolated from whole lumbar spinal cord homogenate of Non-Tg/miR155+/-, SOD1G93A-miR155+/- and SOD1G93A-miR155–/- mice at the age of 120d. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring  Mouse miRNA Assay Kit was used for miRNA expression profile


title: CGH characterisation of non-typeable Streptococcus pneumococcus circulating in Portugal

city: Oeiras

first: Raquel

last: Sá-Leão

address: Av da República

country: Portugal

institute: ITQB António Xavier

summary: Background. Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity. Methods. A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. Results.  NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements. Conclusions.  NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci.  Thus we propose that NT should be routinely identified and reported in surveillance studies.

overall_design: 34 isolates representative of the lineages circulating in Portugal.

first: Débora

last: Tavares

first: Alexandra

middle: S

last: Simões

first: Hester

last: Bootsma

first: Peter

middle: W

last: Hermans

first: Hermínia

last: de Lencastre


title: Regulatory role of SrrAB two-component system in Staphylococcus epidermidis growth and biofilm formation

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: Biofilm formation is considered the most important factor involved in pathogenicity of Staphylococcus epidermidis.We investigated the role of two-component signal transduction system (TCS) srrAB, which was up-regulated under micro-aerobic condition, in the growth and biofilm formation of S. epidermidis.AsrrA-deficient mutant (∆srrA) derived from S. epidermidis1457 (SE1457), exhibited dramatic reduction in growth and biofilm formation underboth aerobic and micro-aerobic conditions, and more sensitive to several different types of antimicrobial agents, H2O2 and SDS. In New Zealand Rabbit model of S. epidermidis biofilm infection, ∆srrA hardly formed biofilm compared to that of SE1457. Phenotypic alteration was restored to the wide-type levelwhen srrAB were complemented into ∆srrA. Further study found that the initial adherence capacity and production of polysaccharide intercellular adhesion (PIA) in ∆srrA were decreased, while extracellular DNA (eDNA) was increased. Transcriptional Analysisby qRT-PCR demonstrated that expression level of icaRin ∆srrA was up-regulated compared to that of SE1457 under aerobic condition, while down-regulated under micro-aerobic condition;icaA and altE were down-regulated under both conditions. Expression of genes involved in respiratory metabolism, such as qoxB(quinol oxidase polypeptide II), ctaA(heme A synthase), and pfl(pyruvate formatelyase), etc. were down-regulated in ∆srrAunder both conditions. Electrophoretic mobility shift assay (EMSA) revealed that phosphorylated SrrA bound to the promoter regions of icaR, icaA, atlE, qoxB,ctaA, andpflB just like binding its own promoter region srr. Taken together, our results demonstrate that srrAB may provide a mechanistic link between respiratory metabolism, environmental signals, and regulation of biofilm formation in S. epidermidis.

overall_design: Microarrays covering different S. epidermidis genomes were used to assess the impact of the two component system srrAB on growth and biofilm formation, by comparing WT with srrA mutant transcriptomes

first: Youcong

last: Wu

first: Tao

last: Zhu

first: Haiyan

last: Han

first: Huayong

last: Liu

last: Xu

first: Yang

first: Xing

first: Patrice

last: Francois

first: Adrien

last: Fischer

first: Li

last: Bai

first: Caiguang

last: Yang

first: Friedrich

last: Gotz

first: Di

last: Qu


title: miRNA profile in SOD-155 microglia

first: Oleg

last: Butovsky

overall_design: Total RNA was isolated from FACS sorted adult FCRLS+ microglia from spinal cords and Ly6CHi splenic monocytes from Non-Tg/miR155+/-, SOD1G93A-miR155+/- and SOD1G93A-miR155–/- mice at the age of 120d. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring  Mouse miRNA Assay Kit was used for miRNA expression profile


title: Differential regulation of microRNAs in skeletal muscle from monozygotic twins discordant for type 2 diabetes

city: Copenhagen

first: jette

last: bork-jensen

address: Tagensvej 20

department: the department of endocrionlogy (diabetes and metabolism)

country: Denmark

institute: Rigshospitalet

summary: Analysis of microRNA expression in vastus lateralis muscle biopsies from 11 genetically identical twin pairs discordant for type 2 diabetes. This eliminates the influence of genotype and leads to the identification of microRNAs that are exclusively influenced by environmental (non-genetic) factors.

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

overall_design: Total RNA containing microRNAs were obtained from muscle biopsies (vastus lateralis) from genetically identical twin pairs (n=11 pairs). All twin pairs were discordant in respect to their glucose tolerance; thus, one twin has diabetes whereas the co-twin has either normal or impaired glucose tolerance.

first: Jette

last: Bork-Jensen

first: Camilla

last: Scheele

first: Daniel

last: Christophersen

first: Emma

last: Nilsson

first: Martin

last: Friedrichsen

first: Denise

last: Fernandez-Twinn

first: Louise

last: Grunnet

first: Thomas

last: Litman

first: Kim

last: Holmstrøm

first: Birgitte

last: Vind

first: Kurt

last: Højlund

first: Henning

last: Beck-Nielsen

first: Jørgen

last: Wojtaszewski

first: Susan

last: Ozanne

first: Bente

last: Pedersen

first: Pernille

last: Poulsen

first: Allan

last: Vaag


title: Comparison of microRNA expression between prostate adenocarcinoma cells, DU-145 and immortalized normal cells, PWR-1E

city: Fort Worth

first: Smrithi

last: Rajendiran

address: 3500 Camp Bowie Blvd

institute: UNT Health Science Center

summary: The primary goal of this experiment was to determine the endogenous miRNA that are differentially expressed between prostate adenocarcinoma cells, DU-145 and prostate immortalized epithelial cells, PWR-1E. Subsequently, we performed other analysis with BLAST and in silico algorithm searches to determine the appropriate miRNA that could regulate a novel gene MIEN1.

