title: let-7 transfection series

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

summary:
micro (mi) RNAs are short noncoding transcripts that post-transcriptionally regulate gene expression by sequence-specific interaction.  Hundreds of human miRNAs have been discovered that collectively have thousands of predicted mRNA targets.  However, despite rapid advances in miRNA identification, accurate determination of targets has slowed their functional characterization in animals.  Here we present a novel computational method called GenMiR++ to discover a regulatory network of functional miRNA-mRNA interactions using sequence information and RNA expression data.  Using this method, we find that tissue-specific patterns of expression of miRNA-targeted genes are surprisingly predictive of whether miRNA-mRNA interactions are functional in other tissues.  We show that our targetting network is an improvement over predictions generated using solely sequence-based approaches and directly demonstrate its biological relevance by exploring miRNA misregulation in retinoblastoma.  We found that downregulation of let-7b in retinoblastoma correlated with elevated levels of GenMiR++ targets, including CDC25A and BCL7A, which were reduced in response to let-7b.  Our miRNA regulatory network provides a large-scale resource of functional targets that will accelerate exposition of miRNA biological roles.
Keywords: miRNA transfection

overall_design: let-7 transfection

first: Jim

last: Huang

first: Tim

last: Corson

first: Gordon

last: Chua

last: Hughes

first: Ben

last: Blencowe

first: Brendan

last: Frey

first: Quaid

last: Morris


title: Top1 and Top2-mediated replication fork integrity

status: Public on Aug 01 2007

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary:
DNA topoisomerases solve topological problems during chromosome metabolism. We investigated where and when Top1 and Top2 are recruited on replicating chromosomes and how their inactivation affects fork integrity and DNA damage checkpoint activation. We show that, in the context of replicating chromatin, Top1 and Top2 act within a 600 bp region spanning the moving forks. Top2 exhibits additional S-phase clusters at specific intergenic loci, mostly containing promoters. TOP1 ablation does not affect fork progression and stability and does not cause activation of the Rad53 checkpoint kinase. top2 mutants accumulate sister chromatid junctions in S phase without affecting fork progression and activate Rad53 at the M/G1 transition. top1 top2 double mutants exhibit fork block and processing, and phosphorylation of Rad53 and γH2A in S phase. The exonuclease Exo1 influences fork processing and DNA damage checkpoint activation in top1 top2 mutants. Our data are consistent with a coordinated action of Top1 and Top2 in counteracting the accumulation of torsional stress and sister chromatid entanglement at replication forks, thus preventing the diffusion of topological changes along large chromosomal regions. A failure in resolving fork-related topological constrains during S phase may therefore result in abnormal chromosome transitions, DNA damage checkpoint activation and chromosome breakage during segregation.
Keywords: ChIP-chip analysis

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE8nnn/GSE8305/suppl/GSE8305_Binding ratio of protein of interest_Top1_Top2_BrdU.txt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE8nnn/GSE8305/suppl/GSE8305_Binding ratio of protein of interest_Top1_Top2_Dpb3.txt

overall_design:
S. cerevisiae chromosomes III–V, and chromosome VI highdensity oligonucleotide microarrays were provided by Affymetrix Custom Express Service (SC3456a520015F, P/N 520015; rikDACF, P/N 510636, respectively). Sequence and position of oligonucleotides on the microarrays are available from Affymetrix. ChIP was carried out as previously described (Katou et al. 2003; Katou et al. 2006): we disrupted 1.5 x 108 cells byMulti-beads shocker (MB400U, Yasui Kikai)  using glass beads. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc.) and anti-Flag monoclonal antibody M2 (Sigma-Aldrich) were used for chromatin immunoprecipitation. ChIPed DNA was purified and amplified by random priming as described (Katou et al. 2003): a total of 10 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp, purified, and the fragments were end-labelled with biotin-N6-ddATP23. Hybridization, washing, staining and scanning were performed according to the manufacturer’s instruction (Affymetrix). Primary data analyses were carried out using the Affymetrix microarray Suite version 5.0 software to obtain hybridization intensity, fold change value, change P-value and detection P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared ChIPed fraction with supernatant fraction by using three criteria. First, the reliability of strength of signal was judged by detection P-value of each locus (P ≥0.025). Second, reliability of binding ratio was judged by change P-value (P ≥ 0.025). Third, clusters consisting of at least three contiguous loci that filled the above Bermejo et al. 26 two criteria were selected, because it was known that a single site of protein–DNA interaction will result in immunoprecipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbours. For the analyses of BrdU incorporation, cells were fixed by ice-cold buffer containing 0.1% azide, and then total DNA from 3 x108
cells was purified. DNA was sheared to 300 bp by sonication, denatured, and mixed with 2μg anti-BrdU monoclonal antibody (2B1D5F5H4E2; MBL). Antibody-bound and unbound fractions were subsequently purified, amplified, labelled and hybridized to the DNA chip.

first: Rodrigo

last: Bermejo

first: Ylli

last: Doksani

first: Thelma

last: Capra

first: Yuki

middle: M

last: Katou

first: Hirokazu

last: Tanaka

first: Marco

last: Foiani


title: Prostate Adenocarcinoma: Candidate Genomic Signatures Prognostic of Biochemical Failure

city: Philadelphia

first: Carmen

middle: Elisa

last: Oquendo

state: PA

address: 421 Curie Blvd

country: USA

institute: University of Pennsylvania

type: Genome variation profiling by genome tiling array

summary:
Prostate cancer is the most common form of non-skin cancer in American men.  Although the 5-year survival rate is 100%, an important proportion of patients will recur after seven years following treatment.  Despite attempts to delineate clinical and molecular prognostic signatures of recurrence, accurate prediction remains an elusive task. The purpose of this project was, therefore, to identify candidate genomic signatures of biochemical failure present at the moment of diagnosis.  To do this, we carried out array comparative genomic hybridization on surgical specimens from a training cohort of patients with PRCA who were followed on average for ten years.  Due to the unstable nature of malignant genomes, we selected non-random genomic aberrations through Significance Testing of Aberrant Copy Number (STAC), a statistical permutation algorithm.  Further analysis of STAC regions between recurrent and non-recurrent groups showed that recurring cases had a greater proportion of gain in 4p14-12, 11p14.3-14.1 or 15q21.1-22.2 in comparison to non-recurrent cases.  All three genomic signatures were independently, better predictors of recurrence than previously known clinical covariates. The importance of these regions in PRCA progression was further validated in publicly available expression data sets, where over-expression of ADAM10, BDNF and CYP19A1 (all coded in the aforementioned regions) was found to increase with progression of disease.  We hypothesize that amplification of ADAM10, BDNF, and CYP19A1 may serve as candidate biomarkers of recurrence to be validated in larger datasets.
Keywords: BAC Array CGH, Biomarker study

first: C

middle: E

first: Priti

last: Lal

first: Michelle

last: Korenblit

first: Kurt

last: D'Andrea

first: Katherine

last: Rinaldi

first: Li

last: Ping

first: Weigen

last: Shang

first: Phyllis

middle: A

last: Gimotty

first: S

middle: B

last: Malkowicz

first: John

last: Tomaszewski

middle: L

last: Nathanson


title: Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a rich medium (labeling:ENZO)

status: Public on Aug 05 2007

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary:
We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70oC.
Keywords: time course

overall_design: Three wild-type T. thermophilus HB8 strains were pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH.  The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC.  Cells were collected after 180, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min, and then crude RNA was extracted.  The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

first: Noriko

last: Nakagawa

first: Aiko

last: Kashihara

first: Shigeyuki

last: Yokoyama

first: Seiki

last: Kuramitsu


title: Microarray expression profliling of mouse whole spleen tissue after infection with L. monocytogenes

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
The infection with the intracellular pathogen Listerial monocytogenes in mice is well characterized resulting in bacterial colonization of various organs, mediated cellular response, and its role in the subsequent clearace of the bacteria, have been well described. In order to comprehensively describe the course of infection and identify molecular events leading to control of infection, we have undertaken whole organ profiling of the mouse spleen after infection.
Keywords: L. monocytogenes infection, spleen, microarray

overall_design: 4-5 weeks old female animals were i.v. infected with a sub-lethal dose L. monocytogenes EGDe and total spleen RNA was isolated on consecutive hours  from 1-4 and days from 1 to 9 post infection. As control pooled RNA of non-infected spleens were used. For each measurement 2-4 chip technical replicates including 1-2 dye swap experiments have been performed.

