title: Postia placenta MAD-698 gene expression in different media

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary:
Transscript profiles of Postia placenta grown on different substrates were analyszed. Array design was based on the DoE's Joint Genome Institute's gene models for P. placenta version 1. The research goal is to identtify genes essential for cellulose depolymerization.

Keywords: Culture condition comparison

overall_design:
From a data set of 12,438 unique alleles, each NimbleGen (Madison, WI) array featured 10 unique 60mers per gene, all in triplicate. The dataset was manually annotated to include only the ‘best allelic model’ among CAZY-encoding genes (SI Table 1, appended as a supplementary file).  Total RNA was purified from 6-day old cultures containing microcrystalline cellulose (Avicel) or glucose as sole carbon source. Three biological replicates per medium were used (6 separate arrays). RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the Postia placenta MAD-698 whole genome 37K expression array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.  One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C.  Array hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C.

Supplementary file 'si_figure_3.jpg' represents a Neighbor-Joining tree of the cytochrome P450 contingent (P450ome) of P. placenta. The tree shows 254 P450 proteins clustered into 11 fungal clans (indicated by different clan specific color at the branch point). The unrooted phylogenetic tree was constructed using MEGA4 phylogenetic analyses program with 1000 bootstrap replications.  Evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset.


title: Overexpression of GLI2 induces genomic instability

status: Public on Jan 06 2009

city: San Francisco

first: Antoine

last: Snijders

state: CA

address: 2340 Sutter Street

department: Cancer Research Institute

country: USA

institute: University of California San Francisco

type: Genome variation profiling by genome tiling array

summary:
We used genome-wide microarray comparative genomic hybridization to investigate the response of control HT1080 cells and HT1080 cells infected with a lentivirus expressing eGFP, GLI2-eGFP or CCND1-RFP to challenge with methotrexate to address the question if GLI2 overexpression induces genomic instability.
Keywords: aCGH

overall_design: Array CGH experiments of cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

first: Bing

last: Huey

first: Ritu

last: Roydasgupta

first: Richard

last: Jordan

first: Brian

last: Schmidt

first: Donna

last: Albertson


title: Gene expression analysis of in vitro cultured tomato plantlets

status: Public on Jan 07 2009

city: Québec

first: Jean-François

last: Dubuc

address: 2440 boul. Hochelaga

country: Canada

institute: Université Laval

summary:
Plants growth and development is highly dependent on the environment. During there lifespan, plants are submitted to changing environmental conditions that requires constant metabolic adjustments. In particular, in vitro cultured plantlets are exposed, throughout micropropagation, to unique growth conditions characterized by distinctive levels of nitrogen, exogenous sugar, light and atmospheric conditions. To resume growth upon transfer ex vitro, in vitro plantlets must acclimatize to natural conditions. In this study, the impact of the in vitro environment on the expression profile of tomato (Solanum Lycopersicum) plantlets was analysed using the microarray and real-time PCR methods. After 20 days of growth in vitro, a significant increase in expression of genes linked to photosynthesis, nitrogen metabolism and salicylic acid signaling pathways was observed. By opposition, the expression of transcripts associated to carbohydrate metabolism and jasmonic acid signaling pathway were reduced. Also, the expression of reactive oxygen scavenging (ROS) enzymes in the mitochondrias, chloroplasts and cytosol were altered in in vitro cultured tomato plantlets. More precisely, the in vitro environment led to increased photosynthetic gene expression, lower sink strength, up-regulation of nitrogen assimilation and induced a specific stress response in tomato plantlets. Our results suggest that the presence of exogenous sugar is an important environmental cue that governs the modified cell ROS pattern, defense-related genes modulation and abnormal physiology of in vitro plantlets.
Keywords: environmental challenge, growth condition comparison, expression profile

overall_design: Three biological replicates consisting of three individual plantlets grown in different vessels (in vitro) or pots (ex vitro) were used for the competitive hybridization. To reduce possible bias due to the difference in the properties of both dyes, two technical replicates consisting of dye swap were realized. The complete experiment required six microarrays.