overall_design: We used two samples, namely, DU-145 and PWR-1E, independently, for miRNA expression

first: Jamboo

last: Vishwanatha


title: Transcriptome of S. cerevisiae during production of D-xylonate

status: Public on Nov 18 2014

city: VTT, Espoo

first: Merja

last: Oja

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Production of D-xylonate in the yeast S. cerevisiae represents an example of bioprocess development for more sustainable production of value-added chemicals from cheap raw material or waste. Previously it was shown that the production of D-xylonate led to its significant intracellular accumulation and to dramatic loss of viability during the production process. In order to identify the physiological or pathological responses associated with D-xylonate production, we performed a time-course transcriptome analysis of D-xylonate production in yeast cultivated in a bioreactor.
Comparison of the transcriptomes of D-xylonate producing strain with control strain showed considerably higher expression in the xylonate producing strain of the genes controlled by the cell wall integrity pathway (CWI) and of some genes previously identified as upregulated in response to the organic acid stress. Surprisingly, also genes encoding proteins involved in translation, ribosome structure and RNA metabolism – the processes commonly found to be down-regulated under virtually every condition causing cellular stress – were upregulated during the D-xylonate production. The overall transcriptional responses were, therefore, very dissimilar to those previously reported as being associated with diverse stresses including the organic acid treatment and production. In addition, it was observed that the consumption of ethanol was slower and the level of trehalose was lower in the D-xylonate producing strain. Validation experiments including Slt2 kinase phosphorylation profiles and the quantitative PCR analyses of selected gene showed remarkably good match with our findings and confirmed the observations made in the transcriptome analysis.
The production of organic acids has a major impact on the physiology of yeast cells. There is, however, very limited overlap at the transcriptional level in responses to treatment or production of different acids. The loss of viability, observed during production and accumulation of D-xylonate, seems to be caused by erroneous interpretation of environmental signals causing a failure in entering the stationary phase and eventually leading to depletion of scarce resources by the affected cells. This, together with intracellular acidification, inevitably results in cell death.

overall_design: The study compares two yeast strains, a D-xylonate producing strain, expressing XylB gene from C. crescentus, and the isogenic parental strain, an industrial hydrolysate tolerant S. cerevisiae strain B67002. The strains were grown in bioreactors and samples for microarrays were taken from 6 time points during the cultivation (0h, 7h, 23h, 47h, 49h and 71h). Three replicate cultures were performed for each strain. The total number of microarrays is 36. Each arrays measures 5,777 genes from Saccharomyces cerevisiae with eight 60-mer probes per gene, with three-fold technical redundancy.

first: Dominik

last: Mojzita


title: DNA methylation study in breast cancer [aCGH]

city: Hannover

first: Jessica

last: Rößler

address: Carl-Neuberg Str. 1

department: Pathology

institute: Medical School Hannover

type: Genome variation profiling by genome tiling array

summary: Addressing the still unresolved question of the existence of CIMP in breast cancer DNA methylation alterations among histological breast cancer subtypes were examined by applying the HM450K BeadChip of Illumina Inc., covering about 480,000 single CpG sites. In addition to the occurrence of the hypermethylator phenotype in breast cancer, its relation to genetic instability and histological subtypes was investigated.

overall_design: Bisulfite converted DNA from 32 fresh-frozen primary breast tissue samples and 4 breast cancer cell lines were hybridized onto the HumanMethylation 450K BeadChip from Illumina Inc. Additionally, 28 of these primary samples were analyzed by array-based comparative hybdridization (aCGH).

first: Ulrich

last: Lehmann

first: Ole

last: Ammerpohl

first: Jana

last: Gutwein

first: Doris

last: Steinemann


title: Identification of microRNAs differentially expressed in zebrafish larvae following immunostimulation

first: Arvind

last: Sundaram

state: Oslo

address: Kirkeveien

summary: To identify key microRNAs involved in innate immune response of zebrafish larvae. Immunostimulation experiments were carried out on 72 hours post fertilisation larvae by exposing them to lipopolysaccharide or peptidoglycan. Samples were collected at 1, 2 and 12 hours after exposure and total RNA was extracted. Transcript level of 246 microRNAs was quantified using microarray and further validated through real-time PCR

overall_design: MicroRNA expression in immunostimulated zebrafish larvae was measured at 1, 2 and 12 hours after exposure to 200 µg/ml of lipopolysaccharide from Salmonella enterica typhimurium or peptidoglycan from Staphylococcus aureus. Experiments were preformed in triplicates

first: Vishwanath

last: Kiron

first: Joaquín

last: Dopazo

first: Jorunn

middle: B

last: Jørgensen

first: Jorge

middle: O

last: Fernandes


title: Expression data from pig (Sus Scrofa) ileum tissue from animals receiving different diets at 5 days after weaning

status: Public on Nov 14 2014

city: Piacenza

first: Lorenzo

last: Bomba

state: Piacenza

address: via Emilia Parmense, 82

department: Istituto di Zootecnica

institute: Università Cattolica del Sacro Cuore

summary:
Weaning is a very critical period for piglets, typically accompanied by lower feed intake, weight loss after weaning and increased mortality. At weaning, piglets are exposed to many stressors, such as loss of mothering, mixing with other litters, end of lactational immunity, and a change in their environment and gut microbiota. After weaning, morphological and histological changes occur in the small intestine of piglets producing a rapid change of feeding regime which is critical for the immature digestive system. Sixteen female piglets were weaned to assess the effect of sorbic acid supplementation on the small intestine tissue transcriptome. At weaning day (T0), 4 piglets were sacrified and tissue samples collected. The remaining 12 piglets were weighted and randomly assigned to different post weaning (T5) diets. Diet A (n=6) contained 5 g/kg of sorbic acid. Diet B (n=6) is the same as Standard diet. Total RNA was isolated from ileum samples to be analyzed using the a CombiMatrix CustomArrayTM 90K platform . Even though diet had no detectable effect during the first 5 days after weaning, outcomes from this study highlighted some of the response mechanisms to the stress of weaning occurring in the piglet gut. A total of 205 differentially expressed genes were used for functional analysis using bioinformatics through BLAST2GO, Ingenuity Pathway Analysis 8.0, and the Dynamic Impact Aproach (DIA). Bioinformatics analysis revealed that Apoptosis, RIG-I-like and NOD-like receptor signaling were altered as a result of weaning. Results suggest that immune and inflammatory responses were activated and likely are a cause of small intestine atrophy as revealed by a decrease in villus height and villus/crypt ratio.
Keywords: weaning, gut, gene expression, sorbic acid, microarray analysis

overall_design: Comparative RNA expression profiles from post weaning and pre weaning ileum tissue of 16 piglets receiving at post weaning two different diets (sorbic acid addition).

first: Andrea

last: Minuti

first: Sonia

last: Moisa

first: Erminio

last: Trevisi

first: Elisa

last: Eufemi

first: Michela

last: Lizier

first: Franco

last: Lucchini

first: Marcin

last: Rzepus

first: Aldo

last: Prandini

first: Filippo

last: Rossi

first: Raffaele

last: Mazza

first: Giuseppe

last: Bertoni

first: Juan

last: Loor

first: Paolo

last: Ajmone-Marsan


title: G2/M transition for stabilizing mouse haploid ESCs: CGH

status: Public on Nov 07 2014

city: Tokyo

first: Saori

last: Takahashi

address: 1-5-45 Yushima Bunkyo-ku, Tokyo

department: Epigenetics

institute: Tokyo Medical and Dental University

summary: To test genome stability of the parthenogenetic haploid embryonic stem cells, we performed array comparative genomic hybridization (aCGH) analysis.

overall_design: Two independent experiments (samples and experimental control) were performed.