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Trinad

last: Chakraborty

first: Svetlin

last: Tchatalbachev


title: Analysis of Gene Expression Under Nitrogen Fixing Conditions in Geobacter sulfurreducens

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

summary:
In this study, expression analysis using electrochemically synthesized Combimatrix 12K DNA microarrays was validated in G sulfurreducens.  Growth under nitrogen fixing conditions and growth in ammonium amended medium, respectively, were the experimental and control conditions.  Expression analysis using this platform was also compared to expression analysis on whole cDNA microarrays.
Keywords: two-condition comparison

overall_design: This was a dual channel experiment used aRNA directly labeled with either cy5 (experimental) or cy3 (control).  Three biological replicates were labeled and hybridized in duplicate (two technical replicates).

first: Bradley

last: Postier

first: Raymond

middle: J

last: DiDonato jr.

middle: R

first: Barbara

last: Methe


title: Effects of aflatoxin on hepatic gene expression in male broiler chicken

status: Public on Jul 31 2007

city: columbia

first: lakshmi

middle: praveena

last: yarru

state: MO

address: 920 east campus dr

department: Division of Animal science

institute: University of Missouri

summary:
Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin.  Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes were identified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. It is hypothesized that genes associated with antioxidant, detoxification and immune systems were downregulated and the genes involved in cell proliferation were up-regulated in birds fed aflatoxin compared to controls
Keywords: aflatoxin, chicken liver, microarrays, gene expression

first: Lakshmi

middle: P

last: Yarru

first: Raja

middle: S

last: Settivari

first: Eric

last: Antoniou

first: David

last: Ledoux


title: sigma32 over-expression in E. coli

city: Madison

first: Kai

last: Zhao

state: WI

address: 2100 University Avenue

department: Oncology

institute: Mcardle Laboratory for Cancer Research

summary:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32 –dependent genes were also determined in a DnaK null mutant to examine the anti- sigma32 function of DnaK.
Keywords = sigma factor
Keywords = regulon
Keywords = microarray
Keywords = Western blot
Keywords = E. coli
Keywords = anti-sigma factor
Keywords: time-course

first: Mingzhu

last: Liu

first: Richard

last: Burgess


title: A transcriptome analysis of the Vibrio fischeri LuxR-LuxI regulon

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

summary:
Acyl-homoserine lactone (acyl-HSL) quorum sensing was first discovered in Vibrio fischeri where it serves as a key control element of the seven-gene luminescence (lux) operon. Since this initial discovery, other bacteria have been shown to control hundreds of genes by acyl-HSL quorum sensing. Until recently, it has been difficult to examine the global nature of quorum sensing in V. fischeri. However, the complete genome sequence of V. fischeri is now available and this has enabled us to use transcriptomics to identify quorum-sensing regulated genes and to study the quorum-controlled regulon of this bacterium. In this study, we used DNA microarray technology to identify over two-dozen V. fischeri genes regulated by the quorum sensing signal N-3-oxohexanoyl-L-homoserine lactone (3OC6-HSL).
Keywords: Comparison of transcriptome profiles

overall_design: Transcriptome profiles of Vibrio fischeri ES114 grown in the absence or presence of exogenously added 3OC6-HSL were compared.

first: Luis

first: Amy

last: Schaefer

first: Everett

last: Greenberg


title: A comparison of the gene expression between the cortical fiber and epithelial cells in mouse eye lens

city: Kyoto

first: Shigekazu

last: Nagata

address: Yoshida. Sakyo-ku

department: Department of Medical Chemistry

institute: Graduate School of Medicine, Kyoto University

summary:
The eye lens is composed of fiber cells, which differentiate from epithelial cells on its anterior surface. In concert with this differentiation, a set of proteins essential for lens function is synthesized, and the cellular organelles are degraded. To understand the molecular mechanism of the lens cell differentiation, we compared the gene expression profiles between epithelial and cortical fiber cells of young mouse lens using a microarray analysis.
Keywords: cell-type comparison

overall_design: To prepare lens epithelial and cortical fiber cells, lenses from 13-day-old mice (5 mice) were soaked in Hank’s balanced salt solution containing 1.26 mM CaCl2 and 0.91 mM MgCl2, and dissected by forceps into capsules that included the adhering epithelial cells and into cortical fiber cells. RNA was then prepared from epithelial and cortical fiber cells.

first: Masaki

last: Nakahara


title: Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation

city: Cambridge

first: Antonis

last: Kirmizis

state: England

address: Gurdon institute, Tennis Court Rd

country: United Kingdom

institute: Antonis Kirmizis

summary:
Modifications on histones control important biological processes through their effects on chromatin structure. Methylation at histone H3 lysine 4 (H3K4) by Set1p is found at the 5’end of active genes and contributes to transcriptional activation by recruiting chromatin remodeling enzymes. An adjacent arginine residue (H3R2) is also known to be asymmetrically dimethylated (H3R2me2a) in mammalian cells6, but its location within genes and its function in transcription are unknown. Here we show that H3R2 is also methylated in budding yeast. Using an antibody specific for H3R2me2a in ChIP-on-Chip analysis we determine the distribution of this modification on the entire yeast genome. We find that H3R2me2a is enriched at all heterochromatic loci, at inactive euchromatic genes and at the 3’-end of moderately transcribed genes. In all cases the pattern of H3R2 methylation is mutually exclusive with the presence of trimethylation at H3K4 (H3K4me3). The inverse correlation reflects the fact that methylation at H3R2 disrupts the ability of the Set1-complex to methylate H3K4. H3R2m2a inhibits specifically the trimethylation of H3K4 because it prevents Spp1 (a Set1-methyltranferase subunit) from binding to histone H3. These results indicate that methylation at H3R2 controls the global distribution of H3K4me3 and provides the first mechanistic insight into the function of arginine methylation on chromatin.
Keywords: ChIP-chip

overall_design: ChIP-chip analysis was performed to determine the genomic distribution of histone modifications H3R2me2a, H3K4me1, H3K4me2, and H3K4me3 in the BY4741 yeast strain.  This analysis was also used to determine the genomic binding of proteins Rap1 and Sir2 in the JHY6-H3WT and JHY6-H3R2A strains. Two biological replicates were carried out for each experiment. ChIP samples were amplified, labelled, and hybridized to 50-mer tiling arrays covering the entire yeast genome at a 64 bp resolution.

first: Helena

last: Santos-Rosa

first: Christopher

last: Penkett

first: Michael

last: Singer

first: Michiel

last: Vermeulen

first: Matthias

last: Mann

first: Jurg

last: Bahler

first: Roland

middle: D

last: Green

first: Tony

last: Kouzarides


title: Global, comparative analysis of tissue-specific promoter CpG methylation.

status: Public on Aug 08 2007

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

type: Methylation profiling by genome tiling array

summary:
Understanding cell-type-specific epigenetic codes on a global level is a major challenge after the sequencing of the human genome has been completed. Here we applied methyl-CpG immunoprecipitation (MCIp) to obtain comparative methylation profiles of coding and noncoding genes in three human tissues, testis, brain, and monocytes. Forty-four mainly testis-specific promoters were independently validated using bisulfite sequencing or single-gene MCIp, confirming the results obtained by the MCIp microarray approach. We demonstrate the previously unknown somatic hypermethylation at many CpG-rich, testis-specific gene promoters, in particular in ampliconic areas of the Y chromosome. We also identify a number of miRNA genes showing tissue-specific methylation patterns. The comparison of the obtained tissue methylation profiles with corresponding gene expression data indicates a significant association between tissue-specific promoter methylation and gene expression, not only in CpG-rich promoters. In summary, our study highlights the exceptional epigenetic status of germ-line cells in testis and provides a global insight into tissue-specific DNA methylation patterns.
Keywords: MCIp-on-Chip

overall_design: The promoter hypomethylation profiles of the two somatic tissues (monocytes and brain) were compared to human testis (reference). The set includes two hybridisations with independent testis samples for each comparison. Each comparison uses a set of two microarrays.

first: Elmar

last: Schilling


title: Temporal Analysis of Candida albicans Gene Expression During Biofilm Development: Phase-Dependent Cellular Activities

city: Urbana

first: Lois

last: Hoyer

state: IL

address: 2001 S Lincoln Ave

department: Pathobiology

institute: University of Illinois

summary:
Candida albicans can form biofilm on the surface of indwelling medical devices.  Biofilm formation is an importanat clinical problem because biofilm-grown cells have decreased susceptibility to antifungal agents.  Microarray technology was used to identify changes in gene expression during biofilm development.  Two biofilm substrates (denture and catheter) were used, with two C. albicans strains tested on each substrate.  Three phases of biofilm development were studies:  early (6 h), intermediate (12 h), and mature (48 h).  Planktonic specimens were collected at the same time points.  Comparison between biofilm and planktonic cell transcriptional profiles at each time point showed differential expression of approximately 3% of the genome in biofilm.  Fewer than half of these genes were up-regulated in biofilm, compared to planktonic cells.  Transcriptional profiles were also analyzed over the time course of biofilm development.  Genes up-regulated during the early phase (6 h) primarily were involved in glycolytic and non-glycolytic carbohydrate assimilation, and amino acid metabolism.  The largest number of differentially expressed genes were identified at the intermediate phase (12 h) of biofilm development where the largest increase in biofilm biomass occurs.  Genes up-regulated at 12 h were involved in transcription, protein synthesis/translation, energy generation, cellular transport, and nucleotide metabolism.  At mature phase (48 h), few genes were up-regulated compared to the 12 h time point.  These data define phase-dependent changes in gene expression that occur during biofilm development and show how genes belong to different, but interconnected, functional categories regulate the morphology and phenotype of C. albicans biofilm
Keywords: phase-dependent gene expression; comparative genomic hybridization; cell type comparison

overall_design: Two independent biological replicates were used in the microarray hybridization analysis.  The experimental design of the array hybridizations was a 4-block (one for each strain and surface combination), simple loop (daisy-chain) design with a dye swap.

first: Kathleen

last: Yeater

first: Jyotsna

last: Chandra

first: Georgina

last: Cheng

first: Pranab

middle: K

last: Mukherjee

first: Xiaomin

last: Zhao

first: Sandra

last: Rodriguez-Zas

first: Kurt

last: Kwast

first: Mahmoud

last: Ghannoum


title: affy_fertility_chicken_exp169

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development.