first: Yves

last: Desjardins


title: Transcriptional profiling of wild-type, mglA point mutant, and fevR (FTT0383) knockout bacteria

city: Stanford

first: Anna

last: Brotcke

department: Microbiology and Immunology

institute: Stanford University

summary:
Time courses and RNA isolation.  Overnight cultures of F. novicida strain U112, GB2, and fevR ko (383) were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml.   Samples were taken throughout the growth curve for RNA isolation and to determine the OD600.   Five samples were taken during the growth curve at 1, 3, 5, and 7.5h and 10h for characterization of single mutants or at 2, 4, 6, and 8h in gro::fevR bypass experiments.  RNA was harvested and a common reference was created from each individual sample.  1ug of either the Sample, or Reference was reverse transcribed and labeled with either Cy5 (samples) or Cy3 (reference) and hybridized to a Francisella microarray previously described in Brotcke, Weiss, et al, Infection and Immunity, 2006.
Groups of assays that are related as part of a time series.
Age: Red channel represents 1ug of RNA from an individual timepoint
Starting OD: Wt, GB2, and FTT0383 (fevR) ko were subbed to an OD of 0.01 in TSB + 0.2% cysteine in 200ml.

Keywords: time_series_design

overall_design: Computed


title: Transcript profiling of Actinobacillus pleuropneumoniae in BALF

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

summary: Actinobacillus pleuropneumoniae is the etiologic agent of contagious pleuropneumonia, an economically important disease of commercially reared swine throughout the world.  To cause this disease, A. pleuropneumoniae must rapidly overcome porcine pulmonary innate immune defenses.  Since bronchoalveolar fluid (BALF) contains many of the innate immune components found in the lung, we examined the gene expression of a virulent serovar 1 strain of A. pleuropneumoniae after exposure to concentrated BALF.  This experiment was also carried out with a malT mutant of the same strain.

platform_organism: Actinobacillus pleuropneumoniae serovar 5b str. L20

overall_design:
Labelled cDNA synthetised from tester condition (namely wt BALF, mutant BHI and mutant BALF) was co-hybridized on the microarray with labelled cDNA from the control condition (wt BHI).  Control was labelled with Cy3.

At least four hybridizations were conducted for each sample combination type. Microarray analysis was carried out using the TM4 Suite of softwares (TIGR) and the SAM algorithm, using a false discovery rate (FDR) value of 0%. For the planktonic and adhesion experiments, Cy5 signal (test) was compared to Cy3 signal (control) in order to obtain a list of significant differentially expressed genes. In order to obtain the list of differentially expressed genes between planktonic growth and adhesion, log2 ratios were compared in TM4 also using the SAM algorithm.

first: Abdul

last: Lone

first: John

middle: H

last: Nash

first: Mario

last: Jacques

first: Janet

middle: I

last: MacInnes


title: Constitutive Expression of FevR (383) in wt, mglA mutant, and FevR mutant bacteria

summary:
Time courses and RNA isolation. Strains were created that constitutively express fevR (FTT0383) transcript by replacing the endogenous fevR promoter with that of groES, and this gro::fevR region was integrated into either the wild-type, mglA mutant (GB2), or fevR knockout.  Overnight cultures of F. novicida strains were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml.  Samples were taken throughout the growth curve for RNA isolation and to determine the OD600.  Four samples were taken during the growth curve at 2, 4, 6, and 8h for characterization of in gro::fevR bypass experiments.  RNA was harvested and a common reference was created by combining equal amounts of RNA from each sample in the experiment.  1ug of RNA from either the samples or common reference was reverse transcribed and samples were labeled with Cy5 (samples) or Cy3 (reference) and hybridized to the Francisella microarray described in Brotcke, Weiss, et al. Infection and Immunity, 2006.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

overall_design: all pairs


title: DNA methylation in B cells

status: Public on Jan 01 2009

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

summary: Using a methylated-DNA enrichment technique (MIRA) in combination with whole genome tiling arrays, we have characterized by MIRA-chip the entire B cell ‘methylome’ of an individual human at 100 base pair resolution.