first: Jiyoung

last: Lee

first: Takashi

last: Kohda

first: Miyuri

last: Kawasumi

first: Masami

last: Kanai-Azuma

first: Tomoko

last: Kaneko-Ishino

first: Fumitoshi

last: Ishino


title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs

status: Public on Nov 06 2014

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3' processing in vitro and in vivo. RBBP6 associates with other core factors, and this interaction is mediated by an unusual ubiquitin-like domain, DWNN (domain with no name), that is required for 3' processing activity. The DWNN is also expressed, via alternative RNA processing, as a small single-domain protein (isoform 3 [iso3]). Importantly, we show that iso3, known to be down-regulated in several cancers, competes with RBBP6 for binding to the core machinery, thereby inhibiting 3' processing. Genome-wide analyses following RBBP6 knockdown revealed decreased transcript levels, especially of mRNAs with AU-rich 3' untranslated regions (UTRs) such as c-Fos and c-Jun, and increased usage of distal poly(A) sites. Our results implicate RBBP6 and iso3 as novel regulators of 3' processing, especially of RNAs with AU-rich 3' UTRs.

overall_design: RBBP6 siRNA or control siRNA was transfected in MCF7 cells in duplicates and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix)

first: Dafne

last: DiGiammartino

first: Koichi

last: Ogami

first: Jossie

last: Yashinskie

first: Mainul

last: Hoque

first: Bin

last: Tian

first: James

middle: L

last: Manley


title: A composite map of copy number variable (CNV) regions in the horse genome and the discovery of CNVs involved in equine XY disorders of sexual development

city: College Station

first: Sharmila

last: Ghosh

address: VMS Building, Rm 107, 4458 TAMUS

department: VIBS

institute: Texas A&M University

summary: 38 horses from 16 diverse breeds and Przewalski's Horse were used to generate a composite CNV map of equine genome. This map was used to detect novel copy number variation in six horses affected with disorder of sexual development (DSD).

overall_design: 38 horses from 16 diverse breeds and Przewalski's Horse, at least one male and one female were taken from each breed, six DSD 'Sex-reversal' samples. Male and DSD samples were hybridized with Thoroughbred1, and female samples were hybridized with Thoroughbred2

first: Zhipeng

last: Qu

first: Erica

last: Fang

first: Pranab

last: Das

first: Jana

last: Caldwell

first: Rytis

last: Juras

first: E

middle: G

last: Cothran

first: Sue

last: MacDonell

first: Daniel

last: Kenney

first: Teri

last: Lear

first: David

last: Adelson

first: Bhanu

last: Chowdhary

first: Terje

last: Raudsepp


title: Nucleosome occupancy measurments in Bptf knockout ESC, MEF and DP thymocytes.

city: Richmond

first: Joseph

middle: William

last: Landry

state: Virginia

address: 401 College Street

department: Human and Molecular Genetics

institute: Virginia Commonwealth University

summary:
NURF is a remodleing complex expressed in many cell types.  Knockout of Bptf, the unique and essental subunit of NURF, results in altered nucleosome occupancy across the genome.
To measure changes in nucleosome occupancy we hybridized nucleosomal DNA overdigested with MNase to 10 bp tiling arrays covering 3.3 Mbp of the mouse genome.

overall_design: Comparison of nucleosome positions in control and Bptf knockout ESC, MEF and DP thymocytes.

first: Zhijun

last: Qiu


title: Renal cells Carcinoma (RCC) Genome variation profiling by genome tiling array with Agilent CGH array

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary: Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.

overall_design: 9 samples was analysed by arrayCGH method using Agilen recommendations. Sample was labeled in Cy5 and co-hybridized with control DNA cy3 labeled.


status: Public on Nov 05 2014

city: Helsinki

first: YOU

last: ZHOU

address: Tukholmankatu 8

institute: Minerva Institute for Medical Research

summary: To determine whether expression microRNAs (miRNAs) in visceral adipose tissue (VAT) is altered in human non-alcoholic fatty liver disease (NAFLD), we first performed miRNA profiling of VAT from subjects with (n=15, macroscopic liver fat >30%) or without (<5%, non-NAFLD, n=15) NAFLD. VAT miRNA expression profiles in the two groups were similar except for a single miRNA, miR-192*, which was 1.9-fold increased in NAFLD. We next overexpressed miR-192* in cultured human adipocytes, measured its effect on the cellular triglyceride content, and characterized these adipocytes by transcriptomic profiling followed by pathway analysis, qPCR and quantification of select cellular proteins.

overall_design: SGBS preadipocytes were transduced with shRNA miR-192* or a non-targeting control miRNA. Growth media was added after four hrs of incubation. The cells were grown in standard medium for 48 hrs without selection, after which the growth medium was replaced with a medium containing 0.5 μg/ml puromycin (Sigma-Aldrich). SGBS adipocytes overexpressing miR-192* or a non-targeting control miRNA were lysed and total RNA was isolated and purified. After verification of the quality of RNA, we performed gene expression analysis in a modified standard Agilent microarray (023043) containing 205 free positions (Agilent) to was verified by 2100 Bioanalyzer (Agilent).

first: You

last: Zhou

first: Vesa

middle: M

last: Olkkonen

first: Raghavendra

last: Mysore


title: Renal cells Carcinoma (RCC) Genome variation profiling by genome tiling array with Perkin Elmer Constituionnal Chip platform

overall_design:
10 samples was analysed by arrayCGH method using Perkin Elmer recommendations. Sample was labeled in Cy3 and co-hybridized with control DNA cy5 labeled.

Please note that normalized data matrix contains logRatio Cy3/Cy5 values with non-unique 'CLONE_ID' identifiers, and thus included as a Series supplementary file.


title: Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

status: Public on Nov 02 2014

city: Sapporo

first: Ryozo

last: Imai

address: Hitsujigaoka 1, Toyohira-ku

department: Hokkaido Agricultural Research Center

institute: National Agriculture and Food Research Organization (NARO)

summary:
A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction.
Keywords: transgenic vs wt Col.-0 comparison

overall_design: Total RNA was extracted from rosette leaves of two independent 3-week-old T1 Arabidopsis Col-0 plants over-expressing TaSK5 driven by 35S promoter and the whole transcriptome was compared with that of wild-type plant. Sample pairs in two independent transformants (OX7 and OX17), referred as biological replicates, were analyzed by the two-color method. Dye-swapped hybridizations were performed in every replicate.

first: Nikolai

last: Christov

first: Petya

last: Christova

first: Hideki

last: Kato

first: Yuelin

last: Liu

first: Kentaro

last: Sasaki


title: Innate and adaptive immunity in zebrafish: time course (zebrafish)

status: Public on Nov 03 2014

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

summary: The interaction between fungal pathogen and host innnate and adaptive immunity during infection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism as the host to study C. albicans infection via systems biology approach. Transcriptome microarray data and histological analysis of surviving fish were sampled at different post-infection time points. Time-course microarray data following primary and secondary infection of zebrafish by Candida albicans were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks for primary and secondary responses of the host.

