title: Expression analysis of Escherichia coli MG1655 K-12 ∆hns/∆stpA from aerobic and anaerobic growth conditions

status: Public on Jun 20 2013

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary:
Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆hns/∆stpA strain from exponental growth under aerobic and anaerobic growth conditions.
The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding.

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

overall_design: A four chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 ∆hns/∆stpA mutant strain under aerobic and anaerobic growth conditions. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 using a high-density tiling array consisting of ~385,000 60mer probes spaced every 12 bp.

first: Huihuang

last: Yan

first: Irene

last: Ong

first: Dongjun

last: Chung

first: Kun

last: Liang

first: Frances

last: Tran

first: Sunduz

last: Keles

first: Robert

last: Landick

first: Patricia

last: Kiley


title: Intestinal Salmonella Typhimurium infection leads to miR-29a induced Caveolin 2 regulation [mRNA]

status: Public on Jun 25 2013

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

country: Germany

institute: Freie Universitaet Berlin

summary: The host response to S.typhimurium infections in ileum was studied after infection of piglets. mRNA and miRNA expression studies were performed to identify interactions of miRNAs and regulated mRNAs in context of mammalian intestinal Salmonella infection using a piglet model.

overall_design: Intestinal samples (~ 2 cm circle segments) were taken at time points 3h, 3d and 28d post infection from ileum of ten S.typhimurium infected piglets (S), ten S.typhimurium infected piglets and additional treated with probiotic strain E.faecium NCIMB 10415 (SP) and five healthy control piglets(C) (EUROC x Pietrain). The piglets were weaned at the age of 28 days and infected with S. typhimurium. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA). For microarray analysis pooled samples of each experimental group were prepared ana partes aequalis from individually isolated total RNA samples, which were collected at the same time point in each group. Common reference was designed from equal amounts of total RNA of each pool and additional total RNA from ascending colon.

first: L

last: Hoeke

first: J

first: A

last: Keller

first: R

last: Einspanier

first: S


title: Chip-chip from Escherichia coli MG1655 K-12, WT and ∆fnr strains

middle: S

country: USA

type: Genome binding/occupancy profiling by genome tiling array

summary:
Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12.  We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263).
The ∆hns/∆stpA strains were also used.
Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure

sample_organism: Escherichia coli str. K-12 substr. MG1655star

overall_design: Mapping of occupancy of FNR, NNS, IHF and ß of RNAP in the genome of Escherchia coli MG1655 K-12 under aerobic or anaerobic growth conditions. Immunoprecipitated DNA compared to INPUT for each sample.


title: CGH analysis of monkey PG-haESCs (parthenogenic haploid embryonic stem cells)

status: Public on Jun 26 2013

city: Shanghai

first: Linyu

last: Shi

address: 320 Yueyang Road

country: China

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

summary: The genomic DNA sample of monkey PG-haESCs were compared to the female adipose cells by comparative genomic hybridization. The data confirmed that these haploid cells sustained genome integrity.

overall_design: The analysis was performed on a Agilent aCGH G3 Rhesus Macaque 4x180K array to analyse the copy number variations in monkey PG-haESCs, and the genomic DNA of femal monkey adipose was used as control, which had the same background with haploid ESCs.

first: Jinsong

last: Li


title: Intestinal Salmonella Typhimurium infection leads to miR-29a induced Caveolin 2 regulation [miRNA]

overall_design: Intestinal samples (~ 2 cm circle segments) were taken at time points 3h, 3d and 28d post infection from ileum of ten S.typhimurium infected piglets (S), ten S.typhimurium infected piglets and additional treated with probiotic strain E.faecium NCIMB 10415 (SP) and five healthy control piglets(C) (EUROC x Pietrain). The piglets were weaned at the age of 28 days and infected with S. typhimurium. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA). For microarray analysis pooled samples of each experimental group were prepared ana partes aequalis from individually isolated total RNA samples, which werde collected at the same time point in each group. Common reference was designed from equal amounts of total RNA of each pool and additional total RNA from ascending colon.


title: microRNA expression for 86 chemo-treated ovarian cancer patients

status: Public on May 17 2013

city: Columbus

first: Andrea

last: Vecchione

state: OH

address: 460W12th Ave

institute: The Ohio state University

summary:
We profile expression in serous epithelial ovarian carcinomas to assess the possibility of an miRNA signature associated with chemoresistance.

Resistance to the available therapies is one of the main causes of low survival of patients with advanced epithelial ovarian cancer, thus representing an emergency in oncology. Here, we profiled miRNA expression in 86 naïve serous epithelial ovarian carcinomas (EOCs) to assess the possibility of miRNAs associated with chemoresistance. We identified 23 miRNAs associated with chemoresistance, of which three (miR-484, miR-642 and miR-217) were confirmed in the validation set (112 independent patients). The study of miR-484 role demonstrated that it regulated the chemoresistance of EOC cells acting not on cancer cells but on tumor vasculature. In particular, miR-484 is produced and secreted by chemosensitive EOC, therefore regulating the production of VEGFB by cancer cells and the expression of VEGFR2 in endothelial cells. Overall, we demonstrated that a three-miR signature can classify the response to chemotherapy and that chemoresistance in EOC relays, at least in part, on the control of tumor angiogenesis, indicating new options in the treatment of these patients.

overall_design: We analyzed tumor samples (<5% of normal tissue) from FFPE blocks of 86 patients with serous ovarian carcinomas.

first: Francesca

last: Lovat

first: Stefano

last: Volinia

first: Gennaro

last: Chiappetta

first: Simona

last: Giglio

first: Maura

last: Sonego

first: Roberto

last: Cirombella

first: Patrizia

last: Pellegrini

first: Daniela

last: Califano

first: Sandro

last: Pignata

last: Losito

first: Vincenzo

last: Canzonieri

last: Sorio

first: Dorothee

last: Wernicke

first: Antonella

last: Stoppacciaro

first: Gustavo

last: Baldassarre

first: Carlo

middle: M

last: Croce


title: A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (ChIP-chip)

status: Public on Jun 07 2013

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary: During limb development, Hoxd genes are transcribed in two waves: Early on, when the arm and forearm are specified and subsequently, when digits form. While the latter phase is controlled by enhancers centromeric to the HoxD cluster, we show here that the early phase requires enhancers located in the opposite telomeric gene desert. The transition between the two types of regulations involves a functional switch between two distinct topological domains, as reflected by a subset of genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently shift to establish new contacts on the opposite side. This transition between two regulatory landscapes generates an intermediate area of low Hox dose developing into the wrist, the transition between our arms and our hands. This intriguing correspondence between genomic and morphological boundaries illustrates the mechanism underlying collinear Hox gene regulation in our developing appendages.

overall_design: Chromatin ImmoPrecipitation on chip (Tiling array): Distribution of H3K4me3 and H3K27me3 in early limb buds at E9.5, E10.5 and proximal late limbs E12.5. Distribution of H3K27me3 in del(8-13) and del(8-13)/del(attP-TpSB3) E10.5 limb buds. Distribution of H3K27me3 in WT and homozygote del(Nsi-Atf2) (Montavon et al., 2011) forelimb autopods.

first: G

last: Andrey

first: D

last: Duboule


title: Expression data from rat liver stem-like WB-F344 cells treated with 3,3’,4,4’,5-pentachlorobiphenyl (PCB 126)

status: Public on May 01 2013

city: Brno

first: Jan

last: Vondracek

address: Kralovopolska 135

department: Department of Cytokinetics

country: Czech Republic

institute: Institute of Biophysics ASCR

summary: Although the tumor promoting effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), coplanar polychlorinated biphenyls (PCBs) and related compounds in liver tissue are primarily attributed to activation of the aryl hydrocarbon receptor (AhR), the underlying molecular mechanisms are still unclear. Liver progenitor (oval) cells have been suggested to constitute a potential target for hepatocarcinogenic chemicals. To better understand AhR-driven pathways we analyzed the transcriptional program in response to coplanar PCB 126 in rat liver progenitor WB-F344 cells using high density microarrays. After 6h treatment, we identified 145 significantly deregulated genes considered to be direct AhR-dependent target genes. The number of differentially regulated genes increased to 658 and 968 genes after 24h and 72h, respectively. Gene ontology analysis revealed that these genes were primarily involved in drug and lipid metabolism, cell cycle and growth control, cancer developmental processes, cell-cell communication and adhesion. Interestingly, the Wnt and TGF-beta signaling pathways, both being involved in developmental and tumorigenic processes, belonged to the most affected pathways. AhR and ARNT-dependent regulation of selected target genes of interest was then confirmed using TCDD as a model AhR agonist, together with pharmacological inhibition of the AhR and by RNA-interference techniques. We demonstrated AhR-dependent regulation of emerging and novel AhR target genes, such as Fst, Areg, Hbegf, Ctgf, Btg2, and Foxq1. Among them, the transcription factor Foxq1, recently suggested to contribute to tumor promotion and/or progression, was found to be regulated at both mRNA and protein levels by AhR/ARNT activation.

overall_design: 18 Total samples were analyzed (3 independent repeats for each treatment and time point). We generated the following pairwise comparisons: Control vs. PCB 126 at 6 h; Control vs. PCB 126 at 24 h; Control vs. PCB 126 at 72 h;

first: Dagmar

last: Faust

first: Pavel

last: Krcmar

first: Lenka

last: Smerdova

first: Jirina

last: Prochazkova

first: Eva

last: Hruba

first: Petra

last: Hulinkova

first: Bernd

last: Kaina

first: Cornelia

last: Dietrich

first: Miroslav

last: Machala


title: Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

city: frederick

first: cedric

last: cagliero

address: 1050 boyles street

institute: NCI/NIH

summary:
To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin
domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast,
‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.