overall_design: Methylated fragments in genomic DNA extracted from B cells were enriched with the MIRA assay and hybridized together with input genomic DNA to NimbleGen's whole genomc tiling array.

first: Tibor

last: Rauch

first: Xueyan

last: Zhong

first: Arthur

middle: D

last: Riggs

first: Gerd

middle: P

last: Pfeifer


title: Gene expression during germination in the Chytridiomycete Blastocladiella emersonii

status: Public on Jan 05 2009

city: Goiania

first: Silvia Maria

last: Salem-Izacc

state: Goias

address: ICB, Campus 2

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Goiás

summary: To investigate global changes in gene expression during B. emersonii germination process, we constructed cDNA microarrays containing 3,563 putative unique genes. Analyses were carried out during germination induced under various environmental conditions. Microarray data revealed that 26% of them are differentially expressed during germination in nutrient medium, in at least one of the time points investigated. Over 500 genes are up regulated during the time course of germination under these conditions, most of them being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are down regulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport and chromosome organization. We also compared germination induced in the presence of nutrients with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth that are induced during germination in nutrient medium do not show increased expression when B. emersonii zoospores germinate in inorganic solution, indicating that nutrients exert a positive regulatory effect on the transcription of these genes.

overall_design: Differentially expressed genes during germination were investigated in a time-course experiment, using RNA samples isolated from cells collected 30, 60 and 90 min after inoculation of zoospores in nutrient medium DM3. The reference sample was zoospore RNA, which was considered the time zero of germination. We also compared germination in nutrient medium with germination induced in inorganic salt solution, triggered either by adenine or potassium ions. In these experiments we considered germination in nutrient medium as the reference sample. There are at least 3 biological replicates (independent harvest) and 2 technical replicates for each array (L-left and R-right).

first: Silvia

middle: M

first: Tie

last: Koide

first: Ricardo

middle: Z

last: Vêncio

first: Suely

middle: L

last: Gomes


title: hepatocellular carcinoma vs. corresponding noncancerous liver or normal liver

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

summary:
Hepatocellular carcinoma (HCC) remains a major health problem worldwide, and HCC patients have a poor prognostic outcome. In this study, we systematically disclose mechanisms of hepatocarcinogenesis, and also effectively identify and validate novel anticancer targets in HCCs.
Keywords: disease state analysis

overall_design: total 58 cDNA microarrays, all experiment samples are hepatocellular carcinoma. RNAs from  33 corresponding noncancerous livers and 5 normal livers were used as the reference, respectively. The tumor samples were labeled with Cy5-dUTP.The nontumor samples were labeled with Cy3-dUTP.


title: Gene expression signatures for 17α-ethinylestradiol and ZM 189,154, singly and combined, in fathead minnow testis

status: Public on Jan 03 2009

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Aquatic organisms are continuously exposed to complex mixtures of chemicals, many of which can interfere with their endocrine system, resulting in impaired reproduction, development or survival, among others. In order to analyze the effects and mechanisms of action of estrogen/anti-estrogen mixtures, we exposed male fathead minnows (Pimephales promelas) for 48 hours via the water to 2, 5, 10, and 50 ng 17α- ethinylestradiol (EE2)/L, 100 ng ZM 189,154/L (a potent antiestrogen known to block activity of all estrogen receptors) or mixtures of 5 or 50 ng EE2/L with 100 ng ZM 189,154/L. We analyzed gene expression changes in the gonad, as well as hormone and vitellogenin plasma levels. Steroidogenesis was down-regulated by EE2 as reflected by the reduced plasma levels of testosterone in the exposed fish and down-regulation of genes in the steroidogenic pathway. Microarray analysis of testis of fathead minnows treated with 5 ng EE2/L or with the mixture of 5 ng EE2/L and 100 ng ZM 189,154/L indicated that some of the genes whose expression was changed by EE2 were blocked by ZM 189,154, while others were either not blocked or enhanced by the mixture, generating two distinct expression patterns. Gene ontology and pathway analysis programs were used to determine categories of genes for each expression pattern.  Our results suggest that response to estrogens occurs via multiple mechanisms, including canonical binding to soluble estrogen receptors, membrane estrogen receptors, and other mechanisms that are not blocked by pure antiestrogens.