A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. We use 4 different hen lines:

-   one line of laying hens with 3 different samples: the just ovulated oocyte, the oocyte collected 24 hours before ovulation (F1 stage), and granulosa cells collected at the F1 stage. We could compare different tissue and developmental stages.

-   one line of hen with rapid growth speed

-   two lines of laying hens

For the 3 last lines we used animals with different fertility levels. We collected the oocyte of the largest follicle before ovulation (F1).

The aim of the study is to identify genes involved in fertility or early embryo mortality.

Keywords: normal vs disease comparison

overall_design: 6 arrays - Gallus gallus

first: Sandrine

last: Balzergue

first: Florence

last: Batellier

first: Sebastien

last: Elis

first: Marie-Laure

last: Martin-Magniette


title: Lobular Carcinoma in situ CGH

status: Public on Jul 27 2007

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

summary:
We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise. Our goal was to use known aberrations within these samples as a benchmark for determining the ability to differentiate between sample noise and real signal.
Keywords: CGH

overall_design: Human genomic DNA from a pool of individuals were hybridized to the Cy5 channel and labeled using indeirect amino alyl dUTP. The genomic DNA was extracted from LCM cells from LCIS and labelled with Cy3 using DOP amplification amino-alyl dUTP.

first: Carolyn

last: Mies

first: Katarzyna

last: Dudycz-Sulicz

first: Don

last: Baldwin

first: Gregory

last: Grant


title: Pre- and postnatal hepatic expression profiles of two pig breeds differing in body composition

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
In order to gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition we aimed to compare samples of pigs of two breeds, the “obese” German Landrace (DL) and the “lean” Pietrain (Pi) obtained at prenatal stages (35, 63, and 91 days post conceptionem) and at adult age (180 days).   In terms of number of genes regulated the most striking differences between DL and Pi were found at adult age with upregulation of key genes of lipid biosynthesis/metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs on the one hand and upregulation of genes of cell growth and/or maintenance, protein syntheses as well as cell proliferation pathways (PPARD, POU1F1, IGF2R) in lean Pi pigs on the other hand. Time course analysis of expression profiles of breed differences from foetal to adult stage and functional cluster analysis of the biological processes confirmed the trend of differences between genetically different obese and lean breeds. The highlighted classes of genes showed common breed-typical expression throughout prenatal development and at adult age. The transcriptional differences between obese and lean pigs involving lipid pathways and cell activity are already initiated during early prenatal development. The information about genetic differences between obese and lean pigs reveals a number of functional candidate genes for traits related to obesity and leaness.
Keywords: pig, oligo-microarray, prenatal liver expression, adult liver expression, obesity, leaness

overall_design: Porcine liver from three prenatal stages (35, 63, and 91 day post conceptionem, dpc) plus adult age (180 days) of 10 animals of each of the breeds DL and Pi, which differ in body composition, were collected. The hepatic gene expression patterns of DL and Pi breeds were compared at each of the four stages of development. Three or four biological replicate microarray hybridisations were performed for each stage with DL pools labelled with Cy5 and Pi pools labelled with Cy3.

first: Siriluck

last: Ponsuksili


title: Sex-dependent and STAT5a-dependent Liver Gene Expression

status: Public on Jul 30 2007

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary:
A series of dual-channel gene expression profiles obtained using Agilent Mouse TOE 75k microarrays was used to examine the sex-dependent and STAT5a-dependent differences in gene expression in adult mouse liver.  This series is comprised of 3 randomly chosen independent male and female wildtype mouse liver cDNA samples and 3 randomly chosen independent male and female STAT5a-deficient mouse liver cDNA samples, totalling 12 samples.  The samples were paired randomly to generate 4 comparisons of M-WT:F-WT, M-WT:M-KO, F-KO:F-WT, F-KO:M-KO.  Comparison of the set of sex-dependent genes with the set of genes responsive to the loss of STAT5a in females shows a small group of the sex-specific genes were also regulated by STAT5a in females.  These results indicate a role for STAT5a in female gene expression to a lesser degree than that shown for STAT5b in males.
Keywords: genetic knockout and sex response

overall_design: A Cy3-labeled cDNA sample is co-hybridized with a Cy5-labeled cDNA sample depending on the comparison being made.  The samples are then dye-swapped and compared again on a second microarray chip.  The two pairs are averaged together, the averages are normalized across the fluorescent reverse pairings, and the normalized ratio is reported along with the two separate intensities.  This is replicated 3 times with independent samples of cDNA for each pair being compared.  There are a total of 4 pairs of conditions being compared for a grand total of 12 samples.

first: Karl

middle: H

last: Clodfelter

last: Miles

first: Valerie

last: Wauthier

first: Minita

middle: G

last: Holloway

first: Xiaohua

last: Zhang

first: Paul

last: Hodor

first: William

last: Ray


title: Mesenteric adipose tissue of rats treated with oleoyl-estrone

status: Public on Jul 25 2007

city: Barcelona

first: Xavier

last: Remesar

address: Av. Diagonal 645

department: Nutrició i Bromatologia

country: Spain

institute: Universitat de Barcelona

summary:
The aim of this work was to determine if  OE treatment affects the expression of genes that regulate lipid metabolism in white adipose tissue. Gene expression in adipose tissue from female treated rats (48 hours) was analysed by hybridization to cDNA arrays and levels of specific mRNAs were determined by Real-Time PCR. Treatment with OE decreased the expression of 232 genes and up-regulated 75 other genes in mesenteric white adipose tissue.
Short-term treatment with OE affects adipose tissue capacity to extract fatty acids from lipoproteins and to deal with fatty acid transport and metabolism.
Keywords: Effects of a drug on gene expression

overall_design:
The rats were given a daily oral gavage of 10 μmol/kg/day of oleoyl-estrone (OED, Barcelona, Spain) in 0.2 ml of sunflower oil during two days, by means of stomach cannulae. Controls received only the oil gavage. After 48 hours of the beginning of treatment, the mesenteric white adipose tissue was  dissected and frozen in liquid nitrogen and stored at -80ºC.
Total RNA was extracted from adipose mesenteric tissue using Tripure isolation kit. Gene expression was analysed by hybridization to cDNA arrays (AtlasTM Rat Array 1.2 from BD-Clontech, Mountain View CA, USA).
Two samples from control animals and two samples from treated animales were analyzed.

first: Anna

last: Salas

first: Véronique

last: Noé

first: Carlos

last: Ciudad

first: Mar

middle: M

last: Romero

first: Remesar

last: Xavier

first: Esteve

last: Montserrat


title: Acid shock responses in Staphylococcus aureus

status: Public on Jul 29 2007

city: Aas

first: Solveig

last: Langsrud

address: Osloveien 1

country: Norway

institute: Matforsk, Norwegian Food Research Institute

summary:
We present a general overview of the changes in the genetic expression along a time curve through the first 20 minutes after acidification to pH 4.5 of exponentially growing cultures of the food pathogenic strain Staphylococcus aureus 50583. A newly developed method for statistical significance testing was used to detect significant gene expression responses. Most responses showed an increase or decrease from time zero to 10 minutes after acidification and then generally a stabilisation in expression level from 10 to 20 min. Increased urease activity appeared to be an important factor in the acid defence along with proton excretion by NADH dehydrogenase and macromolecule repair mechanisms. Oxidative stress responses such as increased expression of thioredoxin genes and upregulation of  pentose phosphate pathway genes to generate more reducing power were also induced. A general reduction in the expression of genes encoding ribosomal proteins and genes involved in nucleotide synthesis as well as fatty acid and lipoprotein metabolism reflected the lowered growth rate after acidification. The pH shock did not appear to trigger major virulence responses or biofilm formation. The metal ion regulation and transport was affected by the acid shock and production of several cofactors such as molybdopterin was increased. Many of the presented observations could be explained, while some represent still unknown mechanisms. The patterns of regulation were confirmed by real time reverse transcriptase PCR. Together these results showed the main responses of S. aureus and will be a good starting point for future more specific in-depth studies of specific gene responses in conjunction with acid stress defence of S. aureus.
Keywords: Time course, stress response

overall_design: S. aureus was inoculated in TSB and and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 the control samples were withdrawn immediately prior to the addition of HCl to directly bring the pH down to 4.5. Samples were withdrawn 2, 5, 10 and 20 min after addition of acid. All samples were directly transferred to RNA Protect Bacteria reagent (Qiagen). This procedure was repeated at three different days for a total of three sample sets (parallels). Separate array experiments were performed on all three parallels.