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

overall_design: A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.

first: Cedric

last: Cagliero

first: Ralph

last: Grand

first: Beatrix

last: Jones

first: Ding

middle: J

last: Jin

first: Justin

last: O'Sullivan


title: Alanine scan of 11 amino acid long novel linear epitope from C.jejuni cj0669 protein [2]

status: Public on May 06 2013

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168 which was previously identified as potentially immunogenig was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was seperated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interaction rabbit polyclonal IgG to C.jejuni was used, while non-specific binding to the epitope sequence was checked using rabbit polyclonal IgG to H. pylori (Abcam ab20459).


title: GSK-3alpha Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1-TAB Stabilization and Regulation of Non-Canonical NF-kB

status: Public on May 31 2013

city: Chapel Hill

first: Albert

last: Baldwin

state: NC

address: 450 West Drive

department: LCCC

institute: UNC-Chapel Hill

summary: Mutations in KRAS occur in a variety of tumors of epithelial origin, driving the oncogenic phenotype.The NF-kB transcription factor pathway is important for oncogenic RAS to transform cells and to drive tumorigenesis in animal models. Recently TAK1, an upstream regulator of IKK which controls canonical NF-kB, was shown to be important for chemoresistance in pancreatic cancer and for regulating KRAS+ colorectal cancer cell growth and survival. Here we show that GSK-3alpha is upregulated by KRAS leading to interaction with TAK1 to stabilize the TAK1/TAB complex to promote IKK activity. Additionally, GSK-3alpha is required for promoting critical non-canonical NF-kB signaling in pancreatic cancer cells. Pharmacologic inhibition of GSK-3 suppresses growth of human pancreatic tumor explants, consistent with loss of expression of genes such as c-myc and TERT.  These data identify GSK-3alpha as a key downstream effector of oncogenic RAS via its ability to coordinately regulate distinct NF-kB signaling pathways

overall_design: GSK-3 inhibition at 2 and 8 hours

first: Deepali

last: Bang

first: Willie

last: Wilson

first: Jen

last: Yeh


title: Early Genomic Amplifications in Blood-Stages of ARMD Plasmodium falciparum Acquiring De Novo Drug Resistance [Expression]

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

summary: While many molecular changes associated with commonly used antimalarials are known, there remain important questions on how parasites arrive at the correct causal molecular solutions in a haploid genome.   We selected for resistance to DSM1, a novel dihydroorotate dehydrogenase (DHODH) inhibitor with a non-biological triazolopyrimidine scaffold, in P. falciparum with the Accelerated Resistance to Multiple Drugs (ARMD) trait.  While direct sequencing revealed no mutations in the target DHODH gene, comparative genomic hybridizations from four independently selected DSM1-resistant clones showed a large, single 34-95kb amplification in each clone. Each amplified region always included the DHODH locus.  The length of this region and the resulting 2- to 3-fold DHODH copy number increase were verified at the RNA and protein level.  DSM1 resistance was stable over several months of in vitro culture.  Additional selection at higher DSM1 concentrations caused further gains in CNVs at the DHODH locus.  The present system validated DHODH as a key target of the triazolopyrimidine antimalarial, DSM1 and, more importantly, captured large, random CNVs as an early step in the initiation of drug resistance in malaria parasites.   This defined system is expected to be valuable for characterizing early, causal molecular steps leading to successful drug resistance

overall_design: RNA from P. falciparum DSM1 resistant cell-line was hybridized against RNA of parental strain, Dd2. DSM1 resistant cell culture was maintained under DSM1 at 333 nM, microarray data were obtained from three hybridizations using RNA from three independent parasite cultures

first: Daniel

middle: L

last: Freeman

first: Jennifer

last: Guler

first: Rapatbhorn

last: Patrapuvich

first: John

last: White

first: Ramesh

last: Gujjar

first: Prakash

last: Pendyala

first: Margaret

middle: A

last: Phillips


title: Expression analysis of  the gacS mutant of Pseudomonas fluorescens SBW25

status: Public on Jun 17 2013

city: Wageningen

first: Xu

last: Cheng

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary: Pseudomonas species are ubiquitous in plant-associated environments and produce an array of volatiles, enzymes and antimicrobials. The biosynthesis of many metabolites is regulated by the GacS/GacA two-component regulatory system. Transcriptome analysis of Pseudomonas fluorescens SBW25 revealed that 702 genes were differentially regulated (fold change>4, P<0.0001) in a gacS::Tn5 mutant, with 300 and 402 genes up- and down-regulated, respectively. Genes that were significantly down-regulated are involved in viscosin biosynthesis (viscABC), protease production (aprA), motility, biofilm formation, and secretory systems. Genes that were significantly up-regulated are involved in siderophore biosynthesis and oxidative stress. In contrast to previous studies with gac-mutants of other Pseudomonas species/strains, the gacS mutant of SBW25 inhibited growth of oomycete, fungal and bacterial pathogens significantly more than parental strain SBW25. A potential candidate for this enhanced antimicrobial activity was a large nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode for an 8-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis of an NRPS gene in this cluster, however, did not lead to a reduction in the antimicrobial activity of the gacS mutant. Collectively these results indicate that a mutation in the GacS/GacA regulatory system causes major transcriptional changes in P. fluorescens SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms.

overall_design: This expression study used total RNA recovered from four separate wild-type cultures of Pseudomonas fluorescens SBW25 and four separate cultures of the gacS mutant.  Expression design was based on the updated genome sequence of Pseudomonas fluorescens SBW25, NC_012660.1 and associated plasmid pQBR0476 with nineteen 60-mer probe  per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.

first: Irene

last: de Bruijn

first: Menno

last: van der Voort

first: Jos

last: Raaijmakers


title: Expression profiling of Ciona intestinalis neurula and mid-tailbud stage embryos expressing altered forms of the transcription factor Ci-Tbx2/3 in the notochord

status: Public on Apr 27 2013

city: New York

first: Anna

last: Di Gregorio

state: NY

address: 345 E 24th Street, room 804A

department: Basic Science and Craniofacial Biology

institute: NYU College of Dentistry

summary:
Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown.  We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region.
We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16).  These constructs were introduced into 1-cell stage embryos and grown to the neurula (N) or mid-tailbud (mTb) stage to capture targets regulated throughout notochord morphogenesis.

overall_design: Ci-Tbx2/3 targets were ascertained using whole-genome custom Affymetrix microarrays to compare the transcription levels of Tbx2/3DBD and Tbx2/3VP16 expressing embryos to wild-type controls (Bra>GFP) at the neurula or mTb stages.


title: Early Genomic Amplifications in Blood-Stages of ARMD Plasmodium falciparum Acquiring De Novo Drug Resistance [Genome variation]

overall_design: gDNA from P. falciparum DSM1 resistant cell-line was hybridized against gDNA of parental strain, Dd2. DSM1 resistant cell culture was maintained under DSM1 at 333 nM, microarray data were obtained from three hybridizations using gDNA from three independent parasite cultures


title: Expression data from maize D11 mutant

status: Public on Apr 25 2013

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

institute: Yangzhou University

summary:
The expression profiling of a newly identified maize dwarf mutant Dwarf11 (D11) was investigated by Affymetrix array. Results showed that transcripts encoding GA biosynthetic and catabolic enzymes ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), and GA 2-oxidase (GA2ox) were up-regulated in the D11 mutant.
We used microarrays to identify the difference of GA-related gene expression in D11 mutant.

overall_design: Stems of D11 mutant and wild type were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: Early Genomic Amplifications in Blood-Stages of ARMD Plasmodium falciparum Acquiring De Novo Drug Resistance

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Expression data of gene knockout Plasmodium falciparum clones

status: Public on May 25 2013

city: Bethesda

first: YAN

last: LUO

address: 9000 Rockville Pike

institute: NHLBI

summary:
The variant antigen, Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), expressed on the surface of P. falciparum infected Red Blood Cells (iRBCs) is a critical virulence factor for malaria. Each parasite encodes 60 antigenically distinct var genes encoding PfEMP1s, but during infection the clonal parasite population expresses only one gene at a time before switching to the expression of a new variant antigen as an immune evasion mechanism to avoid the host’s antibody responses. The mechanism by which 59 of the 60 var genes are silenced remains largely unknown.
We used microarrays to detail the global programme changes of gene expression caused by each gene knockout with a particular view towards which gene knockout results in transcriptional upregulation of the entire var gene family.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Plasmodium falciparum clones, in each of which one of different histone lysine methylation modification enzyme genes was knocked out, were synchronized in the asexual stage and collected at indicated time points post invasion of erythrocytes for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the key epigenetic enzyme that controls silencing of the whole var gene family.