overall_design: Fathead minnows exposed to 5, 10, or 50 ng/L ethinylestradiol, 100 ng/L ZM189,154, or a mixture of 5 or 50 ng/L ethinylestradiol and 100 ng/L ZM189,154. There are four replicates per treatment. We used a reference design.

middle: G

last: Reyero Vinas

first: Kevin

middle: J

last: Kroll

first: Li

last: Liu

first: Edward

last: Orlando

first: Karen

last: Watanabe

first: Maria

middle: S

last: Sepulveda

first: Daniel

last: Villeneuve

last: Perkins

first: Gerald

middle: T

last: Ankley

first: Nancy

last: Denslow


title: Depletion of the Cullin Cdc53p Induces Morphogenetic Changes in Candida albicans

city: Montreal

first: Katharina

last: Trunk

address: 2950 chemin Polytechnique

institute: IRIC-Université de Montréal

summary:
Transcriptional profiling of CDC53 down-regulated Candida albicans cells compared to control cells

Keywords: comparative genomic hybridization, genetic modification

Candida albicans is an important opportunistic human fungal pathogen, which can cause mucosal as well as systemic infections in immunocompromised patients.  Critical for the virulence of C. albicans is its ability to undergo a morphological transition from yeast to hyphal growth mode.  Proper induction of filamentation is dependent on the ubiquitination pathway, which targets proteins for proteasome-mediated protein degradation or activates them for signaling events.  In the present study, we evaluated the role of ubiquitination in C. albicans by impairing the function of the major ubiquitin-ligase complex SCF.  This was done by depleting its backbone, the cullin Cdc53p (orf19.1674), using a tetracycline down-regulatable promoter system.  Cdc53p-depleted cells displayed an invasive phenotype and constitutive filamentation under conditions favouring yeast growth mode, both on solid and in liquid media.  In addition, these cells exhibited an early onset of cell death, as judged from propidium iodide staining, suggesting that CDC53 is an essential gene in C. albicans.  To identify Cdc53p-dependent pathways in C. albicans, a genome-wide expression analysis was carried out that revealed a total of 425 differentially expressed genes (fold change ≥ 2, p-value ≤ 0.05) with 192 up- and 233 down-regulated genes in the CDC53-repressed mutant as compared to the control strain.  GO term analysis identified biological processes significantly affected by Cdc53p depletion, including amino acid starvation response, with 14 genes being targets of the transcriptional regulator Gcn4p, and reductive iron transport.  These results indicate that Cdc53p enables C. albicans to adequately respond to environmental signals.

overall_design: Two-strain experiment, CDC53-repressible cells vs. control cells, both grown in the presence of 20 µg/ml Doxycycline. Four independent biological replicates of total RNA of each strain, dye-swap.