first: Erlend

last: Bore

first: A

first: Tone

last: Rode

first: Askild

last: Holck


title: The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation

status: Public on Jul 20 2007

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
The filamentous bacterium Streptomyces coelicolor differentiates  by forming specialized, spore-bearing aerial hyphae that grow into the air. Using microarrays, we identified genes that are down-regulated in a mutant unable to erect aerial hyphae. Through this route, we identified a previously unknown layer of aerial mycelium surface proteins (the "chaplins"). The chaplins share a hydrophobic domain of ~40 residues (the "chaplin domain"), and all have a secretion signal. The five short chaplins (ChpD,E,F,G,H) have one chaplin domain, whereas the three long chaplins (ChpA,B,C) have two chaplin domains and a C-terminal "sorting signal" that targets them for covalent attachment to the cell wall by sortase enzyme. Expression of the two chaplin genes examined  (chpE, chpH) depended on aerial hyphae formation but not sporulation,  and egfp fusions showed their expression localized to aerial  structures. Mass spectrometry of cell wall extracts confirmed that the short chaplins localized to the cell surface. Deletion of chaplin genes caused severe delays in aerial hyphae formation, a phenotype rescued by exogenous application of chaplin proteins. These observations implicate the chaplins in aerial mycelium formation, and suggest that coating of the envelope by the  chaplins is required for aerial hyphae to grow out of the aqueous environment of the substrate mycelium into the air.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: User Defined

first: Nitsara

last: Karoonuthaisiri


title: A. nidulans wild type and atmA null mutant strains transcriptome analysis in conidia grown for 60, 90 and 120 minutes

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

summary:
ATM is a phosphatidyl-3-kinase-related protein kinase that functions as a central regulator of the DNA damage response in eukaryotic cells. In humans, mutations in ATM cause the devastating neurodegenerative disease Ataxia Telangiectasia. Previously, we characterized the homologue of ATM (AtmA) in the filamentous fungus Aspergillus nidulans. In addition to its expected role in the DNA damage response, we found that AtmA is also required for polarized hyphal growth. In order to investigate which pathways are controlled by AtmA during proliferation and polar growth, we determined the transcriptional profile of A. nidulans wild type and delta atmA mutant strains in different growth conditions. Conidia from both wild type and delta atmA mutant were incubated with 50 mM of hydroxyurea to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. At each time point, the germlings were also harvested by centrifugation and used for competitive microarray hybridizations. Our results indicate several genes that have decreased mRNA expression in the delta atmA mutant which are involved in the formation of a polarized hyphae and control of polar growth; in the synthesis of phosphatidic acid; in the ergosterol biosynthesis; and intracellular trafficking, secretion, and vesicular transport.
Keywords: gene expression array-based, log2 ratio

overall_design:
For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) and delta atmA (IM69) mutant strains were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks and allow to grow for 60, 90 and 120 minutes in a reciprocal shaker (250 rpm) at 37°C. After this time, germilings were harvested by centrifugation and total RNA from each sample was extracted. Hybridization experiments were competitive using probes derived from wild type and delta atmA strain grown for 60, 90 and 120 using wild type RNA as reference in comparison to the mutant strain (delta atmA) in the same experimental time point.  Dye swap hybridizations were performed. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary files linked below).

first: Iran

last: Malavazi


title: Bj_Minimal_Rich

status: Public on Jul 26 2007

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

summary:
Functional genomics of B. japonicum in minimal vs. rich medium. Different nutritional status was compared.
Keywords: stress response

overall_design: Three independent biological materials were prepared. However, total 6 arrays were analyzed due to the dye swap.

first: Gary

last: Stacey

first: David

middle: W

last: Emerich

first: Michael

last: Sadowsky

first: Dong

last: Xu

last: Franck


title: Gene expression in Su(Hw) null larvae

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

summary:
We examined the effects of loss of su(Hw) on gene expression in both carefully staged 3rd instar larvae (selected at the soft white pre-pupae stage) and wing imaginal discs from these animals.  su(Hw) null animals were generated by crossing su(Hw)v mutants with a deficiency (Df(3R)ED5644), homozygous individuals were recognised be the lack of the dominat Tb marker carried on the TM6B marker.
Keywords: ChIP-chip

overall_design: RNA from null larvae was compared with a pool of RNA extracted from wild type (Oregon R) larvae at the same stage.  To control for genetic background we also examined su(Hw)v and Df(3R)ED5644 heterozygotes with the pool - thus 3 genotypes were examined.  For each genotype, 4 independent biological replicates were performed - 2 of these dye swapped with respect to the other two.  The same experimental design and gentoypes were used for the analysis in dissected wing imaginal discs.

first: Boris

middle: E

last: Adryan

first: Gertrude

middle: A

last: Woerfel

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: Marie

last: Quick

first: Lisa

last: Meadows

first: Steven

first: Robert

last: White


title: T4_bisthiazolium effect on the malaria parasite transcriptome

city: Riverside

first: Karine

middle: Gaelle

last: Le Roch

address: 900 University Avenue

department: Department of Cell Biology & Neuroscience

institute: University of California

summary:
Choline analogs represent a novel class of antimalarial compounds with strong potency against drug-sensitive and resistant P. falciparum. Although, these drugs are presumed to target proteins within lipid biosynthesis pathways; their complete mechanism of action and the parasite’s compensatory response remain to be elucidated. We have applied transcriptional profiling to characterize the global response to the choline analog T4 during the P. falciparum intraerythrocytic life cycle
Keywords: Trascriptome analysis of Plasmodium falciparum in response to external stimuli using the affymetrix platform GPL3575

overall_design: Parasites were incubated in complete medium at 8 % parasitaemia and 5 % haematocrit and treated with different concentration of T4.  Drug was added  at 125nM on a mixed or synchronized 25ml cultures.  Parasites were returned to the incubator for 30 minutes, 5, 24, 30 or 36 hours before total RNA extraction.  Transcriptome was analysed and compared between treated and nontreated cultures. Changes observed in the transcriptome were also further compared with the published ife cycle database (Le Roch et al.,Science, 2003)

first: Yingyao

last: Zhou

first: Henri

last: Vial

first: Elizabeth

last: Winzeler


title: A. nidulans wild type and atmA null mutant strains transcriptome analysis for polar growth upon HU-release

first: Gustavo

last: Goldman

summary:
ATM is a phosphatidyl-3-kinase-related protein kinase that functions as a central regulator of the DNA damage response in eukaryotic cells. In humans, mutations in ATM cause the devastating neurodegenerative disease Ataxia Telangiectasia. Previously, we characterized the homologue of ATM (AtmA) in the filamentous fungus Aspergillus nidulans. In addition to its expected role in the DNA damage response, we found that AtmA is also required for polarized hyphal growth. In order to investigate which pathways are controlled by AtmA during proliferation and polar growth, we determined the transcriptional profile of A. nidulans wild type and delta atmA mutant strains in different growth conditions. Conidia from both wild type and delta atmA mutant were incubated with 50 mM of hydroxyurea to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. At each time point, the germlings were also harvested by centrifugation and used for competitive microarray hybridizations. Our results indicate several genes that have decreased mRNA expression in the delta atmA mutant which are involved in the formation of a polarized hyphae and control of polar growth; in the synthesis of phosphatidic acid; in the ergosterol biosynthesis; and intracellular trafficking, secretion, and vesicular transport.
Keywords: gene expression array-based (log2 ratio)

overall_design:
For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) and delta atmA mutant strains were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks containing 50 mM of hydroxyurea (HU) and allow to grow for 5 hours in a reciprocal shaker (250 rpm) at 37°C to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. Hybridization experiments were competitive using probes derived from wild type and delta atmA strain grown for zero, 60, 90 and 120 minutes after HU blockage release using timepoint zero as the reference RNA for the hybridizations (wild type or mutant strain). Dye swap hybridizations were performed. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary files linked below).

first: Iran

last: Malavazi


title: Micromolar fluoride alters ameloblast lineage cells in vitro

city: san francisco

first: Pamela

last: DenBesten

address: 513 Parnassus Ave. Rm S-612

department: Orofacial sciences

institute: UCSF

summary:
Previously characterized ameloblast-lineage cells were used in this study to determine whether micromolar levels of fluoride could be directly affect these cells.
Keywords: substance response

overall_design:
Six samples altogether were analyzed in this study. Every two of them were from a same biological souce and subject to with or without the treatment of 10uM NaF (the only difference between the two samples.)
The experiment was repeated 3 times.

first: Qiaomei

last: Yan

first: Yan

last: Zhang

first: Wu

last: Li


title: LIN-14 mutants

status: Public on Jul 19 2007

last: Stanford Microarray Database

summary:
A temporal gradient of the novel nuclear protein LIN-14 specifies the timing and sequence of stage-specific developmental events in Caenorhabditis elegans. The profound effects of lin-14 mutations on worm development suggest that LIN-14 directly or indirectly regulates stage-specific gene expression. We show that LIN-14 can associate with chromatin in vivo and has in vitro DNA binding activity. A bacterially expressed C-terminal domain of LIN-14 was used to select DNA sequences that contain a putative consensus binding site from a pool of randomized double-stranded oligonucleotides. To identify candidates for genes directly regulated by lin-14, we employed DNA microarray hybridization to compare the mRNA abundance of C. elegans genes in wild-type animals to that in mutants with reduced or elevated lin-14 activity. Five of the candidate LIN-14 target genes identified by microarrays, including the insulin/insulin-like growth factor family gene ins-33, contain putative LIN-14 consensus sites in their upstream DNA sequences. Genetic analysis indicates that the developmental regulation of ins-33 mRNA involves the stage-specific repression of ins-33 transcription by LIN-14 via sequence-specific DNA binding. These results reinforce the conclusion that lin-14 encodes a novel class of transcription factor.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Marta

last: Hristova


title: Identification of differentially-expressed genes between FoxH1 morpholino and control in zebrafish embryos.