first: Lubin

last: Jiang

first: Louis

middle: H

last: Miller

first: Jose

last: Ribeiro


title: CGH of Plasmodium falciparum selected with DSM1

first: Pradipsinh

last: Rathod

type: Genome variation profiling by genome tiling array

summary: Continual challenge of 107 ARMD Dd2 parasites with 0.3µM DSM1, a novel dihydroorotate dehydrogenase (DHODH) inhibitor, reproducibly generated ~5-fold resistance and 3-fold amplification of 30-100Kb DNA, always including the DHODH gene.  Subsequent  3-10µM DSM-1 pressure selected for ~10-fold amplification of the copy number variant (CNV), and over 100-fold resistance.  Target-specific and genome-wide DNA sequencing revealed no additional mutations contributing to DSM1 resistance.

overall_design: Each DSM1-resistant clone is compared to the Dd2 parent reference sample.


title: Analysis of the effects of the methyltransferase encoded by Rv3263  on gene expression in M. tuberculosis

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 60 Prescott St

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: DNA methylation affects gene expression in many organisms. To determine to effects of DNA methylation on gene expression in M. tuberculosis, we genetically deleted a predicted DNA methyltransferase encoded by Rv3263 and subjected wildtype, mutant, and complemented strains to global expression analysis.

overall_design: RNA was extracted from triplicate cultures of wildtype, methyltransferase deletion, and complemented strains.

first: Sarah

last: Fortune


title: Expression data from neonatal rat ovaries following LPS exposure

city: Callaghan

first: Luba

last: Sominsky

state: NSW

address: University Drive

country: Australia

institute: The University of Newcastle

summary: Inflammatory processes play an important role in regulation of ovarian development, in particularly early in life. Neonatal immune challenge by administration of lipopolysaccharide (LPS) has been previously demonstrated to result in diminished ovarian reserve and altered reproductive lifespan. In this study we aimed to characterise the cellular mechanisms that may underpin impaired ovulatory capacity and reduced oocyte development, induced by LPS treatment. Rat pups were administered with LPS or saline on postnatal days 3 and 5. Ovaries were obtained on postnatal day 7 to examine the effect of LPS administration on the ovarian transcriptome.

overall_design: Rat pups were administered intraperitoneally either 0.05mg/kg of LPS (Salmonella Enteritidis) or an equivalent volume of non-pyrogenic saline on postnatal days (PNDs) 3 and 5, and ovaries were obtained on PND 7 for RNA extraction and hybridization on an Agilent-028279 SurePrint G3 Rat GE 8x60K Array platform.

first: Alexander

middle: P

last: Sobinoff

first: Eileen

last: McLaughlin

first: Deborah

last: Hodgson


title: Evolutionary principles of modular gene regulation in Yeasts

city: Cambridge

first: Ilan

last: Wapinski

address: 7 Cambridge Center

institute: Broad Institute

summary: Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts.

sample_organism:
Schizosaccharomyces pombe
Schizosaccharomyces japonicus
Lachancea waltii
Saccharomyces cerevisiae
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis

overall_design: Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau.

first: Dawn

last: Thompson

first: Sushmita

last: Roy


title: Comparison of transcriptome of high differentiation-inducible murine erythroleukemia cells and low differentiation-inducible murine erythroleukemia cells

status: Public on Apr 23 2013

city: Noda

first: Hitoshi

last: Sasaki

state: Chiba

address: 2641 Yamazaki

department: Department of Biological Science and Technology

country: Japan

institute: Tokyo University of Science

summary:
Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSO）, hexamethylene bisacetamide (HMBA） or trichostatin A (TSA） treatment.
We selsected  high differentiation-inducible (HD) and low differentiation-inducible (LD)-MEL cells by recloning of original MEL cells. We screened erythroid differentiation related-genes to compare transcriptome of HD and LD-MEL cells.

overall_design: HD-MEL cells and LD-MEL cells were cultured 6, 12, 24, or 36 hours with 1.0% DMSO, 3.0 mM HMBA, or 15 nM TSA. The RNA of HD-MEL cells and LD-MEL cells were compare same time points of each drug treatment. The expression ratio (HD/LD) was calculated by average of technical quadruplicate microarray experiments includes two dye-swaps.


title: HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

status: Public on Apr 21 2013

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Analysis of histone H3 turnover in wild-type and mutant fission yeast cells by using MNase-ChIP-chip

overall_design: Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose. Cells were crosslinked with 1% Formaldehyde and chromatin was fragmented into mononucleosomes by using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody from wild-type and mutant fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto  44k pombe Agilent oligo arrays. Data were processed using Agilent scanner and Feature Extraction software.

first: Ozan

last: Aygün

first: Sameet

last: Mehta

middle: I


title: Expression profiles of high differentiation-inducible murine erhthroleukemia cells

summary:
Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSO), hexamethylene bisacetamide (HMBA), or trichostatin A (TSA) treatment.
We analyzed expression profiles of high differentiation-inducible (HD) MEL cells during chemical induced differentiation.

overall_design: HD MEL cells were cultured at 1, 6, 12, 24, or 36 hours with 1.5% DMSO, 5.0 mM HMBA, or 30 nM TSA. The RNA of HD-MEL cells before and after chemial treatment were compared. The expression ratio (After chemical treatment/Before chemical treatment) was calculated by average of technical quadruplicate microarray experiments includes two dye-swaps.


title: Phenotypic activation and repression of three ELAV-like proteins in Trypanosoma brucei

status: Public on Apr 18 2013

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

summary: Three potential ELAV-like proteins of T. brucei, including Tb927.3.2930, Tb927.7.5380, and Tb927.8.6650, were either inhibited by RNAi or phenotypically activated by over-expression, followed by microarray analysis of the transcriptome. The results indicated that these ELAV-like proteins regulate the abundance of a large number of T. brucei transcripts, potentially through regulation of mRNA stability.

overall_design: Each of the three ELAV-like proteins were either inhibited by RNAi or over-expressed, in stable transgenic procyclic form cell lines. Total RNA was extracted 48h after tetracycline induction of the constructs (except for total RNA from Tb927.8.6650 RNAi which was extracted 24h after tet-induction). cDNA was synthesized using TaqMan Reverse Transcription Reagents with random hexamer priming (Applied Biosystems), and sent to NimbleGen for labeling and hybridization. Non-induced cells were analyzed in parallel.

first: Zhiquan

last: Lu

first: Reza

last: Salavati


title: A rapid transcriptome response is associated with desiccation resistance in aerially-exposed killifish embryos

status: Public on Apr 15 2013

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

country: France

institute: Université Bordeaux 1

summary: The changes in the transcriptome of Fundulus heteroclitus embryos incubated in water or in air from the blastula stage was investigated.

overall_design: Embryos at blastula stage were sampled after different times under water or air, and at the same temperature, and compared by using a cDNA microarray containing 15.658 probes.

first: Angèle

last: Tingaud-Sequeira

first: Juan

last: Lozano

first: Cinta

last: Zapater

first: David

last: Otero

first: Michael

last: Kube

first: Richard

last: Reinhardt

first: Joan

last: Cerdà


title: Arabidopsis protoplasts : TMV*rep vs. TMV*CP.MP transfected

city: Taipei

first: Cheng-En

last: Chen

address: No.1, Sec.4, Roosevelt Road.

country: Taiwan

institute: National Taiwan University

summary: Transcriptional profiling of Arabidopsis in response to infection with TMV in the initial infection stage (0.5, 4 and 6 hours post inoculation). Analyze the relative transcriptome change of TMV*CP.MP- and TMV*rep-inoculated samples.

overall_design: TMV*rep vs. TMV*CP.MP transfected cells. 2 biological replicates conducted at each time (0.5, 4 and 6 hours post inoculation)

first: Shu-Hsing

last: Wu


status: Public on Apr 24 2013

city: Berkeley

first: Ariel

last: Grostern

state: CA

address: 209 O'Brien Hall

department: Civil & Environmental Engineering

institute: UC Berkeley

summary: Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

overall_design: Two treatments, based on carbon/energy source used for growth: pyruvate and H2/bicarbonate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: H2/bicarbonate vs. pyruvate

first: Lisa

last: Alvarez-Cohen


title: To identify gene markers which differentiate between AERD and ATA with a high discriminative power.