overall_design: Each fish in the first group was intraperitoneally injected with 1 × 10E5 and 1 × 10E7 CFU C. albicans at day 0 and 14, respectively. These infected fish were collected at 1, 2, 3, 6, 14, 17.5, 21 dpi (day post infection). For the second group, a second injection of C. albicans was given on 14th day of the first infeciton, and the repeated infeceted fish were collected at 2, 6, 12, 18, 24, 30, 36, 42 hours post second injection.   1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Each time points contain two biological repeats.

first: Chung-Yu

last: Lan

first: Che

last: Lin

first: Bor-Sen

last: Chen

first: Wen-Ping

last: Hsieh

last: Wong


title: Leigh Syndrome in Drosophila melanogaster: morphological and biochemical characterization of Surf1 post-transcriptional silencing.

status: Public on Nov 04 2014

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

institute: University of Padova

summary: Leigh Syndrome (LS) is the most common early-onset, progressive mitochondrial encephalopathy usually leading to early death. The single most prevalent cause of LS is occurrence of mutations in the hSurf1 gene. LSSurf1 patients show a marked and specific decrease in the activity of mitochondrial respiratory chain complex IV (cytochrome c oxidase, COX). hSurf1 encodes an inner membrane mitochondrial protein involved in COX assembly. We established a D. melanogaster model of LS based on the post-transcriptional silencing of CG9943, the Drosophila homolog of hSurf1. Knock down of Surf1 was induced (i) ubiquitously, which led to larval lethality; (ii) in the mesodermal derivatives, which led to pupal lethality; (iii) in the central nervous system, which allowed survival; and (iv) at specific developmental stages. A biochemical characterization was carried out in knock down individuals, which unexpectedly revealed defects in all complexes of the mitochondrial respiratory chain (MRC) included the F-ATP synthase (complex V) in larvae, and a COX-specific impairment in adults. Silencing of Surf1 expression in Drosophila S2R+ cells led to loss of COX activity associated with decreased oxygen consumption. We conclude that Surf1 is essential for COX activity and mitochondrial function in D. melanogaster, and provide a new tool to clarify the pathogenic mechanisms of LS.

overall_design: Gene expression profiling was carried out on controls and Surf1 Act-Gal4 KD third stage and first stage Drosophila larvae using the Drosophila 2.0 custom platform (Agilent Technologies). Total RNA was obtained from the whole body of 1st instar larvae for each genotype. Four biological replicates were analyzed for controls and Surf1 KD samples respectively for a total of 8 microarray experiments

first: Caterina

last: Da Re

first: Sophia

last: von Stockum

first: Mauro

last: Zordan

first: Massimo

last: Zeviani

first: Paola

last: Cisotto

first: Alberto

last: Biscontin

last: Millino

first: Paolo

last: Bernardi

first: Rodolfo

last: Costa


title: Gene expression in NIL-DOG1 and rdo5-1

status: Public on Nov 01 2014

city: koeln

first: Yong

last: Xiang

address: Carl-von-Linne-Weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: We have identified RDO5 as a phosphatase that promotes seed dormancy, most likely independent from ABA and DOG1. To obtain an indication about the genetic and molecular pathways by which RDO5 functions, we performed a transcriptomic comparison between rdo5-1 and its wild-type NIL-DOG1 at different seed stages, using the Arabidopsis Affymetrix AGRONOMICS1 tiling microarrays

overall_design: RNA was extracted from siliques at 14 days after pollination, freshly harvest seeds and 6 hours imbibed seeds. The transcriptome analysis was carried out using Affymetrix microarrays (Arabidopsis AGORONOMICS1 genome array)

first: Wim

last: Soppe


title: Sex-specific changes of placental transcriptome in response to a n-3 LCPUFA supplementation of pregnant women

status: Public on Oct 30 2014

city: Freising-Weihenstephan

first: Bernhard

last: Bader

address: Gregor-Mendel Straße 2

department: Clinical Nutritional Unit - ZIEL-Research Center for Nutrition and Food Sciences

institute: Technische Universität München

summary:
Previously, we have examined the effect of maternal dietary n-3 LCPUFA supplementation during pregnancy to reduce offspring obesity risk. Considering the involvement of the placenta in fetal programming, we here analyzed the sexually dimorphic potential of placental gene expression, its response to the n-3 LCPUFA intervention and their correlation to offspring obesity risk.
The placenta is implicated to play a key role in mediating fetal /metabolic programming of the offspring in utero. For human and mouse models, it has been reported that male and female fetuses differentially respond to in utero environmental stimuli. Moreover, sexual dimorphism is also known for placental gene expression, LCPUFA metabolism and adipose tissue distribution. Therefore, we explored whether the maternal n-3 LCPUFA intervention during pregnancy has a sex-specific impact on the term placental transcriptome in a defined subpopulation of the INFAT (impact of nutritional fatty acids during pregnancy and lactation on early human adipose tissue development) study. In addition, we assessed the relationships between sex-specific placental gene expression and sex steroids levels, and expression changes of specific genes and offspring obesity risk. Overall, human term placentas show sexually dimorphic gene expression and respond sex-specifically to dietary maternal n-3 LCPUFA intervention during pregnancy with more pronounced effects on gene expression and estradiol-17β/testosterone ratio in female than male placentas.

overall_design: Human term placentas were obtained at birth from participants of the INFAT study, which were randomly assigned at the 15th week of gestation to either a control (healthy nutrition during pregnancy) or the n-3 LCPUFA supplementation group (1020g docosahexaenoic acid and 180g eicosapentaenoic acid per day). For this analysis, placentas were selected that were derived from spontaneous birth, where no induction of labor, anesthetics or analgesics was used. Placenta pieces were sampled according to a standardized protocol and the isolated RNAs (n=16), pooled from four different locations within one placenta, were labeled and hybridized to Affymetrix NuGO_Hs1a52018 arrays. The microarray data was analyzed for (i) the factor n-3 LCPUFA intervention by pooling the data of male and female placentas, (ii) the factor n-3 LCPUFA intervention considering offspring sex by using a model including a sex term, (iii) the factor sex separately in the control and the intervention group and (iv) the factor n-3 LCPUFA intervention separately in male and female placentas.

first: Berhard

first: Eva-Maria

last: Sedlmeier


title: Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-Htt deficient mice

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

type: Methylation profiling by genome tiling array

summary:
The serotonin transporter (5-HTT) gene-linked polymorphic region has been suggested to play a modulatory role in mediating the effects of early-life stress on psychopathology rendering carriers of the low-expression short (s)-allele more vulnerable to environmental adversity in later life. Here we analyzed the effects of prenatal stress (PS), 5-Htt genotype, and an interactin of both on DNA methylation in the hippocampi of female C57BL/6 mice.
Here, we applied Methylated DNA ImmunoPrecipitation (MeDIP) in a maternal restraint stress paradigm to perform a global promoter DNA methylation screen: Hippocampal DNA of wild type and 5-Htt +/- mice in stressed and control environments were analyzed to define genotype- (G) and environment-dependent (E) as well as GxE-interactive effects on promoter DNA methylation in the brain region, where marked effects were expected.