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary:
The Forkhead Box H1 (FoxH1) protein is a co-transcription factor recruited by phosphorylated Smad2 downstream of several TGFbetas, including Nodal-related proteins.  We have reassessed the function of zebrafish FoxH1 using antisense morpholino oligonucleotides (MOs) ( 5’ TGCTTTGTCATGCTGATGTAGTGGG  3’) as compared with a control morpholino (MO) with no specific target (5’ TAGTTAAGCCTAGCTCTCATAAACT  3’). Probing FoxH1 morphant RNA by microarray, we identified a cohort of five keratin genes – cyt1, cyt2, krt4, krt8 and krt18 - that are normally transcribed in the embryo’s enveloping layer (EVL) and which have significantly reduced expression in FoxH1-depleted embryos.
Keywords: 40% epiboly-stage embryos, injected with either 8 ng of a 25mer morpholino (MO) with no specific target or 8 ng of a 25mer MO with reverse complementary to the 5’ untranslated region of the zebrafish foxH1 gene.

overall_design: 34k expression arrays were generated by printing Oligo nucleotides from three different sets (MWG, Compugen and Operon) onto epoxy slides. Total RNA from 50 FoxH1 MO- and 50 control MO-injected embryos was amplified using an Ambion kit (Cat#1753), labeled with Cy dyes and hybridized overnight to the oligo chip.  This procedure was performed three times independently, including one dye swap, and cRNA from FoxH1 morphants and control embryos were co-hybridized for a total of three hybridizations.

first: Benjamin

last: Feldman

first: Wuhong

last: Pei

first: Houtan

last: Noushmehr

first: Abdel

last: Elkahloun


title: Whole genome analysis of mRNA decay in P. falciparum reveals a lengthening of mRNA half-life during the IDC

city: San Francisco

first: Joseph

middle: L

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California San Francisco

summary:
The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms.  Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiological role, and plays an important role in determining levels of gene expression.  We have used a genome wide approach to characterize mRNA decay in Plasmodium falciparum.  We found that globally, rates of mRNA decay increase dramatically during the asexual intraerythrocytic developmental cycle.   During the ring stage of the cycle, the average mRNA half-life was 9.5 minutes, yet this was extended to an average of 65 minutes during the late schizont stage of development.  Thus a major determinant of mRNA decay rate appears to be linked to the stage of intraerythrocytic development.  Furthermore, we have found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening.  These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes.  Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies.  Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intraerythrocytic development.  This type of genome wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.
Keywords: Plasmodium falciparum treated with actinomycin D

platform_organism:
Saccharomyces cerevisiae
Plasmodium falciparum

overall_design: We analyzed a series of microarrays representing timepoints up to 240 minutes after addition of the transcription inhibitor actinomycin D.  This experiment was repeated for the ring, trophozoite, schizont and late schizont stages to measure stage-specific mRNA decay.

first: Jennifer

last: Shock

first: Kael

last: Fischer


title: Basal Epidermis from UVB-irradiated Mc1r and Kit mutants

summary:
Total RNA was extracted from the basal epidermis derived from UVB-irradiated P2.5 normal (Mc1r+/Mc1r+; Kit+/Kit+), Mc1r-mutant (Mc1re/Mc1re) and Kit-mutant (Kit/W-v/Kit/W-v) mice. Biological replicates (cy5) were labelled and co-hybridized with a reference RNA sample (cy3) to a 35K mouse cDNA microarray.
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Craig

last: April


title: Analysis of the trithorax Group (trxG) genes ash2 and ash1 wing imaginal disc transcriptomes.

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

summary:
The absent, small or homeotic discs 2 (ash2) gene, a member of the trithorax Group (trxG) of transcriptional regulators, is functionally related to ash1. However, ASH2 and ASH1 belong to distinct multimeric complexes of unknown composition and it is unclear how they act to regulate transcription. In this study, examination of gene expression profiles in wing imaginal discs from ash2 and ash1 mutants revealed their transcriptomes are very similar and correlate with wing phenotypes.
Keywords: loss of function analysis

overall_design: Wing imaginal discs from alleles ash2^I1, ash2^112411 and ash1^22 were dissected. Four microarrays were hybridized for each experiment (total of 12 experiments) in biological replicate pairs, such that the total RNA from the sample used as a starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

first: Mireia

last: Angulo

first: Miguel

last: Pignatelli

first: Florenci

last: Serras

first: Montserrat

last: Corominas


title: Female Rhesus Monkey hypothalamic gene expression profiling during puberty

status: Public on Jul 17 2007

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

summary:
Transcriptional profilling of the female primate hypothalamus during normal puberty. Total RNA samples from hypothalami from juvenile (JUV), early pubertal (EP) and mid pubertal (MP) female monkeys were used to compare pairwise against the JUV group.
Keywords: Normal gene expression profiling

overall_design: Tree-condition experiment, EP vs. JUV and MP vs. JUV. Biological replicates: 4 JUV, 4 EP and 4MP. Four replicates per array.

first: Christian

last: Roth

first: Claudio

last: Mastronardi

first: Hollis

last: Wright

first: Ricardo

last: Cabrera

first: Alison

last: Mungenast

first: Sabine

last: Heger

first: Heike

last: Jung

last: Dubay

first: Sergio

middle: R

last: Ojeda


title: HMEC nine-condition expression profiling

city: Los Angeles

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

summary:
Exposure to air particulate matter is associated with increased cardiovascular morbidity and mortality. One of the possible mechanisms is by promotion of atherosclerosis mediated by synergy of particulate matter chemicals and oxidized phospholipids on vascular endothelial cells. We treated human microvascular endothelial cells (HMEC) in triplicate wells with diesel exhaust particles (DEP) extract at a concentration of 5 and 25 mcg/ml, oxidized 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphorylcholine (ox-PAPC) at concentrations of 10, 20 and 40 mcg/ml or combination of DEP at 5 mcg/ml plus ox-PAPC at  10, 20 and 40 mcg/ml. The 3600 most variably expressed genes were employed to construct a weighted gene co-expression network to assess the degree of connectivity. Module enrichment analysis showed that three modules (Brown, Green and Yellow) were highly significant (p< 0.0001) in enriched genes regulated by the treatments. These three modules exhibited patterns of synergistic/additive interaction and were enriched in pathway genes relevant to vascular inflammation. The in-vivo relevance of this gene clustering analysis was established by demonstrating that liver gene expression of hypercholesterolemic mice exposed to ultrafine particles exhibited significant upregulation of similar gene pathways, as predicted by the in-vitro synergy.
Keywords: Expression profiling comparison, effect of DEP vs. ox-PAPC vs. DEP plus ox-PAPC

overall_design: This experiment compares gene expression profiles of HMEC exposed to DEP, ox-PAPC or DEP plus ox-PAPC by Illumina HumanRef-8 v1 Expression Beadarrays. This design allowed to establish the genome wide synergistic effects of co-regulation induced by DEP and ox-PAPC.

first: KeWei

last: Gong

first: Wei

last: Zhao

first: Ning

last: Li

first: Berenice

last: Barajas

first: Michael

last: Kleinman

first: Constantinos

last: Sioutas

first: Steve

last: Horvath

first: Aldons

middle: J

last: Lusis

first: Andre

last: Nel

first: Jesus

last: Araujo


title: Sex-dependent and strain-dependent gene liver gene expression

first: David

last: Waxman

summary:
A series of dual-channel gene expression profiles obtained using Agilent Mouse TOE 75k microarrays was used to examine the sex-dependent differences in gene expression across three outbred mouse strains, 129J x Black Swiss, 129J x BALB/c, and ICR.  This series is comprised of samples obtained from 3 pools of randomly chosen independent cDNA samples of male and female 129Jx BALB/c mice and 3 randomly chosen independent cDNA samples of male and female 129J x Black Swiss mice and 5 randomly chosen independent cDNA samples of male and female ICR mice.  The ICR mice were randomly distributed into three and two member pools for each sex and two of the 5 samples for each sex were independently hybridized separately as well.  Comparison of the sex-specific genes for the three outbred strains generated lists of strain-dependent and strain-independent sex-specific genes.
Keywords: sex response and strain response

overall_design: A Cy3-labeled cDNA sample is co-hybridized with a Cy5-labeled cDNA sample depending on the comparison being made. The samples are then dye-swapped and compared again on a second microarray chip. The two pairs are averaged together, the averages are normalized across the fluorescent reverse pairings, and the normalized ratio is reported along with the two separate intensities. This is replicated 3 times with independent samples of cDNA for the 129J x BALB/c and 129J x Black Swiss Mice and 2 times each for the ICR pools and single samples. There are a total of 3 outbred strains being compared for a grand total of 10 samples.