first: Patrick

last: Gendron

first: Andre

last: Nantel

first: Sebastien

last: Lemieux

first: Terry

last: Roemer

first: Martine

last: Raymond


title: Gene expression in cotton stems and roots accumulating starch

status: Public on Jan 04 2009

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS

summary:
Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production.
Keywords: starch accumulating, stem, root

overall_design: Genes expression was compared between cotton stems that were low in starch and accumulating starch. Gene expression was also compared between cotton roots that were low in starch and accumulating starch. A total of three microarrays were used. One dye swap was used. Material from the field were harvested 2 weeks apart. Greenhouse grown material were planted at two week intervals and harvested at the same time. NOTE that the channel representing the low starch material only gave about half of the total signal than the high starch samples. QPCR of 9 genes confirmed differential expression of 8 of them. QPCR also confirmed similar expression of two genes not predicted to be differentially expressed by the microarray analysis. Therefore no correction was made for the apparent difference in the hybridization of high and low starch samples.

middle: W


title: Prostate miRNA expression profiles

status: Public on Jan 11 2009

city: Research Triangle Park

first: Michael

middle: D.

last: Mattie

address: Five Moore Drive

department: Genomics Research

institute: GlaxoSmithKline

summary:
Comparison of miRNA expression profiles in normal and malignant prostate tissues.
Keywords: microarray analysis of microRNA expression profiles

overall_design: MicroRNA expression was compared between normal prostate tissue from either young subjects that died of trauma, or normal adjacent to tumor, and prostatic tumors in older prostate cancer patients.  RNA was isolated from frozen tissue sections, enriched for the miRNA fraction, which was subsequently labeled and hybridized to miRNA microarrays for expression profiling analysis.

first: Christopher

last: Haqq

first: Jeff

last: Simko

first: Charlotte

last: Dai

first: Peter

last: Carroll

last: Chew


title: Pearl millet seedlings infected with rust (Puccinia substriata)

city: Pretoria

first: Bridget

middle: Genevieve

last: Crampton

address: PO Box 395

country: South Africa

institute: CSIR Biosciences

summary:
Transcriptional profiling of rust-infected pearl millet seedlings over time [0h, 20h, 5d and 8d post infection (pi)].

Keywords: Time course, Stress response

overall_design: Loop design.  All time points compared with time = 0 h in data analysis.  Two biological replicates per sample, and one technical dye swap replicate.

first: Ingo

last: Hein

first: Dave

middle: K

last: Berger


title: Pearl millet seedlings treated with salicylic acid (SA)

summary:
Transcriptional profiling of SA-treated pearl millet seedlings over time [0, 12, 24 and 48 hours post treatment (hpt)].

Keywords: Time course, Stress response


title: Treatment of human monocyte-derived dendritic cells with Saccaromyces cerevisiae in exponential growth phase

city: Firenze

first: Luca

last: Beltrame

address: Viale Pieraccini 6

department: Department of Pharmacology

country: Italy

institute: University of Firenze

summary:
In vitro experiment of stimulation of monocyte-derived dendritic cells with Saccaromyces cerevisiae in exponential growth phase. This experiment was performed to verify the comparability of microarray
experiments using a pathway based logic (Beltrame et al., PLoS 2009) by comparing the analysis of this sample with other seven public data  sets on monocyte-derived dendritic cells subjected to different stimuli retrieved from GEO

Keywords: Case-control, transcriptional profiling, dendritic cells

overall_design: A case-control experiment consisting of 3 case samples (stimulated dendritic cells) compared to 3 paired (from the same donor) samples

first: Lisa

last: Rizzetto

first: Raffaele

last: Paola

first: Philippe

last: Rocca-Serra

last: Gambineri

first: Cristina

last: Battaglia

first: Duccio

last: Cavalieri


title: Dictyostelium discoideum amoeba stage library

city: Pocatello

first: Maureen

last: Brandon

state: ID

address: Mail Stop 8007

department: Biological Sciences

institute: Idaho State University

summary: We identified 3418 genes transcribed at a level of at least two copies each. We identified many transcripts involved in protein translation, cell maintenance and metabolism, as expected for vegetative cells. The most highly expressed cell signaling genes include ubiquitin, smlA, and nucleotide exchange factors RasGEF F and Ras GEF G. Additionally, we identified many genes previously reported to be expressed only during later stages of development including dutA, actin8, thioredoxin3, culmination specific protein 45D, discoidin II and yelA.