status: Public on Apr 08 2013

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

summary: Aspirin-exacerbated respiratory disease (AERD) has association with severe asthma and aspirin can cause asthma to worsen, often in the form of a severe and sudden attack. The oral aspirin challenge (OAC) is the gold standard to confirm the diagnosis of AERD but it is time consuming and produces serious complications in some cases. Therefore more efficient and practical method is needed to predict AERD patients. The aim of the present study was to identify AERD-related gene expression in peripheral blood mononuclear cells (PBMCs) and examine the diagnostic potential of these candidate gene(s) for predicting AERD. To do this, RNAs from 24 subjects with AERD and 18 subjects with aspirin-tolerant asthma (ATA) were subjected to microarray analysis of ~34,560 genes. In total, 10 genes were selected as candidate gene markers by applying p ≤ 0.001(t-test) and ≥ 8-fold change and to correct for multiple comparisons, the false discovery rate (FDR) analyses were performed. By applying multiple logistic regression analysis, among possible 1023 models (210–1), a model consisting of CNKSR3, SPTBN2, and IMPACT was selected as candidate set, because this set showed the best AUC (0.98) with 88% sensitivity and 89% specificity. For validation, mRNA levels by real-time PCR on PBMCs from two population sets in a gene-chip study and another replication sample: 20 AERD, 20 ATA, and 8 normal controls, were significantly different between groups with 100% sensitivity and 100% specificity in each of the two population sets. However, IMPACT gene didn’t differentiate between AERD and normal controls. The set of the two genes (CNKSR3 and SPTBN2) showed the best AUC (0.96) with 88% sensitivity and 94% specificity in a gene chip study sample. In addition, this set showed perfect discriminative power with AUC (1.0, 100% sensitivity and 100% specificity) in each of the two population sets: the gene-chip samples and the replication samples. It also showed perfect discrimination for AERD form NC (AUC 1.0) and ATA from NC (AUC 1.0). In conclusion, we developed the two gene markers (CNKSR3 and SPTBN2) of PBMC which differentiate between AERD and ATA with a perfect discriminative power. These gene markers may be an efficient and practical method useful for predicting AERD.

overall_design: Total 24 AERD (Aspirin-exacerbated respiratory disease) and 18 ATA(aspirin-tolerant asthma) samples were used to find bio-markers using 35K op-array.

first: Choon-Sik

last: Park


title: Screening for novel immunogenic proteins of Campylobacter jejuni NCTC 11168

status: Public on Apr 06 2013

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: The screening of a cDNA derived expression library of Campylobacter jejuni NCTC 11168 expressed in E. coli using a fusion construct and specific HaloTag interaction to a modified surface is shown. 1536 different clones were screened including positive (hisJ, cjaA, peb1a) and negative (argC, pyrC, gapA) reference proteins. The goal of the screening was to identify potential novel immunogenic proteins from C. jejuni by selecting clones showing a high signal intensity in comparison to the known antigens used as positive markers. Afterwards, the most promising clones were sequenced to identify the gene and corresponding protein, and these proteins were then investigated further. Consequently, 22 novel immunogenic proteins could be identified.

platform_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: In total, 1536 (4 x 384) different lysates were spotted on different microarray slides. Each slide contained 3600 distinct spots, separated into two compartments of 1800 spots each. Each compartment comprised quadruplicate replicates of each sample lysate with controls being analysed with more replicates. As controls we used: hisJ, cjaA and peb1 (3 x 40 replicates) as positive reference proteins, as they have been described as immunogenic before; argC and pyrC (2 x 40 replicates) as negative reference proteins; two sets of E. coli cell lysates without fusion proteins expressed, namely Acella electrocompetent cells (40 replicates) and KRX (32 replicates); and a buffer control (24 replicates). Therefore, each set of replicate slides contained 376 different samples and 8 controls. Each screening was performed with three replicate slides. Consequently, a total number of 12 slides were screened (4 sets of samples x 3 replicates each). For identification, rabbit polyclonal antibody to C. jejuni (Acris AP24002PU-N) as primary and goat polyclonal to rabbit IgG conjugated with ChromeoTM-546 (Abcam ab60317) as secondary antibody were used. The top compartment was incubated first with primary antibody, while the bottom compartment was incubated with PBS at the same time. Afterwards, both compartments were incubated with secondary antibody.


title: Analysis of Colletotrichum orbiculare infection of N. benthamiana

status: Public on Apr 09 2013

city: Yokohama

first: Pamela

last: Gan

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Plant Sciences

institute: RIKEN

summary:
Species from the genus Colletotrichum are the causal agents of anthracnose which contribute to significant losses to the production of commercially grown crops.  The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, as well as Colletotrichum gloeosporioides, which infects a wide range of fruits and vegetables, were sequenced.  A custom microarray was designed for Colletotrichum orbiculare and used to assess gene expression during infection of Nicotiana benthamiana.
Gene expression of Colletotrichum orbiculare growing on its host Nicotiana benthamiana was assessed at 24 hours post inoculation, 3 days post inoculation and 7 days post inoculation.  Mycelia growing in vitro and ungerminated conidia were used as controls.  Three replicates were performed for each time point.

overall_design: Pamela, Gan

first: Kyoko

last: Ikeda

first: Hiroki

last: Irieda

first: Mari

last: Narusaka

last: O'Connell

first: Yoshihiro

first: Yoshitaka

last: Takano

first: Yasuyuki

last: Kubo

first: Ken

last: Shirasu


title: Lenalidomide and Pomalidomide inhibit Multiple Myeloma-induced osteoclast formation and RANKL/OPG ratio in myeloma microenvironment targeting the expression of adhesion molecules.

status: Public on Apr 13 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Multiple myeloma (MM)-induced osteoclast (OC) formation occurs in close contact with MM cell infiltration into the bone marrow (BM) due to the imbalance of the receptor activator of NF-kappa-B ligand (RANKL)/osteoprotegerin (OPG) ratio in favor of RANKL in the micorenvironment. Soluble factors including CCL3/MIP-1?, IL7 and IL-3 also contribute to the increased OC formation in MM.The immunomodulatory drugs (IMiD®s) directly inhibit OCs, however their effect on the mechanisms involved in MM-induced OC formation are not known and have been investigated in this study. We found that both Lenalidomide (LEN) and Pomalidomide (POM), at concentration ranging reached in vivo, significantly blunted RANKL up-regulation normalizing the RANKL/OPG ratio in human BM osteoprogenitor cells (PreOBs) co-cultured with MM cells and inhibited CCL3/MIP-1? production by MM cells. The reduction of CD49d expression on MM cells, a molecule critically involved in RANKL up-regulation in the micorenvironment, accompanied this effect. Consistently the pro-osteoclastogenic property of the conditioned medium of MM cells co-cultured with PreOBs was reduced in the presence of both IMiD®s. By microarray analysis we further investigated the effect of POM and LEN on the transcriptional profile of both MM cells and PreOBs. We found a significant down-regulation in MM cells, in addition to CD49d, of genes belonging to the adhesion molecules family such as ITGA8 and ICAM2 (CD102) induced by both IMiD®s compounds. In conclusion our data suggest that POM and LEN inhibits MM-induced OC formation through the inhibition of RANKL/OPG ratio targeting the expression of adhesion molecules by MM cells.

overall_design: This series of microarray experiments contains the gene expression profiles of JJN3 cell line cultured in presence of POM (100 µM), LEN (100 µM) or vehicle in triplicate flasks for 24 hours, respectively. Preparation of biotin-labeled cRNA, hybridization to GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc., Santa Clara, CA, USA) and scanning of the chips (7G Scanner, Affymetrix Inc.) were carried out according to manufacturer's protocols. Expression values were extracted from cell intensity files, using GeneAnnot custom chip definition files. The CDF Packages for R/Bioconductor (http://www.bioconductor.org/) version 2.2.0 was based on GeneAnnot annotation Version 2.0 and publicly available at http://www.xlab.unimo.it/GA_CDF/. The data were normalized using Robust Multi-array Average procedure.

first: Bolzoni

last: Marina

first: Storti

last: Paola

first: Bonomini

last: Sabrina

first: Todoerti

last: Katia

first: Guasco

last: Daniela

first: Peronaci

last: Marco

first: Toscani

last: Denise

first: Agnelli

last: Luca

first: Neri

last: Antonino

first: Giuliani

last: Nicola


title: Verification of immunogenic nature by microarray screening

city: Potsdam

first: Sebastian

last: Hoppe

summary: Screening of 22 novel proteins derived from Campylobacter jejuni NCTC 11168 identified prior via screening of cDNA libraries. The full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink. Screening was performed using three different polyclonal antibodies to Campylobacter jejuni and detection was achieved by goat polyclonal antibody to rabbit IgG conjugated with Chromeo-546. In order to assess their potential immungenic nature and rank the proteins investigated, comparative analysis using already described antigens from C. jejuni were used in the assay.

overall_design: Each microarray was separated into different incubation chambers using the ProPlate (Grace Biolabs) multi-well gaskets. While for two slides (2009 and 2447), three chambers were used, the remaining slides were designed to use 16 different compartments. Each compartment could be incubated with different antibodies and represent individual replicates of the slides. As positive references, hisJ and cjaA were used. For negative controls, argC and gapA were used, and the crude lysates of the expression host (Acella E. coli) and buffer were spotted as well. For slides 2009 and 2447, three-well gaskets were used allowing for seven replicates per sample, while only incubation with one antibody. Slides 416033 and 416826 used 16-well gaskets and only hisJ and argC as protein references. Samples and controls were spotted in quadruplicate. Finally, for 1000 and 1001, samples were spotted in triplicate, whereas controls were spotted in quadruplicate using hisJ, cjaA, argC and gapA as protein references.