first: Karl

last: Clodfelter

first: Miles

last: Gregory

first: Valerie

last: Wauthier

first: Minita

last: Holloway

first: Xiaohua

last: Zhang

first: Paul

last: Hodor

first: William

last: Ray


title: Resistance Exercise Reverses Aging in Human Skeletal Muscle

status: Public on Jul 16 2007

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary:
Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training.
Keywords: resistance exercise, muscle, aging

overall_design: A muscle biopsy was taken from the vastus lateralis muscle of the right or left leg (randomized) before exercise or immobilization (young people, N = 26 total) and before (N = 25), and after (N = 14), the training period in older adults, ~20 cm proximal to the knee joint using a 5mm Bergström biopsy needle. The muscle was dissected of fat and connective tissue, immediately frozen in liquid nitrogen, and stored at -80°C for subsequent analysis. All subjects were required to abstain from strenuous physical activity for 48 h prior to the muscle biopsy.

first: Mark

last: Tarnopolsky

first: Kenneth

last: Beckman

first: Krysta

last: Felkey

first: Alan

last: Hubbard


title: Role of S. cerevisiae Hap1 in oxygen-regulation

status: Public on Jul 28 2007

city: Princeton

last: Hickman

state: NJ

address: Washington Road

department: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

summary:
Expression microarray experiments were performed to identify all of the aerobic and hypoxic transcripts in wild-type cells.  The role of Hap1 in the regulation of transcription was examined by monitoring gene expression in hap1 deletion cells.
Keywords: gene expression, strain comparison, response to hypoxic conditions

overall_design: Three replicates were performed for wild-type cells, and three replicates for hap1 deletion cells.  Biological replicates were performed in each case, with separate cultures grown on different days.  For each microarray, an aerobic sample was compared to a hypoxic sample.

first: Fred

last: Winston


title: Ductal Carcinoma in situ CGH

city: Cambridge

first: Mitchell

last: Guttman

institute: Broad Institute

summary:
We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise. Our goal was to use known aberrations within these samples as a benchmark for determining the ability to differentiate between sample noise and real signal.
Keywords: aCGH

overall_design: Human genomic DNA from a pool of individuals were hybridized to the Cy5 channel and labeled using indeirect amino alyl dUTP. The genomic DNA was extracted from LCM cells from DCIS and labelled with Cy3 using DOP amplification amino-alyl dUTP.

first: Carolyn

last: Mies

first: Katarzyna

last: Dudycz-Sulicz

first: Don

last: Baldwin

first: Gregory

last: Grant


title: Identification of GSNO response network in E. coli

first: Laura

last: Jarboe

address: 420 Westwood Pl

department: Chemical and Biomolecular Engineering

institute: University of California, Los Angeles

summary:
This project used transcriptomic analysis of the S-nitrosoglutathione (GSNO) response in E. coli, and associated regulatory mutants, to identified the molecular targets of and response to GSNO during aerobic growth in minimal media.

Keywords: Comparative genomic response

overall_design: Samples were treated with either 100 or 500 micromolar GSNO and the 5-minute response was analyzed.  The resulting transcriptome data was analyzed with network component analysis (NCA) to identify perturbed regulators and pathways.

first: Daniel

last: Hyduke

first: Linh

last: Tran

first: Katherine

last: Chou

first: James

middle: C

last: Liao


title: A microRNA component of the p53 tumor suppressor network

city: Seattle

first: Lee

last: Lim

state: WA

institute: Rosetta Inpharmatics

summary:
This series consists of samples taken from cell lines transfected with miR-34 duplexes or luciferase control siRNAs.
Keywords: other

overall_design: Please see Nature submission: He et al, 2007.

first: Lin

last: He

first: Xingyue

middle: P

first: Elisa

last: de Stanchina

first: Zhenyu

last: Xuan

first: Yu

last: Liang

first: Wen

last: Xue

first: Lars

last: Zender

first: Jill

last: Magnus

first: Dana

last: Ridzon

first: Aimee

last: Jackson

first: Peter

middle: S

last: Linsley

first: Caifu

last: Chen

first: Scott

last: Lowe

first: Michele

last: Cleary

last: Hannon


title: SparcTm1Cam129SvEv bone vs 129Sv/Evcontrol bone

status: Public on Jul 11 2007

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

institute: Cardiff University

summary:
Sparc null mutants have been generated independently via two targeted mutations in exons 4 and 6. Previous studies have identified low turnover osteopenia in the exon 4 knockout (on a mixed 129Sv/C57Bl/6 background). Since both Sparc null mutations have been shown to result in complete absence of Sparc protein, similar phenotypic outcomes are likely. However, genetic background and/or linkage disequilibrium effects can influence phenotype; abnormalities attributed to a given mutation have often been later found to be caused by closely linked genetic anomalies or strain effects.  Ideally therefore, different inactivating mutations should be tested in various mouse strains; similar phenotypic outcomes can then confidently be assigned to the mutated gene. We have evaluated the bone phenotype in the Sparctm1cam exon 6 knockout on a purebred 129Sv/Ev background at 4 and 9 months, using physical measurement, mechanical strength tests and DXA scanning. We have also quantified bone marrow adiposity and circulating leptin levels to assess adipose tissue regulation anomalies in these mice. 129Sv/EvSparctm1cam null mice show decreased bone mineral density and bone mineral content. Increased mechanical fragility of bone was also evident, largely in line with previous studies. However, differences were also noted. Increased body weight and levels of bone marrow adiposity, but decreased circulating leptin concentrations were identified at 4 months, but not at 9 months. Circulating leptin concentrations were reportedly increased in Sparc exon 4 null animals, suggesting that leptin concentrations may be influenced more by genetic background than by the absence of Sparc. 129Sv/EvSparctm1cam null mice have shorter femurs; this difference was not noted in prior studies, possibly due to increased variation owing to use of a hybrid strain. Molecular phenotyping was carried out using mouse HGMP NIA microarrays with cortical femur samples at various ages, using semi-quantitative RT PCR validation. Array studies have identified 429 genes expressed in normal bone. Six genes (Sparc, Zfp162, Bysl, E2F4 and two ESTs) are differentially regulated in 129Sv/EvSparctm1cam cortical femur versus 129Sv/Ev controls. We confirm low turnover osteopenia as a feature of the Sparc null phenotype, identifying the usefulness of this mouse as a model for human osteoporosis.
Keywords: disease state analysis, time course, genetic modification, osteoporosis, knockout mouse

overall_design: This study compared Sparc null bone, which is osteopenic, with that from matched wild type controls. SparcTm1Cam129SvEv knockout mouse bone at two timepoints, 4months and 9 months, were compared via microarray with strain, age and sex matched 129Sv/Evcontrol bone (male mice were used in all cases). Bone RNA was extracted from 0.5cm midsections of mouse flushed cortical femur. Samples from more than one mouse (litter mates of the same genotype) were pooled in order to maximize yield. Different RNA samples were labelled using the Cy Scribe direct labelling kit (GE Healthcare) and hybridised separately to 5 repetitions of each array type. Fluors were switched. After scanning and image analysis, samples were normalised globally via division by the mean spot value and were analysed with SAM (Significant Analysis of Microarrays). Genes that were two fold differentially regulated with a delta value of 0.5 were selected. In a separate analysis, we removed genes that were below background + 2SD in both channels (average background was calculated using empty spot values), and selected those genes that were more than 2 fold differentially regulated in 8/10 repetitions (the array contains duplicate spots, so 5 reps +2 spots per array = 10 repetitions per experiment). We compared the SAM genelist with the manually generated one and selected genes that appeared on both lists for RT PCR confirmation.