overall_design: We isolated total RNA from Dictyostelium amoeba growing in HL5 media with shaking and at a density of 2.4 X 10(7) cells/ml using Ambion RNAqueous isolation kit. We prepared the SAGE library using an Invitrogen kit and being careful to reduce the amount of ditags in the concatemer ligation reaction to 25% of the manufacturer's suggested mass. Concatemers were sequenced at the Molecular Research Core Facility on the campus of Idaho State University using an Applied Biosystems 3100 Genetic Analyzer. We identified SAGE tags by comparison to the Dictyostelium genome sequence available on the dictybase website.

first: Tiffany

last: Whitney

first: Melissa

last: Mott

first: Douglas

last: Gardner

middle: A


title: Enriched genes in the primary mouth of Xenopus laevis

city: Cambridge

first: Amanda

middle: Jane Graham

last: Dickinson

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Identification of genes enriched in the presumptive primary mouth.  Dissected tissues from the primary mouth anlage and two other anterior regions for comparison, the anterior dorsal and ventral plus cement gland.

overall_design: tissues were dissected and pooled from 75-100 embryos and total RNA extracted.

first: Hazel

last: Sive


title: Regulator trafficking on bacterial transcription units in vivo

first: Rachel

middle: Anne

last: Mooney

address: 1550 Linden Drive

department: Biochemistry

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: The in vivo trafficking patterns on DNA by the bacterial regulators of transcript elongation Sigma70, Rho, NusA, and NusG and the explanation for high promoter-proximal levels or peaks of RNA polymerase (RNAP) are unknown.  Genome-wide ChIP-chip on E. coli revealed distinct association patterns of regulators as RNAP transcribes away from promoters (Rho first, then NusA, and then NusG). However, the interactions of elongating complexes with these regulators, including a weak interaction with Sigma70, did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from Sigma70 peaks in the direction of transcription and co-occurred with NusA and Rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes.  However, inhibition of Rho did not increase RNAP levels within genes downstream of the RNAP peaks, suggesting the peaks are caused by a mechanism other than simple Rho-dependent attenuation.

overall_design: Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta' subunit), Sigma70, NusA, NusG, or Rho.  Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~24bp spacing across the entire genome.  The series contains 17 total datasets.

first: Sarah

middle: E

last: Davis

first: Jason

last: Peters

first: Jennifer

last: Rowland

first: Aseem

last: Ansari

first: Robert

middle: C

last: Landick


title: 17b-Trenbolone study

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary: We investigated the genomic transcriptional response of female fathead minnows (Pimephales promelas) to an acute (4 day) exposure to 0.1 or 1.0 µg/L of, 17β-trenbolone (TB), the active metabolite of an anabolic androgenic steroid used as a growth promoter in cattle and a contaminant of concern in aquatic systems. Our objectives were to investigate the gene expression profile induced by TB, define biomarkers of exposure to TB, and increase our understanding of the mechanisms of adverse effects of TB on fish reproduction. In female gonad tissue, microarray analysis using a 22K oligonucleotide microarray (EcoArray Inc., Gainesville, FL) showed 99 significantly upregulated genes and 741 significantly downregulated genes in response to 1 µg TB/L. In particular, hydroxysteroid (17β) dehydrogenase 12a (hsd17b12a), zona pellucida glycoprotein 2.2 (zp2.2), and protein inhibitor of activated STAT, 2 (pias2) were all downregulated in gonad.

overall_design: 4 control samples compared to 4 exposed samples, ovary.