overall_design: MeDIP-based promoter DNA methylation screen

first: Karla

last: Schraut

first: Daniel

last: van den Hove

first: Klaus

middle: P

last: Lesch


title: Transcriptome response to vanadium stress in rice roots

status: Public on Nov 11 2014

city: Tainan

first: Hao-Jen

last: Huang

address: No.1, University Raod,

department: Life Sciences

institute: National Cheng Kung University

summary: Trace concentrations of vanadium (V) have several benefits for plant growth, but high concentrations are toxic. To help characterize the cellular mechanisms underlying the toxic effects of V in plants, we present the first large-scale analysis of rice root responding to V during the early stages (1 and 3 h) of toxicity. Exposure to V triggered changes in the transcript levels of several genes related to cellular metabolic process, response to stimulus and transporters. Gene expression profiling revealed upregulated levels of genes associated with signaling and biosynthesis of auxin, abscisic acid (ABA) and jasmonic acid (JA) in V-treated rice roots. In addition, V upregulated the expression of ATP-dependent GSH-conjugated transport, ATP binding cassette (ABC) transporter, and markedly downregulated of the expression of divalent cation transporters, drug/metabolite transporter (DMT) and zinceiron permease (ZIP). Among the V-specific responsive transcription factors and protein kinases, the most predominant families were NAC (NAM, ATAF, CUC) transcription factor, receptor-like cytoplasmic kinase VII (RLCK-VII) and leucinerich repeat kinase VIII (LRR-VIII). These microarray data provide a new insight into the molecular mechanism of the rice roots response to V toxicity. Trace concentrations of vanadium (V) have several benefits for plant growth, but high concentrations are toxic. To help characterize the cellular mechanisms underlying the toxic effects of V in plants, we present the first large-scale analysis of rice root responding to V during the early stages (1 and 3 h) of toxicity. Exposure to V triggered changes in the transcript levels of several genes related to cellular metabolic process, response to stimulus and transporters. Gene expression profiling revealed upregulated levels of genes associated with signaling and biosynthesis of auxin, abscisic acid (ABA) and jasmonic acid (JA) in V-treated rice roots. In addition, V upregulated the expression of ATP-dependent GSH-conjugated transport, ATP binding cassette (ABC) transporter, and markedly downregulated of the expression of divalent cation transporters, drug/metabolite transporter (DMT) and zinceiron permease (ZIP). Among the V-specific responsive transcription factors and protein kinases, the most predominant families were NAC (NAM, ATAF, CUC) transcription factor, receptor-like cytoplasmic kinase VII (RLCK-VII) and leucinerich repeat kinase VIII (LRR-VIII). These microarray data provide a new insight into the molecular mechanism of the rice roots response to V toxicity.

overall_design: Comparison of mock control and rice seedlings treated with 1 mM vanadate. Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h.; Biological replicates: 3 control replicates, 3 vanadate-treated replicates.

first: Chung-Yi

last: Lin


title: Human HEK 293T cells transfected with pEGFP-survivin gene

status: Public on Oct 21 2014

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary: Transcriptional profiling of human embryonic kidney 293 cells comparing transfected control pEGFP-C1 (empty vector) with pEGFP (survivin vector).

overall_design: One condition experiment; survivin transfected cell as test sample vs empty vector transfected cell as reference; one dye swap replicate

first: Gonzalo

last: Fernandez

first: Diego

last: Rodriguez

first: Manuel

last: Valenzuela

first: David

middle: J

last: Munroe

first: Carlos

last: Rosas

last: Lemus

first: Natalia

last: Diaz

first: Mathew

middle: C

last: Wright

first: Lissete

last: Leyton

first: Julio

last: Tapia

first: Andrew

middle: F

last: Quest


title: Bradyrhizobium japonicum_Bacteroids vs. Bacteria grown in HM-Arabinose

city: Columbia

last: Emerich

state: MO

address: 117 Schweitzer Hall

department: Biochemistry

institute: University of Missouri-Columbia

summary: A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes essential for symbiotic nitrogen fixation.

overall_design: Four independent biological replicates for bacteroids and free-living cells. Total of 8 arrays including dye swap.

first: Sooyoung

last: Franck

first: William

first: Sean

middle: R

last: Birke

first: Woo-Suk

last: Chang

first: Dipen

last: Sangurdekar

first: Eddie

last: Cytryn

first: Trupti

last: Joshi

first: Michael

last: Sadowsky

first: Gary

last: Stacey

first: Dong

last: Xu


title: Real-time quantitative PCR analysis of mouse lungs

city: Hamilton

first: Ali

middle: A

last: Ashkar

address: 1280 Main St. West

institute: McMaster University

summary: 2 IL-15 KO AND 2 C57BL/6 mice were injected with 5X10^5 cells of the polyoma Middle T (pMT) primary breast tumor cell line intraveneously(IV).  2 days post injection, the lungs were harvested and one lobe of the lung was used to extract RNA from.  We then utilized the SABBiosciences RT^2 Profiler PCR Array for Mouse cytokines and Chemokines to determine levels of cytokine/chemokines that were different in these 2 mice at this time point.  We were interested in the immune responses that may change in response to tumor cells entering and establishing in the lung (as a model of metastasis) in the presence or absence of IL-15.

overall_design: qPCR gene expression profilling performed on the lungs 2 IL-15 KO(test) and 2 C57BL/6 (control), 2 days post IV tumor cell injection.  Equal amounts of total RNA per subject were used in the assay.