title: Identification of novel immunodominant proteins from Campylobacter jejuni and the characterization of linear epitopes

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

overall_design: Refer to individual Series


title: Alanine scan of 11 amino acid long novel linear epitope from C. jejuni cj0669 protein

summary: A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168, which was previously identified as potentially immunogenic, was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence.

overall_design: Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was separated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interactions, rabbit polyclonal IgG to C. jejuni was used, while unspecific binding to the epitope sequence was checked using rabbit polyclonal IgG to Salmonella enterica.


title: Engineering ABT-737 Resistance in MYC-driven Lymphomas Identifies DHX9 as a Drug Response Modifier

status: Public on Apr 03 2013

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Many traditional cytotoxic agents used in the treatment of cancer function by eliciting an apoptotic response in tumor cells.  However, evasion of apoptosis by BCL-2 family members is often deregulated prior to therapeutic intervention leading to treatment failure. To address this, ABT-737 was rationally designed to target BCL-2-like family members and has shown promising results against tumor cells dependent on BCL-2 for their survival. One shortcoming is that MCL-1, a member of the BCL-2 family is poorly inhibited by ABT-737 and is a major cause of resistance. To gain insight into biological pathways that could circumvent this resistance, we designed an shRNA screen to identify novel sensitizers to ABT-737 by engineering MYC driven lymphomas that were resistant to ABT-737 due to endogenous MCL-1 expression. Utilizing this model, we performed a shRNA drop-out screen and identified Dhx9 as a target whose suppression sensitizes cells to ABT-737. DHX9 loss lead to replicative stress signaling, which in turn potently induced the BH3-only proteins, NOXA and PUMA, in a p53-dependent manner to curtail MCL-1 activity. Induction of NOXA is essential for ABT-737 sensitization. Our results ascribe a novel role for DHX9 in the replicative stress pathway and link DHX9 activity to p53 function in vivo.

overall_design: Comparison of Arf-/-Eu-myc/Bcl-2 lymphomas expressing either control Rluc.713 or Dhx9 shRNA, Dhx9.1241


title: CpG Oligodeoxynucleotides treatment of Anopheles mosquitoes

status: Public on Apr 02 2013

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

summary: In the present study, we have investigated the effect of CpG Oligodeoxynucleotides (CpG-ODN) on the outcome of Plasmodium infection of the mosquito vectors Anopheles stephensi and Anopheles gambiae and on the modulation of mosquito immunity to Plasmodium. Anopheles mosquitoes inoculated with CpG-ODN showed significant reduction of Plasmodium infection rate and intensity. Microarrays were used to profile transcription of fat-body from CpG-ODN-treated mosquitoes. Mosquitoes were dissected 18h after ODN inoculation (immediately before feeding). Batches of 20 to 30 fat bodies (abdomen without midgut, ovaries and malpighian tubule]) were dissected in cold DEPC-treated phosphate-buffered saline (PBS) and processed for RNA preparation. Mosquitoes treated with CpG-ODNs are less susceptible to Plasmodium infection. Transcription profile of fat body indicates that protection was associated with coagulation/wound healing, while melanization appears to be depressed.

overall_design: Anopheles gambiae s.s. mosquitoes were reared at 25 ºC and 75% humidity with a 12-hour light/dark cycle. Adult mosquitoes were maintained on a 10% glucose solution. Three- to four-day-old female mosquitoes were cold-anaesthetized and inoculated intratoraxically with 69nl of a 0.1mM CpG-oligodeoxynucleotide (0604 -5’ TCCATGACGTTCCTGATGCT 3’) solution or with the same volume of elution buffer using a Nanoject micro-injector (Drummond Scientific). Mosquitoes were left to rest for 18h. Batches of 20 to 30 fat bodies (abdomen without midgut, ovaries and malpighian tubule) were dissected in cold DEPC-treated phosphate-buffered saline (PBS) and processed for RNA preparation. Two independent experiments were performed for each treatment.

first: Ana

last: Gabriel


title: Altered expression of microRNAs in PC-3 sphere cells of prostate cancer compared with PC-3 adherent cells

status: Public on Apr 01 2013

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: Metastatic prostate cancer is a leading cause of cancer-related death in men. Cancer stem cells (CSCs) are involved in tumor progression and metastasis, including in prostate cancer. There is an obvious and urgent need for effective cancer stem cells specific therapies in metastatic prostate cancer. MicroRNAs (miRNAs) are an important class of pervasive genes that are involved in a variety of biological functions, especially in cancer. The goal of this study was to identify miRNAs involved in prostate cancer metastasis and cancer stem cells.

overall_design: Several published reports have demonstrated that non-adherent spheres culture is increasingly used as an effective method to enrich and identify stem cells or putative CSCs.In our previous study, we enriched prostate cancer stem cells from PC-3 sphere cells in serum-free suspension culture and characterized their CSCs properties.Thus, we used spheres as a prostate cancer stem cells model to elucidate its metastatic mechanisms. We examined the miRNA expression profiles of PC-3 sphere cells of prostate cancer compared with PC-3 adherent cells by miRNA microarray.

first: Xinlan

last: Fan

first: Weixi

last: Deng

first: Guangzheng

last: Zhong

first: Qingqing

last: Cai

first: Tianxin

last: Lin


title: miRNA expression profiles in the serum of diabetic cats

status: Public on Apr 11 2013

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

summary: BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats.  METHODS: Total RNA was extracted from 400 µl serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats.  RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL  cats.  CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM.

overall_design: Blood was drawn from two groups of cats: 8 healthy cats and 8 cats suffering from diabetes. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 16 serum samples were analyzed and the groups were compared. Due to technical problems during hybridization (leaking chamber), sample 1_4_B (Serum_diabetic_8) was not included into analysis.

first: Stefan

last: Bauersachs

first: Stefanie

last: Fleischhacker


title: Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Naturally occurring genetic polymorphisms influence patterns of gene expression in normal tissues, and can provide a molecular view of the component cell lineages and signaling pathways responsible for normal tissue architecture. Analysis of the coordinated changes in this architecture that take place during tumor development can help to identify the functional roles of oncogenes or tumor suppressors and provide potential new therapeutic targets. We have applied a network analysis approach to a set of 92 normal human lung samples from cancer patients and their matched adenocarcinomas. We have identified networks associated with particular cell lineages (alveolar type 2 pneumocytes and Clara cells) in normal lung and document the changes in these networks that accompany transformation to adenocarcinomas. Expression of the transcription factor NKX2-1 (TTF1) is linked to surfactant protein markers of the alveolar type 2 lineage in normal and transformed lung cells, but its network is rewired in tumors to include pathways linked to cell growth such as glutaminase (GLS2). Analysis of mitotic networks revealed the presence of novel components such as the kinase VRK1 that are preferentially linked to the mitotic cycle in tumors but not in normal lung. We show that shRNA-mediated inhibition of VRK1 cooperates with inhibition of PARP signaling to inhibit growth of lung tumor cells. Targeting of genes that are recruited into tumor mitotic networks may provide a wider therapeutic window than that seen by inhibition of integral components of the mitotic machinery such as Aurora kinases.

overall_design: 87 lung adenocarcinomas and 92 adjacent uninvolved lung tissue samples, 85 matched pairs

first: Il-Jin

last: Kim

first: Minh

middle: D

last: To

first: Patrick

last: Pham

first: Kevin

first: Brian

last: Jo

first: Kuang-Yu

last: Jen

first: Dan

last: Raz

first: Jae

first: Jian-Hua

last: Mao

last: Jablons

first: Allan

last: Balmain


title: Cebpa regulates gene transcription in basophils

city: Denver

first: Xiaopeng

last: Qi

state: CO

address: 1400 Jackson Street,

institute: National Jewish health

summary: To investigate the mechanisms by which C/EBPa drives basophil differentiation and maintains basophil identity, we examined whether or not C/EBPa promotes basophil molecular programming and simultaneously represses mast cell molecular programming. We performed genome-wide gene expression profiling on basophils and mast cells and found that 6798 genes were shared by mast cells and basophils; 2033 genes were expressed 2-10 (log2 1-3.3)-fold higher in basophils (differentially expressed in basophils); and 413 genes were expressed greater than 10 (log2 3.3)-fold in basophils (highly expressed in basophils).  On the other hand, we found 569 genes were expressed 2-10 (log2 -1 to -3.3) fold higher in mast cells and 171 genes were highly expressed in mast cells [greater than 10 fold (log2 -3.3)]. We treated purified basophils prepared from Cebpaf/f RosaYFP/creER mice and Cebpa+/+ RosaYFP/creER control mice with or without 4HT treatment for five days.  Gene expression in the treated basophils was analyzed using microarray analysis. Overall, deletion of C/EBPa in basophils resulted in a reduction of mRNA expression for 248 genes and led to an increase in mRNA expression for 255 genes.  The majority of the C/EBPa-regulated genes were either differentially or highly expressed in basophils or mast cells.