last: Dorts

first: Catherine

last: Richter

last: Wright-Osment

first: Mark

middle: R

last: Ellersieck

first: Donald

last: Tillitt


title: Nitrate and starvation dependent transcription in Aspergillus nidulans

city: Vienna

first: Harald

last: Berger

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Applied Life Sciences, Vienna

summary:
Nitrogen metabolism in Aspergillus nidulans is subject to regulation by the GATA transcription factor AreA which is required for the utilization of a wide range of nitrogen sources other than glutamine or ammonium. The level of AreA activity is regulated by intracellular glutamine levels that vary in response to nitrogen supplementation. For nitrate assimilation, which involves two transporters (CrnA, CrnB), nitrate reductase (NiaD) and nitrite reductase (NiiA), the respective genes are subject to regulation at the level of transcription, including nitrogen metabolite repression mediated by AreA and induction mediated by nitrite or nitrate, mediated by a second transcription factor, NirA. Both transcription factors act synergistically to regulate the expression of all four structural genes when nitrogen is limiting or either nitrate or nitrite is available. In this study we dissect the nitrogen limitation effect mediated by AreA form the nitrate/nitrite specific effect mediated by NirA on the transcriptome level.
Keywords: Nitrate/nitrogen limitation response

overall_design: Wild type pabaA1 (WT) strain and nirA637 pabaA1 (nirA loss of function (nirA637)) strains were used in this study. First, WT repressed (ammonium) was compared to WT induced (nitrate) obtaining all genes that are differently transcribed by either nitrogen limitation and/or nitrate induction. Seven biological repetitions were analyzed on seven microarray slides, including 3 dye swaps. Second, WT repressed was compared to WT starved (no nitrogen source available) to obtain genes that are regulated by AreA mediated nitrogen limitation. Four biological repetitions were analyzed on four slides including two dye swaps. Third, nirA637 repressed was compared to nirA637 induced also to obtain AreA dependent genes and genes that are nitrate but not AreA dependent. Four biological repetitions were analyzed on four slides including two dye swaps.

first: Joseph

last: Strauss


title: Defining Behavioral and Molecular Differences Between Summer and Migratory Monarch Butterflies

city: Worcester

first: Steven

last: Reppert

address: 364 Plantation St

department: Neurobiology

institute: University of Massachusetts Medical School

summary: In the fall, Eastern North American monarch butterflies (Danaus plexippus) undergo a magnificent long-range migration.  In contrast to spring and summer butterflies, fall migrants are juvenile hormone deficient, which leads to reproductive arrest and increased longevity.  Migrants also use a time-compensated sun compass to help them navigate in the south/southwesterly direction en route for Mexico.  Central issues in this area are defining the relationship between juvenile hormone status and oriented flight, critical features that differentiate summer monarchs from fall migrants, and identifying molecular correlates of behavioral state.  Here we show that increasing juvenile hormone activity to induce summer-like reproductive development in fall migrants does not alter directional flight behavior or its time-compensated orientation, as monitored in a flight simulator.  Reproductive summer butterflies, in contrast, uniformly fail to exhibit directional, oriented flight.  To define molecular correlates of behavioral state, we used microarray analysis of 9417 unique cDNA sequences.  Gene expression profiles reveal a suite of 40 genes whose differential expression in brain correlates with oriented flight behavior in individual migrants, independent of juvenile hormone activity, thereby separating molecularly fall migrants from summer butterflies.  Intriguing genes that are differentially regulated include the clock gene vrille and the locomotion-relevant tyramine beta hydroxylase gene.  In addition, several differentially regulated genes (37.5% of total) are not annotated, suggesting unique functions associated with oriented flight behavior.  We also identified 23 juvenile hormone-dependent genes in brain, which separate reproductive from non-reproductive monarchs; genes involved in longevity, fatty acid metabolism, and innate immunity are upregulated in non-reproductive (juvenile-hormone deficient) migrants.  The results link key behavioral traits with gene expression profiles in brain that differentiate migratory from summer butterflies and thus show that seasonal changes in genomic function help define the migratory state.