first: Amy

middle: E

last: Gillgrass


title: A  Circulating Antibody Panel for Pre-transplant Prediction of FSGS Recurrence after Kidney Transplantation

city: San Francisco

first: Tara

last: Sigdel

state: CA

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

summary: Recurrence of focal segmental glomerulosclerosis (rFSGS) after kidney transplantation is a cause of early and accelerated graft loss. Immuneadsorption can alleviate renal dysfunction and suggests that circulating antibodies (Ab) are likely implicated in disease pathogenesis. To evaluate pathogenic Ab in rFSGS, we processed 141 unique serum samples from patients with and without primary rFSGS (n=64) and 34 non-FSGS control, transplanted at five (US and EU) hospitals. 9000 antigens were screened in pre-transplant sera by protein arrays and 10 Ab targeting glomerular antigens were selected for ELISA validation. A panel of 7 Ab (CD40, PTPRO, CGB-5, FAS, P2RY11, SNRPB2 and APOL2) could predict post-transplant FSGS recurrence with 92% accuracy. Pre-transplant elevation of anti-CD40 Ab levels alone had a substantial impact (78% accuracy) on the identification of rFSGS risk after transplantation. Epitope mapping of CD40 with customized peptide arrays and rFSGS sera demonstrated altered immunogenicity of the extracellular CD40 domain in rFSGS. Immunohistochemistry of CD40 demonstrated a differential expression of these antigens in FSGS compared to non-FSGS. Anti-CD40 Ab purified from rFSGS patients were uniquely pathogenic in human podocyte cultures; injection of these Ab resulted in heightened proteinuria, independently and in combination with suPAR in a rodent model, abrogated by injection of monoclonal Ab to CD40. In conclusion, a panel of 7 Ab can identify primary FSGS patients at high risk of recurrence prior to transplantation, allowing for customized therapies and improved patient selection for transplant. Intra-renal CD40 is an important axis of disease pathogenesis, and human trials of anti-CD40 therapies are warranted to evaluate their efficacy in preventing rFSGS and improving graft survival.

overall_design: The purpose of the study was to identify potential auto-Abs associated with rFSGS. We used a discovery set of pre-transplant sera from 20 unique patients with biopsy confirmed diagnosis of primary FSGS as their cause of ESRD, of which 10 had progressed to rFSGS within the first post-transplant year and 10 did not have recurrence of proteinuria or histological disease after transplantation (nrFSGS).

first: Marianne

last: Delville

first: Changli

last: Wei

first: Jing

last: Li

first: Szu-Chuan

last: Hsieh

first: Alessia

last: Fornoni

first: George

last: Burke

first: Patrick

last: Bruneval

first: Maarten

last: Naesens

first: Annette

last: Jackson

first: Nada

last: Alachkar

first: Guillaume

last: Canaud

first: Christophe

last: Legendre

first: Dany

last: Anglicheau

first: Jochen

last: Reiser

first: Minnie

last: Sarwal


title: Expression of microRNAs and their target genes and pathways associated with ovarian follicle development in cattle

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: Development of ovarian follicles is controlled at the molecular level by several gene products whose precise expression leads to regression or ovulation of follicles. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through sequence-specific base pairing with target messenger RNAs (mRNAs) causing translation repression or mRNA degradation. The aim of this study was to identify miRNAs expressed in ovarian follicles, localize their expression within the theca and/or granulosa layers and their putative target genes/pathways that are involved in bovine ovarian follicle development. By using miRCURY microarray (Exiqon) we identified 14 and 49 differentially expressed miRNAs (P < 0.01) between dominant and subordinate follicles in theca and granulosa cells, respectively. The expression levels of four selected miRNAs were confirmed by qRT-PCR. To identify target prediction and pathways of differentially expressed miRNAs Union of Genes option in DIANA miRPath v.2.0 software was used. The predicted targets for these miRNAs were enriched for pathways involving oocyte meiosis, Wnt, TGF-beta, ErbB, Insulin, P13K-Akt and MAPK signaling pathways. This study identified differentially expressed miRNAs in the theca and granulosa cells of dominant and subordinate follicles, and clearly implicates them in having important roles in regulating known molecular pathways that determine the fate of ovarian follicle development.

overall_design: Dominant and subordinate follicles were extrated from bovine heifers on day 2.5-3.5 of oestrus cycle. Theca and granulosa cells were isolated from each sample. Dominant and subordinate follicles in each tissue were compared.

first: Anna

last: Zielak-Steciwko

first: John

last: Browne

first: M

last: Gajewska

last: Dzięcioł

first: T

last: Szulc

first: Alexander

last: Evans


title: Expression analysis of motile strain of Sphingomonas sp. A1

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

institute: Kyoto University

summary:
Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1
All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.

overall_design: A two chip study using total RNA recovered from wild-type and motile strains of Sphingomonas. sp A1 grown in 0.5% alginate medium.

first: Yukie

last: Maruyama

first: Chie

last: Hayashi

first: Masahiro

last: Kobayashi

first: Kousaku

last: Murata


title: Analysis of the mesSR regulon in M. catarrhalis

city: Dallas

first: Eric

last: Hansen

address: 5323 Harry Hines Blvd

department: Microbiology

country: USA

institute: University of Texas Southwestern Medical Center

summary: Transcription profile analysis of a wild type ETSU9 strain and its isogenic non-polar in frame mesR mutant.

overall_design: One condition experiment, WT-mesR mutant. WT-mesR mutant, biological replicates: 3 independently grown bacterial cultures. One replicate per array. Each WT-mesR mutant, biological replicate was independently labelled with each of the dyes

first: Maria

last: Labandeira-Rey

first: Christine

last: Pybus


title: Analysis of genes regulated by Akirin and Brahma upon IMD pathway activation in drosophila S2 cells

city: STRASBOURG

first: Nicolas

last: MATT

address: 15 rue René Descarte

department: IBMC

institute: CNRS

summary: This micro-array helps establishing the function of Akirin, a nuclear protein with unknown domains, a putative interacting partner, in the transcriptional regulation of the targets of Relish, a NF-kB factor required to fight Gram(-) bacteria infection in Drosophila melanogaster.

overall_design: S2 cells were knocked down for Relish, Akirin and immune-challenged by Calcium-phosphate transient transfection of dsRNA and over-expressing PGRP-LC vector. Positively transfected cells were sorted by co-expressed Tomato and RNA was purified and analysed by a micro-array

first: François

last: Bonnay

last: Matt

first: Laurent

last: Troxler


title: NFkB perturbation followed by genome-wide allelic-expression data assessment

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

institute: McGill University and Génome Québec Innovation Centre

type: Expression profiling by genome tiling array

summary: We developed a method that perturbs transcription factor followed by monitoring genome-wide allelic expression measurements in living cells. As a model for this novel approach, we chose the factor NFκB.

overall_design: We performed TNF-α induction coupled to inhibition of NFκB in LCLs followed by Allelic Expression (AE) analysis on Illumina HumanOmni5-Quad BeadChips. Samples used included two HapMap trios: one from the CEU (GM12891, GM12892, and GM12878) and one from the YRI (GM19239, GM19238, and GM19240) population. NF-κB knockdown was validated using RT-PCR of known gene targets for NFkB. Differential AE was assessed on Illumina HumanOmni5-Quad BeadChips for each experimental condition: (1) inhibition with Helenanin followed 1 hour later by activation by TNF-α (TN); (2) activation by TNF-α (tnfalpha); (3) DMSO; (4) no treatment (notmt).