overall_design: In this study, we compared gene expression in basophils and mast cell and identified genes which specifically expressed in basophils and mast cells. By using Cebpa conditional knock out mice, we identified Cebpa regulated genes in basophils.

first: Hua

last: Huang


title: DNA damage checkpoint kinases regulate a global network of transcription factors

status: Public on Mar 31 2013

city: La Jolla

first: Eric

last: Jaehnig

address: 9500 Gilman Dr

department: Laboratory of Cancer Genetics

institute: Ludwig Institute for Cancer Research

summary: DNA damage results in the activation of checkpoint kinases, which phosphorylate downstream effectors that inhibit the cell cycle, activate DNA repair, and cause widespread changes in transcription. However, the specific connections between the checkpoint kinases and downstream transcription factors (TFs) are not well understood. Here, we introduce a strategy for mapping regulatory networks between kinases and TFs involving integration of kinase mutant expression profiles, transcriptional regulatory interactions, and phosphoproteomics. We use this approach to investigate the role of the Saccharomyces cerevisiae checkpoint kinases (Mec1, Tel1, Chk1, Rad53, and Dun1) in the transcriptional response to DNA damage caused by methyl methanesulfonate (MMS). The result is a global kinase-TF regulatory network in which Mec1 and Tel1 signal through Rad53 to synergistically regulate the expression of more than 600 genes. This network implicates at least nine TFs, including Msn4, Gcn4, SBF (Swi4/Swi6), MBF (Swi6/Mbp1), and Fkh2/Ndd1/Mcm1, nearly all of which have sites of Rad53-dependent phosphorylation, as downstream regulators of checkpoint kinase-dependent genes. We also identify a major DNA damage-induced transcriptional network acting independently of Rad53 and other checkpoint kinases to regulate expression of genes involved in general and oxidative stress responses.

overall_design: Expression was profiled with and without treatment in several genetic backgrounds (gene deletion strains)

first: Dwight

last: Kuo


title: Epitope mapping of potential novel immunogenic proteins of Campylobacter jejuni NCTC 11168

first: Sebastian

last: Hoppe

department: Bioanalytics and Biosensorics

summary: A number of seven proteins were selected during immunoscreening and further analyses. The proteins were in silico divided into overlapping 15-mer oligopeptides with an overlap of 11 residues. The microarrays were incubated with different antibodies to C. jejuni, Escherichia coli and Salmonella enterica.

overall_design: Each microarray was separated into three individual incubation chambers using ProPlate 3-Well modules. Within each incubation chamber, each peptide was spotted in triplicate with the controls spotted nine times each. The controls included human-IgG, rabbit-IgG, mouse-IgG and myelin basal protein (MBP). Each chamber was incubated independently using different polyclonal antibodies to C. jejuni, and for specificity testing, with an antibody to E. coli or S. enterica. Thus, samples 4_1, 4_2, 5_1 and 5_2 represent epitope mapping of three proteins with C. jejuni antibodies, while 6_1, 6_2, 7_1 and 7_2 represent the data after incubation with an E. coli antibody investigating unspecific interactions of the antibody to the potential linear epitopes from C. jejuni. Finally, for four different proteins from C. jejuni, the set two indicated by S2 was performed. Here, S2_6_1, S2_7_1, S2_7_2, S2_8_1 and S2_8_2 indicate epitope mapping after incubation with antibodies to C. jejuni, while the remaining samples were performed to test these latter 4 proteins for specificity by incubation with antibody to S. enterica.


title: The global gene expression pattern by KDX1 over-expression

city: Seoul

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

institute: Korea university

summary: We did transcription profiling on the effect of KDX1 over-expression.

overall_design: Analysis was performed with wild type and KDX1 over-expressed cells ( pRS426-KDX1). Yeast cells were grown on SD-ura medium. Yeast cells were grown overnight at 30°C . The culture was refreshed to 0.2 O.D and grown at 30°C  for 5h 30min. Cells were collected and processed for RNA extraction.

first: Miwha

first: Cheol-won

last: Yun


title: Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

institute: Chinese Acadamy of agricultural science

summary:
Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were predominantly expressed in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.
In conclusion, a whole rice genome oligonucleotide microarray was used to profile gene expression across five tissues of the perennial wild sorghum S. propinquum. Expression patterns of the five tissues were consistent with the different functions of each organ, and RT- and RI-enriched genes revealed clues regarding molecular mechanisms of rhizome development. Plant hormones, including ABA, GA, and SA, function as key regulators of rhizome gene expression and development. To shed further light on the identities of rhizome-specific genes, rhizome-enriched candidates were identified using QTL co-localization and comparative analysis.

overall_design: In this study, the specific gene expression patterns across five tissues, including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in Sorghum propinquum, especially in the rhizome, were characterized by using a rice genome array. Three independent biological replicates for each tissue from individual plants were performed. The reference was equivalent to a mix of the 5 tissues.

first: Ting

last: Zhang

first: Xiuqin

last: Zhao

first: Liyu

first: Xiaoyue

last: Liu

first: Ying

last: Zong

first: Linghua

last: Zhu

first: Daichang

last: Yang

first: Binying

last: Fu


title: Analysis of the Aedes aegypti transcriptome during flavivirus infection

city: New Haven

first: Tonya

last: Colpitts

state: CT

address: 300 Cedar St, TAC S410

department: Internal Medicine, Section of Infectious Diseases

institute: Yale University School of Medicine

summary:
Microarray analysis on days 1, 2 and 7 post-infection with dengue, yellow fever and West Nile virus in Aedes aegypti Rockefeller strain mosquitoes
RNA was purified and hybridized with Nimblegen X4 microarray chips using 81-mer probes designed from 18,000 open reading frames (ORF) found in the Ae. aegypti genome, with 2 different probes per ORF

overall_design: Nimblegen X4 array format, 81mer probes, RNA samples taken mostly in triplicate, microarray analysis done in triplicate. Thirty seven samples in total. Fold change data with infection/mock on the Series record.

first: Erol

last: Fikrig


title: Hypoxia-inducible factor (Hif)-1 knockdown blocks tumor growth, myeloma-induced angiogenesis and bone destruction in vivo

first: Luca

last: Agnelli

summary: In multiple myeloma (MM), hypoxia-inducible transcription factor-1 (HIF-1) is overexpressed in the MM cells of the hypoxic bone marrow (BM) microenvironment. Herein, we explored in MM cells the in vitro and in vivo effects of persistent HIF-1 inhibition by expression of a lentivirus shRNA pool on proliferation, survival and transcriptional and pro-angiogenic profiles. Among the significantly modulated genes (326 and 361 genes in hypoxic and normoxic condition, respectively), we found that HIF-1 inhibition in the human myeloma cell line JJN3 downregulates the pro-angiogenic molecules VEGF, IL8, IL10, CCL2, CCL5, and MMP9. Interestingly, several pro-osteoclastogenic cytokines were also inhibited, such as IL-7 and CCL3/MIP-1. The effect of HIF-1 inhibition was assessed in vivo in NOD/SCID mice both in subcutaneous and intratibial models, indicating in either case a dramatic reduction of weight and volume of the tumor burden as a consequence of HIF-1 knockdown. Moreover, a significant reduction of the number of vessels per field and VEGF immunostaining were observed. Finally, in the intra-tibial experiments, HIF-1 inhibition significantly blocks JJN3-induced bone destruction. Overall, our data indicate that HIF-1 suppression in MM cells significantly blocks MM-induced angiogenesis and reduces both tumor burden and bone destruction in vivo, strongly indicating HIF-1 as an emerging therapeutic target in MM.

overall_design: The transcriptional profiles on JJN3 transduced with shRNA anti-HIF-1 (JJN3-anti-HIF-1), as compared to those infected with the control vector pLKO.1 (JJN3-pLKO.1), have been analyzed either in hypoxic or normoxic conditions. To perform gene expression profiles, total RNA was purified using the RNeasy Total RNA Isolation Kit (Qiagen, Valencia, CA). Preparation of biotin-labeled cRNA, hybridization to GeneChip Human Genome U133 Plus 2.0 Arrays and scanning (GeneChip¨ Scanner 3000 7G, Affymetrix Inc.) were performed according to manufacturer's protocols.

first: Marina

last: Bolzoni

first: Paola

last: Storti

first: Gaetano

last: Donofrio

first: Irma

last: Airoldi

first: Eugenia

last: Martella

first: Daniela

last: Guasco

first: Denise

last: Toscani

first: Mirca

last: Lazzaretti

first: Ken

last: Patrene

first: Marco

last: Peronaci

first: Andrea

last: Smargiassi

first: Cristina

last: Mancini

first: Martine

last: Amiot

first: Antonino

last: Neri

first: Simona

last: Colla

first: Judy

last: Anderson

first: Franco

last: Aversa

first: David

last: Roodman

first: Nicola

last: Giuliani


title: Growth phase dependent gene expression of Salmonella Typhimurium SL1344 parental strain and isogenic ∆relA, ∆spoT ppGpp null strain

status: Public on Jul 03 2013

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

country: United Kingdom

institute: Institute of Food Research

summary: Transcriptional profiling of Salmonella Typhimurium SL1344 parental starin and isogenic ∆relA, ∆spoT ppGpp null strain grown in LB medium with RNA samples talken at AD600=1.0 (mid log, ML), 2.3 (early stationary phase, ESP), 3.0 (mid stationary phase MSP) and 3.6 (Late stationary phase (LSP)