first: Bronwen

last: Evans

first: Timothy

last: Wells

first: Carole

last: Elford

first: Martin


title: LongSAGE transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

status: Public on Jul 07 2007

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary:
The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.
Keywords: Emiliania, gene expression, nutrients, SAGE, phosphate, nitrogen

overall_design: Emiliania huxleyi CCMP 1516 was obtained from the Provasoli-Guillard Center for the Culture of Marine Phytoplankton, Bigelow Laboratories.  Cultures were grown at 18°C on a 14 h:10 h light:dark cycle (140 µmol quanta m-2 s-1).  Nitrogen and phosphate replete (Replete: 35 µM NO3- and 1.5 µM PO43-), low nitrogen (-N: 10 µM NO3-) and low phosphate (-P: 0 µM PO43-) cells were grown in f/50 medium without Si.  Locally collected seawater was filtered (pore size, 0.2 µm) and autoclaved.  Filter-sterilized inorganic nutrients, trace metals and vitamins (thiamin, biotin and B12) were added after autoclaving.  The cells were grown in 8 L batch cultures.  The growth of cultures was monitored daily by cell number counted on a hemacytometer, and by relative fluorescence using a Turner Designs AU Fluorometer.  Replete cells were harvested in mid-log phase while –N and –P cells were harvested at the onset of stationary phase for SAGE analysis.

first: Sonya

middle: T

last: Dyhrman

first: Sheean

last: Haley

first: Shanda

last: Birkeland

first: Louis

last: Wurch

first: Michael

last: Cipriano


title: High resolution time-course data of regenerating Dorsal Root Ganglion neurons

status: Public on Jul 09 2007

city: Amsterdam

first: Floor

last: Stam

address: de Boelelaan 1087

department: Institute for Neurosciences

country: Netherlands

institute: Vrije Universiteit

summary:
Successful regeneration of injured neurons requires a complex molecular response that involves the expression, modification and transport of large numbers of proteins. The neuronal proteins responsible for the initiation of regenerative neurite outgrowth are largely unknown. Dorsal root ganglion (DRG) neurons display robust and successful regeneration following lesion of their peripheral neurite, whereas outgrowth of central neurites is weak and does not lead to functional recovery. We have utilized this differential response to gain insight in the early transcriptional events associated with successful regeneration. Surprisingly, our study shows that peripheral and central nerve crushes elicit very distinct transcriptional activation, revealing a large set of novel genes that are differentially regulated within the first 24 hours after the lesion. A large number of known regeneration associated genes were retrieved in our study, and, in addition, hundreds of novel genes possibly involved in the transcriptional regulatory network underlying successful regeneration. Please refer to Stam et al., Eur. J. Neurosci 25:3629 (2007).
Keywords: time course

overall_design:
For this study, we used an interwoven loop design. Each RNA sample consists of a pool of 3 animals. Each sample was hybridized at least three times. Each dye was used at least once for each sample.

See below supplementary file (coefs&se.xls) for the top-level processed data.

The excel file has two worksheets, one with the coefficients (gene regulation relative to t0) and the other with the standard errors (se). The first column is the gene ID as defined in the platform file and the sample files.

first: Nicola

last: Armstrong

first: Mathisca

last: de Gunst

first: Yi

last: Zhang

first: August

middle: B

last: Smit

first: Joost

last: Verhaagen


title: Effect pck or ppc expression on intracellular ATP

city: Bucheon

first: Pil

last: Kim

state: Gyunggi

address: 43-1 Yokkok2-dong

country: South Korea

institute: Catholic Univ. of Korea

summary:
Up-regulation of motility genes and biosynthesis genes were found in the pck expressing high ATP cell by transcriptome analysis while catabolism genes were down-regulated.
Keywords: response depends on intracellular ATP concentration derived by pck or ppc overexpression

overall_design:
1. pck or ppc overexpressing E. coli at early log phase using glucose-minimal medium
2. pck or ppc overexpressing E. coli at chemostat culture (D=0.1 h-1)using LB-glucose medium

first: Yeong-Deok

last: Kwon

first: Sang-Yup

last: Lee


title: Identification of a transcriptional fingerprint of estrogen exposure in rainbow trout liver

status: Public on Jul 13 2007

city: Logan

first: Abby

middle: D

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

summary:
The goal of this study was to identify a set of hepatic genes regulated by ligand-dependent activation of the estrogen receptor in juvenile rainbow trout (Oncorhynchus mykiss) that can serve as a biomarker of estrogen exposure. A custom rainbow trout oligo DNA microarray, which contains probes targeting approximately 1450 genes relevant to carcinogenesis, toxicology, endocrinology and stress physiology was utilized to identify transcriptional “fingerprints” of in vivo dietary exposure to 17β-estradiol (E2), tamoxifen (TAM), estradiol + tamoxifen (E2+TAM), diethylstilbestrol (DES), dehydroepiandrosterone (DHEA), dihydrotestosterone (DHT) and cortisol (CORT). Estrogen exposure altered the expression of up to 49 genes involved in reproduction, immune response, cell growth, transcriptional regulation, protein synthesis and modification, drug metabolism, redox regulation and signal transduction. E2, DES and DHEA regulated 18 genes in common, mostly those associated with vitellogenesis, cell proliferation and signal transduction. Interestingly, DHEA uniquely regulated several complement component genes of importance to immune response. While the effect of TAM on E2-induced changes in gene expression was mostly antagonistic, TAM alone increased expression of VTG1 and other genes associated with egg development and immune response. Few genes responded to CORT treatment, and DHT significantly altered expression of only one gene targeted by the OSUrbt array. Hierarchical cluster and principal components analyses revealed distinct patterns of gene expression corresponding to estrogens and non-estrogens, though unique patterns could also be detected for individual chemicals. A set of estrogen-responsive genes has been identified that can serve as a biomarker of environmental exposure to xenoestrogens.
Keywords: estrogen transcriptional profile, chemical transcriptional fingerprint

overall_design: Eight experimental treatments were selected to examine hepatic gene expression in response to estrogens, a selective estrogen receptor modulator (SERM) and non-estrogens. Treatments and concentrations (calculated with respect to diet wet weight) are as follows:  control (CON), 5 ppm 17β-estradiol (E2), 50 ppm tamoxifen (TAM), 5 ppm E2 + 50 ppm TAM (E2+TAM), 2 ppm diethylstilbestrol (DES), 500 ppm dehydroepiandrosterone (DHEA), 5 ppm dihydrotestosterone (DHT) and 5 ppm cortisol (CORT). Test chemicals were purchased from Sigma-Aldrich (St. Louis, MO) and were added directly to the oil portion of the OTD. Experimental treatments were administered for 14 days, and feeding occurred five days per week. Total hepatic RNA was extracted in TRIzol reagent according to supplier’s instructions. Equal amounts of RNA from each individual liver sample were sub-pooled according to tank (four males pooled per tank) resulting in three biological replicates for each treatment. A reference RNA pool was made by combining equal amounts of RNA from all individual male CON liver samples (12 liver samples total). For detection of gene expression on the OSUrbt array, the Genisphere 3DNA Array 350 kit (Hatfield, PA) was used in a dye-swap, reference sample design following the supplier’s protocol. During reverse transcription (SuperScript II, Invitrogen) of total RNA (7 μg) using the supplied Genisphere oligo d(T) primers, each biological sample was tagged separately with a capture sequence for one of two fluorescent dendromer reagents, Cy3 or Cy5. Each reverse transcription reaction also included spiked in mRNA corresponding to the SpotReport Alien Oligo controls. Corresponding reference RNA was reverse transcribed with the capture sequence for the opposite reagent (Cy3 or Cy5). To account for any differences in dye labeling efficiency, technical replicates were performed for two of the three biological replicates in which the capture sequence tags were swapped between the sample and reference. Thus, five arrays per experimental treatment were processed, including the CON treatment.

first: David

last: Williams


title: BCL6 ChIP on chip using a Nimblegen custom tiling array

city: Bronx

first: Ari

last: Melnick

state: NY

address: 1300 Morris Park Ave - Chanin 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

summary:
To determine whether BCL6 binds to the certain locus we performed genomic localization studies by chromatin immunoprecipitations (ChIP) using a densely tiled custom oligonucleotide microarray covering the genomic loci of different genes.
Keywords: ChIP-chip, Transcription Factor localization

overall_design: The experiment was performed in Ramos cell. Triplicate ChIP with BCL6 or actin (negative control) antibodies were cohybridized to the arrays versus the respective input chromatin.The fold enrichment for each oligonucleotide was calculated as the ratio of Cy5 vs. Cy3. Any peaks involving >5 oligonucleotides and with > 2.5 fold enrichment were considered potentially positive hits.