first: Alicia

last: Schiavi

first: Bing

last: Ge


title: Characterization of the inflammatory phenotype of Mycobacterium avium subspecies paratuberculosis

city: Corvallis

first: Luiz

last: Bermudez

state: Oregon

address: 105 Dryden Hall

department: Biomedical Sciences

institute: Oregon State University

summary: Understanding the pathogenic mechanisms and host responses to Johne's disease, caused by Mycboacterium avium subspecies paratuberculosis (MAP), is complicated by a number of challenges of the disease progression and lack of ex vivo models to study the disease.  We describe novel cell culture passage model which mimics the course of infection in vivo.  Using this model we determined that cell culture passaged MAP develops an inflammatory phenotype initiating higher levels of pro-inflammatory cytokines and chemokines compared to levels initiated by non-passaged MAP.  To verify that the MAP phenotypes were changing, we conducted transcriptome analysis of each population during the passage model and identified a change in gene expression, specifically and upregulation of genes involved in the biosynthesis of lipid components within the cell.  Lipidomic analysis showed dramatically different lipid profiles between the 2 populations.  These transcriptome changes were validated by the identification of high levels of upregulated transcripts from MAP-infected cattle ileal tissue.  In total, this study described a novel model used to show that MAP changes phenotype during intracellular passage, thus changing its lipid profile and triggering an inflammatory response in the host leading to the severe clinical phage of Johne's disease.

sample_organism: Mycobacterium avium subsp. paratuberculosis

overall_design: In total 6 slides were analyzed.  Of the 2 phenotypes under investigation, the P0 samples (non-inflammatory) were analyzed in triplate and the P2 samples (inflammatory) were analyzed in triplicate.  Each slide fluorescence intensity was measured at PMT400, 600 and 750. Each oligo on each slide was spotted in triplicate and each slide had its own internal controls.

first: Jamie

last: Everman

first: Torsten

last: Eckstein

first: Jonathan

last: Rousey

first: Paul

last: Coussens

first: John

last: Bannantine


title: Bradyrhizobium japonicum_Bacteroids Time Course

first: David

last: Emerich

summary: A time-course transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed to characterize senescence genes.

overall_design: Four independent biological materials for bacteroids and free-living cells at 6 time points. Seven or eight arrays including dye swap are presented at each time point.

first: Sooyoung

last: Franck

first: Kent

last: Strodtman

first: Jing

last: Qiu


title: Human Breast Cancer Cell MCF-7: Control vs. Gli1 Transfected

city: shanghai

first: juan

last: xu

address: 21F, 415 fengyang road

institute: endocrinology

summary: Transcriptional profiling of breast cancer cell line MCF-7 stably transfected with  pcDNA3.1-Gli1 comparing control ones transfected with CON

overall_design: Total RNA of cells transfected with con or pcDNA3.1-GLI1 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Microarray analysis of Gli1-MCF-7 vs. pcDNA3.1-MCF-7 cells in dye-swap experiment

first: Juan

last: Xu

first: Gaoxiang

last: Huang


title: A receptor protein links plant cell wall surveillance with hormone signaling

status: Public on Oct 06 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
The growth and shape of plants is mainly defined by the properties of their cell walls, which dynamically adapt to internal and external cues. Therefore, the cell wall is under constant surveillance to relay feedback information to the cell interior. However, very little is known about how cell wall signaling is integrated with intracellular growth regulation. Here, we have identified a receptor-like protein, RLP44, which conveys information from the cell wall to the brassinosteroid hormone signaling pathway by interacting with the regulatory receptor-like kinase BAK1. This conditional RLP44-mediated signaling activation is required for normal development and stress responses, requires functional brassinosteroid receptor, but is partially independent of the hormone ligand.
We sought to identify transcriptional changes in the PMEIox transformant in which an altered pectin modification leads to an induction of the brassinosteroid signalling pathway. In addition we determined which fraction of these expression changes was reverted in the cnu1 and cnu2 suppressor mutants of PMEIox, respectively. Complete transcriptome analysis was performed on Col-0 wild-type as well as the PMEIox transformant and the cnu1 and cnu2 suppressor mutant seedlings grown in the dark for four days.

overall_design: 3 Biological replicates of etiolated seedlings grown for 4 days in the dark were harvested on successive weeks.

first: Sebastian

last: Wolf


title: Affymetrix SNP array data for human prostate tumor samples

status: Public on Oct 20 2014

city: Boston

first: Carmen

last: Priolo

state: MA

address: 1 Blackfan Circle

institute: Brigham and Women's Hospital

summary: Metabolomics was used to identify metabolic fingerprints of AKT1 activation or MYC overexpression in human prostate tumors. Genomics was used to determine how many of these tumors had a genetic aberration underlying signaling activation.

overall_design: Copy number analysis of Affymetrix 250K SNP arrays was performed for 59 human prostate tumors and 6 normal prostate samples.

first: Massimo

last: Loda


title: Real-time quantitative PCR analysis of microRNA expression in Primary human Bronchial Epithelial cells (PBECs) from healthy or asthmatic subjects

status: Public on Sep 19 2014

city: Southampton

first: Victor Paky

last: Bondanese

address: Southampton General Hospital, Tremona Road

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton, UK

summary: The goal of this study is to compare the base-line microRNA expression of asthmatic and healthy PBECs. PBECs were grown in-vitro up to passage 2 before harvest.

overall_design: RT-qPCR based microRNA array expression profiling. PBECs were isolated from 5 healthy and 5 asthmatic donors. Total cellular RNA from each sample was processed and analyzed independently.

first: Victor-Paky

first: Tilman

last: Sanchez-Elsner


title: Protein−DNA binding in the absence of specific base-pair recognition

status: Public on Oct 01 2014

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)−DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF−DNA binding preferences. We used high-throughput protein−DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying re- peat symmetries. Based on statistical mechanics modeling, we iden- tify a new protein−DNA binding mechanism induced by DNA se- quence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed gov- erns protein−DNA binding preferences.

overall_design: Four custom protein binding microarray (PBM) experiments of human transcription factors were performed. Briefly, the PBMs involved binding his-tagged transcription factors c-Myc, Max, and Mad1(Mxd1) to double-stranded 180K Agilent microarrays in order to determine their binding specificity for GTCACGTGAC DNA binding sites flanked by repetitive DNA elements with different symmetries and correlation length scales. Briefly, we represent three categories of 36-bp sequences: 1) 28800 probes centered at a GTCACGTGAC site and flanked by repetitive elements (probe names starting with Ariel_); 2) Unbound probes (or negative controls); and 3) Bound probes, which correspond to randomly selected genomic regions bound in vivo by c-Myc, Max, or Mad2 (ChIP-seq P < 10^(-10) in HeLaS3 or K562 celld (ENCODE)), which contain at least two consecutive 8-mers with universal PBM E-score > 0.4 (Munteanu and Gordan, LNCS 2013). Each DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot (raw files) as well as the median intensity over the 6 replicate spots (normalized data). The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).