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

overall_design: Each array used labelled cDNA against a common genomic DNA reference. Triplicate biologically independent RNA samples were arrayed for each of the 2 strains at each of the 4 growth phases

first: Arthur

last: Thompson

first: Vinoy

last: Ramachandran


title: Osmotic regulation of hepatic choline metabolism

city: Düsseldorf

first: Thor

last: Gehrmann

address: Moorenstrasse 5

department: Klinik für Gastroenterologie

institute: Universitätsklinikum Düsseldorf

summary: Betaine critically contributes to the control of hepatocellular hydration and provides protection of the liver from different kinds of stress. This study investigates to what extent hepatocellular hydration changes affect the expression levels of enzymes involved in the metabolism of betaine and related organic osmolytes by using qRT-PCR gene expression studies in rat hepatoma cells as well as metabolic and gene expression profiling in 5,10 - methylene tetrahydrofolate reductase (MTHFR) deficient primary hepatocytes. The results demonstrate a coordinated regulation of betaine degradation and synthesis under anisoosmotic conditions. Expression of betaine degrading enzymes is downregulated by hyperosmolarity and strongly induced by hypoosmolarity. In contrast, synthesis of glycerophosphocholine from phosphoethanolamine and conversion of choline to betaine are both induced by hyperosmolarity but decreased under hypoosmotic conditions. In addition we evaluated the flux of choline and its derivates in liver and plasma of methylene tetrahydrofolate reductase knockout (Mthfr-/-) mice by tandem mass spectrometry. Analyses of system-wide alterations of osmolyte metabolism with microarray studies revealed expression changes similar to those after hypoosmotic exposure in this betaine depletion model. In conclusion, regulation of betaine synthesis and degradation and concomitant changes in intracellular osmolyte concentrations contribute to long-term adaptation to anisoosmotic exposure of the liver.

overall_design: Expression of 280 genes were analyzed in wild type and mthr-/- mice (n=7) with spotted oligonucleotides.

first: Lars

last: Hoffmann

first: Gernot

last: Brauers

first: Dieter

last: Häussinger

first: Ertan

last: Mayatepek

first: Freimut

last: Schliess

first: Bernd

last: Schwahn


title: Genomic Analysis of Microdissected Inflammatory Breast Cancer

status: Public on Mar 29 2013

city: Houston

first: Takahiro

last: Kogawa

state: TX

address: 1515 Holcomb Blvd

department: Breast Medical

institute: MD Anderson

summary: Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status.

overall_design: Genomic profiling of 20 inflammatory breast cancer (IBC), 20 non-IBC and 5 normal was studied.

first: Wendy

last: Woodward

first: Naoto

middle: T

last: Ueno


title: JA-inducible genes in the wild-type rice leaves.

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Jasmonates is inductively produced as a major plant hormone responsible for defense reactions in plants against both biotic and abiotic stresses, such as pathogen infection and mechanical wounding.  We identified JA-inducible genes in the wild-type rice leaves 0 - 4 h after JA treatment using 44k microarray.

overall_design: Expression profiling in the wild-type rice leaves treated with jasmonic acid for 0.5, 1, 2, and 4 h was compared with that in the untreated wild-type rice leaves using two-color method with three biological replicates.

first: Kanako

last: Miyamoto

first: Takafumi

last: Shimizu

first: Koji

first: Hisakazu

last: Yamane

first: Hideaki

last: Nojiri


title: Induced erythropoiesis during acute anemia in Atlantic salmon

status: Public on Mar 26 2013

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Study was performed to improve understanding of erythropoiesis (EP) induced by acute anemia in Atlantic salmon. Fish was injected with a low dose of hemolytic compound phenylhydrazine (PHZ). Treatment resulted in moderate but significant reduction of hematocrit (Hct) and increased transcription of cardiac erythropoietin (epo) at 2 days post challenge (dpc), and epo receptor (epor) in spleen from 2 to 4 dpc. Oligonucleotide microarrays were used to characterize the events of EP in the spleen.  These results were compared to gene expression profiles of untreated mature red blood cells (RBC) in order to search for erythroid-specific genes. Splenic responses suggested a prevalence of protective mechanisms at the first stage, characterized by induced xenobiotic metabolism and responses to oxidative and protein stress. Erythroid-specific regulation was evident at 2 dpc and enhanced by 4 dpc, and gene expression profiles witnessed a rapid establishment of RBC phenotype although Hct levels remained low. A large group of genes showed a strong correlation to globins by expression profiles. In addition to epor this included genes of heme and iron metabolism, scavengers of free radicals and chaperones, channels and transporters, markers of erythrocytes, regulators of proliferation and cell cycle arrest and many genes with unidentified roles in RBC differentiation. Induced EP in spleen was characterized by specific features, such as upregulation of virus-responsive genes and sustained high expression of proapoptotic genes including caspases. Transcriptome changes suggested an association between EP and suppression of several developmental programs including adaptive immune responses. In conclusion, acute hemolysis and resulting anemia rapidly induced EP in the spleen of Atlantic salmon, which showed both common characteristics for all vertebrates as well as fish-specific properties.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon was injected with a single dose of PHZ (6 mg/kg body mass) or saline. Spleen samples for microarray analyses were collected after 2 and 4 days. Additonally, red blood cells (RBC) were compared with spleen

first: A

first: G

last: Timmerhaus

first: S

last: Jorgensen

first: H

last: Takle


title: Global Gene Expression of Dehalococcoides Within a TCE-Dechlorinating Community Under Conditions of Periodic Substrate Supply

status: Public on Mar 01 2013

city: Berkeley

first: Kimberlee

last: West

address: 207 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

summary: A microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long-term trichloroethene (TCE)-degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time-points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 d) when Dhc had been starved of substrate for nine days. 90% of the Dhc ORFs that were detected in the ANAS DNA were found to be expressed as RNA sometime during the time course, demonstrating extraordinary utilization of the streamlined genome. 97% of these transcripts were differentially expressed during the time course, indicating efficiency of transcription through regulation in Dhc. Most Dhc genes were significantly down-regulated at T3, responding to a lack of substrate as would be expected. The tceA and vcrA genes, which code for proteins with known chlorinated ethene reduction functions, were highly expressed at both T1 and T2, whereas two other putative reductive dehalogenase genes (DET0173 and DET1545) were most highly expressed at T2, likely in response to the presence of VC. Hydrogenases were most highly expressed at T1, reflecting their important role in accumulating electrons used to initiate reductive dechlorination and other biosynthesis pathways. Cobalamin transport genes were preferentially expressed at T2, reflecting an increase in corrinoid transport as chloroethenes were degraded and a decrease in activity of the transport system after dehalogenation was complete. This is the first application of a microarray targeting a known genus, including both core genomes and identified strain-specific genes, applied to improve our understanding of transcriptional dynamics within an undefined microbial community.

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: Replicate samples were independently collected, and simultaneously but individually extracted, fragmented, labeled, and hybridized to arrays. Three DNA samples (one from each of the three replicate cycles) and nine RNA samples (one from each of the three time-points in each of the three replicate cycles) were prepared for microarray analysis.

first: Patrick

last: Lee

first: David

middle: R

last: Johnson

first: Stephen

last: Zinder

first: Lisa

last: Alvarez-Cohen


title: Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

status: Public on Feb 20 2013

city: St. Paul

first: Steve

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary: Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development.  We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups.  There are numerous differences in the distribution of H3K27me3 among tissues.  In contrast, we found the distribution of H3K27me3 among the two genetic backgrounds to be quite similar.  The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3.  Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled.  A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species.  However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication.  Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns.  Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets.  This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues.

overall_design:
B73 tissues for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels.
histone modification mutants for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels.
Mo17 tissues for h3k27 analysis: Samples contain antibody pulldown (IP) and control genomic DNA (input) channels.

first: Irina

last: Makarevitch

first: Nathan

last: Springer

first: Steven

first: Amanda

last: Waters


title: The miRNA pathway controls rapid changes in activity-dependent synaptic structure at the Drosophila melanogaster neuromuscular junction (miRNA array)

status: Public on Feb 01 2013

first: Scott

last: Barbee

address: 2190 E. ILIFF Ave.