middle: M

first: Stella

last: Ranuncolo

first: Jose

last: Polo

first: John

last: Greally

first: Roland

last: Green

first: Martin

last: Carrol


title: Added effects of acute heat-stress on the clinical signs associated with fescue toxicosis

city: Columbia

first: Raja

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

summary:
Intake of ergot alkaloids associated with endophyte-infected fescue (E+) has adverse effects on animal health and productivity, which is collectively, termed fescue toxicosis. These effects are exacerbated under hot and humid (summer) conditions. A rat model for this condition was used to evaluate the effect of endophytic toxins on hepatic gene expression under acute (three days) heat stress (HS). Core temperature (Tc) was monitored continuously in rats (n=12) implanted with telemetric transmitters. Rats were fed ad libitum an E+ diet and maintained under thermoneutral (TN) conditions (21 ˚C) for five days, followed by TN or HS conditions (31 ˚C) for three days. Feed intake (FI) and body weight (BW) were measured daily. Both E+ and HS induced alterations in hepatic genes were evaluated using DNA microarrays. Intake of E+ reduced FI and BW under TN and HS conditions from pretreatment level, with greater reduction occurring during HS period. Core temperature at TN did not change from pretreatment level, but increased during HS. Genes associated with ATP synthesis, immune function, chaperone activity, and antioxidant function were reduced in E+HS vs E+TN. Present findings suggest that rats respond to E+ during heat stress by inducing hepatic CYP3A4 expression and suppressing chaperone, antioxidant and immune systems, which could ultimately increase the stress resulting in various pathological abnormalities.
Keywords: Stress response

overall_design:
The experimental schedule consisted initially of an 8 day recovery period after i.p. implantation of telemetric temperature transmitters (Model VM-FH; Mini-Mitter Company, Inc., Bend, OR). This was followed by a 5 day pretreatment period, during which Tc, FI and BW were collected to establish a baseline for statistical analysis (Spiers et al., 2005). During recovery and pretreatment periods, rats were fed the E- diet, whereas during the 8 day treatment period, the rats were fed the E+ (91.5 µg of EV.kg of BW-1.day-1) diet. At the end of 5 days of treatment, rats were divided into two groups, one maintained under continuous HS (31 °C) and the other continuing at TN for three additional days. During treatment Tc was collected at 10 minute intervals, with daily measurement of FI and BW at 0800 hour. At the end of the study, rats were anesthetized by i.m. injection of a xylazine (13 mg/mL)-ketamine (87 mg/mL) cocktail (0.1 mL/100g) and exsanguinated, and liver was collected and weighed. A transverse section from the middle lobe of liver (~5 g) was fixed in 10% neutral buffered formalin for immunohistochemistry (IHC) and terminal dUTP nick-end labeling (TUNEL), and another portion (~5 g) was snap-frozen in liquid nitrogen for microarray, real time-PCR, and antioxidant enzyme activity analysis.

The data, as submitted, was entered into JMAANOVA. In JMAANOVA, intensity based LOWESS normalization was performed on the data. The analysis was performed, using array as random effect and dye and treatment as fixed effect and ANOVA was performed using 500 permutations. Step Up FDR was used for the analysis.

first: RAJA

last: SETTIVARI

first: LAKSHMI

last: YARRU

first: ERIC

last: ANTONIOU

first: DONALD

last: SPIERS


title: Bj_Bacteroid

city: Arlington

first: Woo-Suk

last: Chang

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

summary:
Transcriptional profiling of bacteroids isolated from the soybean root nodules.
Keywords: life style comparison

overall_design: Three independent biological materials were prepared for bacteroids and free-living cells. Total 6 arrays including dye swap were analyzed.

first: Gary

last: Stacey

last: Emerich

first: Michael

last: Sadowsky

first: Dong

last: Xu

first: Sooyoung

last: Jeong


title: Bj_Salt

summary:
Functional genomics of B. japonicum exposed to osmotic stress caused by 50 mM NaCl.
Keywords: stress response

overall_design: Three biological replicates were prepared. However, total 4 arrays were hybridized with the dye swap.

first: David

first: Eddie

last: Cytryn


title: A PhoP point mutation discriminates between the virulent H37Rv and avirulent H37Ra strains of Mycobacterium tuberculosis

status: Public on Jul 05 2007

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
To uncover mutations underlying the attentuation of H37Ra, we embarked on sequencing its genome using a novel massive parallel pyrosequencing technology.
Comparison with the virulent H37Rv parental strain revealed only few polymorphisms, one of which was located in the DNA binding domain of the transcriptional regulator PhoP.
Keywords: Expresion profiling

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycobacterium tuberculosis H37Ra

overall_design: To investigate the phenotypic consequences caused by the mutations in the H37Ra genome, we compared the mRNA expression profiles of H37Rv and H37Ra in a protracted time course study.

first: Jong

last: Lee

last: Krause

first: Joerg

last: Schreiber

first: Robert

last: Stein

first: Stefan

middle: H

last: Kaufmann


title: In vitro generation of human high-density-lipoprotein-resistant Trypanosoma brucei brucei

status: Public on Jul 04 2007

first: Andrew

last: McArthur

summary:
The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei.
Keywords: Trypanosoma, VSG, antigenic switching, HDL-resistance

overall_design: Bloodstream stages of the Lister strain 427 T. b. brucei  (MiTat 1.2),  expressing VSG221, were used  in these studies.  Cells were cultured in HMI-9 medium with the addition of heat inactivated fetal bovine serum (FBS) (10%) and Serum Plus (10%).  T. b. brucei 427-221 is an antigenically stable line and contains a single copy of the vsg221 gene within the 221 expression site (221ES). At a cell density of approximately 1,000,000 cells/ml, T. b. brucei 427-221 were exposed to various amounts of human HDLs for 24 h in a 6 well plate.  Surviving trypanosomes were counted using a hemocytometer then diluted into fresh HMI-9 medium and allowed to recover for 5-14 days.  Once the cells had grown to a density of approximately 1,000,000 cells/ml, they were once again incubated with human HDLs.  Each round of selection was performed with increasing concentrations of human HDLs and freezer stocks were prepared for each surviving population.  Over nine months we conducted eight rounds of human HDL selection, resulting in a population of T. b. brucei that survived incubation with 800 μl of human HDLs (160 lytic U).

middle: G

first: Sara

last: Faulkner

first: Monika

middle: W

last: Oli

first: Rudo

last: Kieft

first: Laura

last: Cotlin

first: Justin

last: Widener

first: April

last: Shiflett

last: Cipriano

first: Sarah

last: Pacocha

first: Shanda

last: Birkeland

first: Stephan

last: Hajduk


title: Transcriptome Analysis of Alkali Shock and Alkali Adaptation in Listeria monocytogenes 10403S

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary:
Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. This study compared the transcriptome patterns of alkali stressed and non alkali stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which this important pathogen adapts and/or grows during short or long-term alkali stress. Transcription profiles associated with alkali shock (AS) responses were obtained by DNA microarray analysis of mid-exponential cells suspended in pH 9 media for 15, 30 or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained by DNA microarray analysis of cells grown to mid-exponential phase in pH 9 media . Comparison of AS and AA transcription profiles with profiles from control (pH 7.0) cells identified over 2,000 genes that were differentially expressed under alkaline conditions. Rapid (15min) changes in expression included upregulation of genes encoding for multiple metabolic pathways, (including those associated with Na+/H+ antiporters), ABC transporters of functional compatible solutes such as carnitine, motility and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30min and more) responses to AS and adaptation during growth in alkaline conditions (AA), included modest changes in mRNA concentrations, and genes involved in proton export.
Keywords: Time course study of gene expression response to alkaline shock and adaptation

sample_organism:
Listeria monocytogenes
Listeria monocytogenes 10403S

overall_design:
Overnight cultures of L. monocytogenes 10403S were inoculated (1:100) into 20 ml of BHI (pH 7) in a 50 ml Erlenmeyer flask, and incubated at 30°C with shaking at 200 rpm. Growth was monitored by measuring OD600, using a Beckman DU-65 spectrophotometer.
Cells to be subjected to alkali shock (AS) were harvested by centrifugation (8,000g x10min at 4°C) from 20 ml of this culture when the optical density at 600 nm reached 0.4. Recovered cells were washed, and immediately resuspended in 20 ml pre-warmed (30°C) pH 9 MBHI (test) or neutral MBHI (pH 7 control) for 15, 30 or 60 min.
Cells to be examined in terms of alkali adaptation (AA) were produced by inoculation of the overnight culture (1:100) into 20ml of MBHI adjusted at pH 9 (test) or pH 7 (control), and incubation at 30°C until they reached OD600 0.4.
In array analysis several controls were employed to minimise technical and biological variations, and ensure the quality of the data, i.e. i) each ORF was present in duplicate in each array, ii) each RNA preparation was used to make probes for at least two-separate arrays with reversal of incorporated dye and iii) three independent RNA batches from each condition were analysed. Only differences of ≥ 2 fold change in the levels of gene expression, which also had P values of 0.05, were recorded as significant.

first: Efstathios

last: Giotis

first: Arunachalam

last: Muthaiyan

first: Brian

last: Wilkinson

first: Ian

last: Blair

first: David

middle: A

last: McDowell


title: Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

status: Public on Jul 02 2007

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

institute: University of Calgary

summary:
The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe], a [NiFeSe] and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1 and hyn2 genes, respectively. In order to understand their cellular functions the expression levels of these hydrogenases, along with the growth rate analysis of mutant strains, was determined during growth on defined media under 3 different conditions. These conditions incuded lactate or hydrogen at either 5% or 50% (vol/vol) used as the sole electron donor for sulfate reduction.
Keywords: Electron donor change

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference. After total intensity normalization the SAM (significance analysis of microarrays) was used to find differentially expressed genes.

first: Hung-So

last: Park

first: Gerrit

last: Voordouw

first: Zhili

last: He

first: Jizhong

last: Zhou