title: Identification of known and novel germ cell cancer specific (embryonic) miRs in serum by high throughput profiling

status: Public on Oct 02 2014

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC

summary: Very recently, a number of independent studies showed that serum levels of embryonic micro-RNA (miR) clusters 371-3 and 302abc/367 are predictive for the presence of testicular type II germ cell tumors. These miRs could be used to sensitively detect SE and EC components which are indeed known to express these miRs [1-7]. This study investigates ca 750 miRs in a high throughput approach to validate these previously identified markers and identify novel potential miR markers for testicular type II germ cell tumors.  1. Belge, G., et al., Serum levels of microRNAs miR-371-3: a novel class of serum biomarkers for testicular germ cell tumors? Eur Urol, 2012. 61(5): p. 1068-9.  2. Dieckmann, K.P., et al., MicroRNAs miR-371-3 in serum as diagnostic tools in the management of testicular germ cell tumours. Br J Cancer, 2012. 107(10): p. 1754-60.  3. Gillis, A.J., et al., Targeted serum miRNA (TSmiR) test for diagnosis and follow-up of (testicular) germ cell cancer patients: a proof of principle. Mol Oncol, 2013. 7(6): p. 1083-92.  4. Gillis, A.J., et al., High-throughput microRNAome analysis in human germ cell tumours. J Pathol, 2007. 213(3): p. 319-28.  5. Murray, M.J. and N. Coleman, Testicular cancer: a new generation of biomarkers for malignant germ cell tumours. Nat Rev Urol, 2012. 9(6): p. 298-300.  6. Murray, M.J., et al., Identification of microRNAs From the miR-371~373 and miR-302 clusters as potential serum biomarkers of malignant germ cell tumors. Am J Clin Pathol, 2011. 135(1): p. 119-25.  7. Voorhoeve, P.M., et al., A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell, 2006. 124(6): p. 1169-81.

overall_design: 35 serum samples were profiled for ca. 750 micro RNAs. These consisted of serum from 10 patients with non-seminomas (2 YS, 2 TE, 2 EC and 4 mixed NS which all contained EC) and 14 SE cases. Controls (C) consisted of serum from 3 individuals with normal testis tissue showing adequate spermatogenesis (Johnson Score 8-10) and serum from 8 patients with non-GCT testicular masses. These contained on epidermoid cyst, three epidermis cysts, one low grade liposarcoma, two neuro-endocrine tumors and a case of paratesticular hemorrhage.

first: Ton

last: van Agthoven

first: Ad

last: Gillis

first: Sunali

last: Patel

first: Kathleen

last: Hayashibara

first: Kathy

middle: Y

last: Lee

first: Leendert

middle: H

last: Looijenga


title: Transcriptome analysis of gilthead sea bream Sparus aurata liver upon exposure to low temperature

status: Public on Aug 27 2014

city: Legnaro

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: In Sparus aurata,  seasonal temperature variations outside the normal thermal range, may trigger physiological responses leading to pathologies and death. In the present study two groups of wild sea bream were exposed for 21 days to two temperature regimes: 16 ± 0.3 °C (control group) and 6.8 ± 0.3 °C (cold-exposed group). Samples were collected during the acute phase (0, 6 and 24 hours after temperature drop) and upon chronic exposure (21 days).

overall_design: A comparative analysis of gene expression was conducted between S. aurata  exposed to 6.8°C. Two groups of wild sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in duplicate groups in four 5 m3 circular recycling tanks and acclimated over one month at 16 °C (Di Marco et al. 2010). Fish were then exposed for 21 days to two different temperature treatments: 16 ± 0.3 °C (control groups) and 6.8 ± 0.3 °C (cold groups). Both groups were fasted during the trial. Warm and cold water temperature conditions were maintained by supplying tanks with two separate re-circulating systems equipped with mechanical and biological filters. Cold water conditions were achieved by inducing two consecutive temperature drops:   water was firstly gradually cooled from 16 °C to 12 °C at a rate of 1°C day -1 and then reduced from 12 °C to 6.8 °C within 24 h. This temperature was then kept for 21 days.  Ten fish per treatment were sampled at different intervals during acute: 0 (T1), 6 (T2) and 24 hours (T3), and chronic exposure (21 days; T4) to low temperature. Fish were firstly anaesthetized in a solution of tricaine methanesulphonate (300 mg/l; MS 222, Finquel) in a 30-litre bucket and then euthanized by severing their spinal cord. Liver samples (about 30 mg) were collected from each specimen, incubated in RNA later at 4 °C for 24 h and then stored at -20 °C.    Total RNA was extracted from tissue samples using the RNAeasy Mini Kit (Qiagen, Hilden, Germany). RNA concentration was determined using a UV-Vis spectrophotometer NanoDrop® ND-1000 (NanoDrop Technologies, Wilmington, USA). RNA integrity and quality was evaluated by means of Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and Expert software according to Ferraresso et al. (2008). RNA integrity number (RIN) index was calculated for each sample that provides a numerical assessment of RNA integrity. This value facilitates the standardization of the quality interpretation; only RNAs with RIN >8 were used for further microarray experiments. Once single RNA samples were extracted and measured, 3 pools (Pool_A consisting of four individuals, Pool_B and _C of three) per each sampling-time point were prepared. This was aimed at getting a sufficient statistical power which is reached by a minimum of three biological replicates per analysed point and at reducing microarray analysis cost. To perform DNA microarray analyses has been used the microarray platform GPL6467 (Ferraresso et al. 2008). Sample labelling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. For each of 24 liver pools 500 ng of total RNA were linearly amplified and labelled with Cy3-dCTP, using the Low RNA Input Linear Amplification Kit PLUS one-color (Agilent Technologies). A total of 24 Agilent 4 x 44K sea bream microarrays (12 samples from both control and cold groups) were then hybridized. An Agilent G2565BA DNA microarray scanner was used to scan arrays at 5 µm resolution, Feature Extraction Software 9.5.1 was then used to process and analyse array images. The software returns a series of spot quality measures in order to evaluate the goodness and the reliability of spot intensity estimates. Filtering and cyclic lowess normalization were performed using R statistical software (http://www.r-project.org/).

first: Luca

last: Bargelloni

first: Alba

last: Mininni

first: Serena

last: Ferraresso

first: Tomaso

last: Patarnello


title: Array competitive genomic hybridization of three Saccharomyces cerevisiae strains vs. DBY8268

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

institute: Dickinson College

summary: A six array study using total gDNA recovered from two separate cultures of each of three different strains of Saccharomyces cerevisiae (YB-210 or CRB, Y389 or MUSH, and Y2209 or LEP) and two separate cultures of Saccharomyces cerevisiae DBY8268.  Each array measures the hybridization of probes tiled across the Saccharomyces cerevisiae genome.

overall_design: Biological replicates: 2 for each strain, 2 for control. Grown and harvested in parallel. One replicate per array.

first: Audrey

last: Gasch