department: Biological Sciences

institute: University of Denver

summary: It is widely accepted that long-term changes in synapse structure and function are mediated by rapid activity-dependent gene transcription and new protein synthesis. A growing amount of evidence suggests that the microRNA (miRNA) pathway plays an important role in coordinating these processes. Despite recent advances in this field, there remains a critical need to identify specific activity-regulated miRNAs as well as their key messenger RNA (mRNA) targets. To address these questions, we used the larval Drosophila melanogaster neuromuscular junction (NMJ) as a model synapse in which to identify novel miRNA-mediated mechanisms that control activity-dependent synaptic growth. First, we developed a screen to identify miRNAs differentially regulated in the larval CNS following spaced synaptic stimulation. Surprisingly, we identified five miRNAs (miRs-1, -8, -289, -314, and -958) that were significantly downregulated by activity. Neuronal misexpression of three miRNAs (miRs-8, -289, and -958) suppressed activity-dependent synaptic growth suggesting that these miRNAs control the translation of biologically relevant target mRNAs. Functional annotation cluster analysis revealed that putative targets of miRs-8 and -289 are significantly enriched in clusters involved in the control of neuronal processes including axon development, pathfinding, and growth. In support of this, miR-8 regulated the expression of a wingless 3’UTR (wg 3’ untranslated region) reporter in vitro. Wg is an important presynaptic regulatory protein required for activity-dependent axon terminal growth at the fly NMJ. In conclusion, our results are consistent with a model where key activity-regulated miRNAs are required to coordinate the expression of genes involved in activity-dependent synaptogenesis.

overall_design: larval CNS of UAS-ChR2 x C380-Gal4 following synaptic stimulation

first: Katherine

last: Nesler


title: The miRNA pathway controls rapid changes in activity-dependent synaptic structure at the Drosophila melanogaster neuromuscular junction (RT-PCR)

overall_design: Three technical replicates (each in raw data) of three biological replicates of wild-type (CantonS) larvae in two treatment groups: (1) 5x spaced high K; (2) or 0x mock stimulation.


title: OsJAR1−related JA-inducible genes in osjar1 tos17 mutant rice leaves.

first: Kazunori

last: Okada

summary: Jasmonates is inductively produced as a major plant hormone responsible for defense reactions in plants against both biotic and abiotic stresses, such as pathogen infection and mechanical wounding. Jasmonoyl isoleucine is known to be a bioactive compound of jasmonate and plays a pivotal role for plant defenses. We identified OsJAR1−related JA-inducible genes in osjar1 tos17 mutant (osjar1-2) rice leaves 0 - 2 h after JA treatment using 44k microarray.

overall_design: Expression profiling in the wild-type rice leaves treated with jasmonic acid for 0, 0.5, 1, and 2 h was compared with that in the osjar1 mutant  leaves treated with jasmonic acid for 0, 0.5, 1, and 2 h using two-color method with three biological replicates.

first: Kanako

last: Miyamoto

first: Takafumi

last: Shimizu

first: Koji

first: Hisakazu

last: Yamane

first: Hideaki


title: Expression analysis of Mycobacterium avium subsp. paratuberculosis K-10 within macrophage cell line

status: Public on Jan 22 2013

city: Madison

first: CHIA-WEI

last: WU

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Once entering the cell, M. avium subsp.paratuberculosis is known to survive harsh microenvironments, especially those inside activated macrophages.  To improve our understanding of M. avium subsp.paratuberculosis pathogenesis, we examined the phagosome maturation associated with transcriptional responses of M. avium subsp.paratuberculosis during macrophage infection.  Monitoring cellular markers, only live M. avium subsp.paratuberculosis bacilli were able to prevent phagosome maturation and reduce its acidification.  On the transcriptional level, over 300 of M. avium subsp.paratuberculosis genes were significantly, differentially regulated in both naïve and IFN-γ-activated macrophages.  These genes include the sigma factor H (sigH) that was shown to be important during persistent infection in M. tuberculosis.

overall_design: Bacterial total RNA was purified from Mycobacterium avium subsp. paratuberculosis that was infected into J774A.1 cells grown with or without interferon-gamma activation at 2 or 24 h post-infection. RNA from bacteria incubated with PRMI-1640 medium for 2 h, which was the infection conditon, is used as control condition. Each condition has two biological replicates. Each hybridization represents expression levels of all 4,350 annotated genes with 20 60-mer oligonucleotides and with three technical replicates.

first: Chia-wei

last: Wu

first: Adel

last: Talaat


title: The transcriptional profilling of the thermosensitive self-incompatible het-R het-V strain undergoing cell death by incompatibility

status: Public on Jan 01 2013

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

institute: Institut de Génétique et Microbiologie UMR 8621

summary: In the filamentous fungus Podospora anserina, cell death by incompatibility can be monitored using the conditional self-incompatible (SI) het-R het-V strain. SI strains are homokaryotic strains bearing incompatible het genes in all nuclei. The co-expression of these het genes triggers cell death in all the cells and hence in the entire mycelium. The het-R het-V SI strain, bearing the two incompatible het-R and het-V genes, proved particularly convenient as cell death triggering is thermosensitive (J. Labarère et al., 1973, C R Acad Sci Hebd Seances Acad Sci D, 276) and is induced by a simple shift in growth temperature (from 32°C to 26°C).The development of this cell death reaction has been recorded for 4 h after transfer to the restrictive temperature. A time course (T0h to T4h) of the transcriptomic response to the temperature shift has been explored in parallel within SI (het-R het-V) and wild type (compatible het-r hetV) s strains.

overall_design: With Platform GPL10116 : reference design with 2 strains: a WT strain and het-R het-V self-incompatible strain (J. Labarère et al., 1973, C R Acad Sci Hebd Seances Acad Sci D, 276).  Each strain with four biological replicates; the common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5.

first: Corinne

last: Clavé


title: DNA copy number profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma

status: Public on Jan 24 2013

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients.
METHODS: We performed gene expression profile, high-density single nucleotide polymorphism array, and mutation analyses using formalin-fixed ICC samples from 149 patients. Associations with clinico-pathological traits and patient outcomes were examined for 119 cases. Class discovery was based on a non-negative matrix factorization algorithm and significant copy number variations (CNV) were identified by GISTIC analysis. Gene set enrichment analysis was used to identify signaling pathways activated in specific molecular classes of tumors, and to analyze their genomic overlap with hepatocellular carcinoma (HCC).
RESULTS: We identified 2 main biological classes of ICC. The inflammation class (38% of ICCs) is characterized by activation of inflammatory signaling pathways, overexpression of cytokines, and STAT3 activation. The proliferation class (62%) is characterized by activation of oncogenic signaling pathways (including RAS, mitogen-activated protein kinase, and MET), DNA amplifications at 11q13.2, deletions at 14q22.1, mutations in KRAS and BRAF, and gene expression signatures previously associated with poor outcomes for patients with HCC. CNV-based clustering was able to further refine these molecular groups. We identified high-level amplifications in 5 regions, including 1p13 (9%) and 11q13.2 (4%), and several focal deletions, such as 9p21.3 (18%) and 14q22.1 (12% in coding regions for the SAV1 tumor suppressor). In a complementary approach, we identified a gene expression signature that was associated with reduced survival times of patients with ICC; this signature was enriched in the proliferation class (P<0.001).
CONCLUSIONS: We used an integrative genomic analysis to identify 2 classes of ICC. The proliferation class has specific copy number alterations, many features of the poor-prognosis signatures for HCC, and is associated with worse outcome. Different classes of ICC, based on molecular features, might therefore require different treatment approaches.

overall_design: DNA copy number profiling was performed using formalin-fixed, paraffin-embedded intrahepatic cholangiocarcinoma tissues obtained at the time of surgical resection.

first: Daniela

last: Sia

first: Augusto

last: Villanueva

first: Vincenzo

last: Mazzaferro

first: Jordi

last: Bruix

first: Myron

last: Schwartz

last: Friedman

first: Josep

last: Llovet


title: The miRNA pathway controls rapid changes in activity-dependent synaptic structure at the Drosophila melanogaster neuromuscular junction

first: Scott

last: Barbee

type:
Other
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: Evolutionary insights into scleractinian corals using comparative genomic hybridizations

status: Public on Nov 22 2012

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary:
Background
Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization).

Results
Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate.

Conclusions
The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.

sample_organism:
Acropora cervicornis
Acropora palmata
Orbicella faveolata
Siderastrea radians

overall_design: Microarray experiments were performed as follows. Appropriate Cy3 and Cy5 labeled DNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70μl. The hybridization mixtures were boiled for 2 min at 99°C and allowed to cool at room temperature for 5 min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 55°C. Microarrays were washed once in 2 × SSC, 0.03% SDS heated to 55 °C for 5 min. followed by one wash in 1 x SSC and another wash in 0.2 x SSC for 5 min each. The slides were kept in 0.2 × SSC until analysis. Slides were dried via centrifugation and scanned using an Axon 4000B scanner. The experimental setup followed a reference design, i.e., all samples were hybridized against the same pool of labeled A. palmata DNA. For each species, a total of four hybridizations were performed, including two dye swap hybridizations in order to account for potential dye bias i.e. two hybridizations with Cy3 labeled M. faveolata DNA against a Cy5 labeled A. palmata reference and two hybridizations with Cy5 labeled M. faveolata DNA against a Cy3 labeled Cy3 A. palmata reference were performed. The same hybridization scheme was used for A. cervicornis and S. radians.

first: Manuel

last: Aranda

first: Michael

last: DeSalvo

first: Till

last: Bayer

first: Monica

last: Medina