overall_design:
A total of 40 monarch butterflies were used for the microarray analysis.  Of the 40, 10 (5 male/5 female) were summer butterflies (Designated as S) and 30 were fall butterflies.  The fall butterflies were further divided into three groups: 10 (5 male/5 female) were untreated (F); 10 (5 male/5 female) were treated with methoprene (M), which is a juvenile hormone analog and induces the development of reproductive organs in migrant butterflies; and 10 (5 male/5 female) were treated with vehicle only (V).   We collected total brain RNA from each of the 40 butterflies.  The brain RNAs were amplified and then used to  probe a custom Nimblegen array that was designed to analyze the 9,417 unique cDNA sequences established in our published EST library (http://titan.biotec.uiuc.edu/cgi-bin/ESTWebsite/estima_start?seqSet=butterfly).
Our main interest is to find genes involved in migration.  This includes genes regulating oriented flight behavior of the butterfly and genes that regulate reproductive status.  To identify these genes, we approached the microarray data in two ways.
First, we identified the potential genes involved in oriented flight behavior using the following strategy.  We compared the summer group to each of the three fall groups (untreated, methoprene-treated, and vehicle-treated) for males and for females, and looked for gene regulation patterns common among the three comparisons for each sex.  Because the comparisons were done separately for males and females, and our behavioral data did not show significant sex differences in flight orientation, we focused on the common differentially regulated genes that were shared between males and females.  Accordingly, we identified 40 cDNAs that were differentially regulated between summer butterflies and fall migrants, irrespective of sex.
Second, we looked for the juvenile hormone-response genes.  Again, we performed sex-specific statistical analyses, and compared the summer and the fall groups, and the methoprene-treated and vehicle-treated migrants.  We then screened for shared genes between the two groups for each sex. We next examined cDNAs that were differentially regulated in both males and females, to determine juvenile hormone-regulated genes involved in more global processes (e.g., longevity and fatty acid metabolism) that would not be expected to be sex-specific.  We identified 23 putative juvenile hormone-response genes that were common between males and females.

first: Haisun

last: Zhu

last: Gegear

first: Amy

last: Casselnab

first: Sriramana

last: Kanginakudru

middle: M


title: CGH analysis of 39 Lactococcus lactis strains.

status: Public on Dec 31 2008

city: Nijmegen

first: Jumamurat

last: Bayjanov

address: Geert-Groteplein

country: Netherlands

institute: CMBI

summary:
Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data. Therefore, we have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis, cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.

Keywords: CGH, CGH analysis, orthology, Lactococcus lactis

sample_organism:
Lactococcus cremoris
Lactococcus lactis subsp. lactis
Lactococcus lactis subsp. hordniae

overall_design: We analyzed 39 CGH arrays, where on each array different strain of L. lactis was hybridized.

first: Douwe

last: Molenaar


title: Identification of the Escherichia coli HU regulon

city: ORSAY

first: Jacques

last: Oberto

address: Université Paris XI, Bâtiment 409, pièce 200

department: CNRS UMR 8621

country: France

institute: Instutit de Génétique et Microbiologie

summary:
The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase.

The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables.
Keywords: genotype, growth phase

overall_design: We used microarrays to investigate global bacterial gene expression in five genotypes of E. coli C600: WT (JO2057), hupA (JO2081), hupB (JO2083), hupAB (JO3020) and rpoS (MW30) at three growth growth phases: exponential, transition and stationary and in three growth media: LB, M9 minimal Glucose and M9 minimal Glycerol. The most relevant experiments were carried out in duplicate: the wild type (JO2057) and the hupAB (JO3020) strains were tested in the exponential and stationary phase, in LB. Wild type and hupAB strains were also tested in single experiments at the transition phase in LB. The single hupA (JO2081) and single hupB (JO2083) mutants were tested at the three growth phases in LB. Wild type and hupAB strains were compared in single experiments both in M9 Minimal Glucose and M9 Minimal Glycerol at the exponential and stationary phase. The last chips were used to test respectively the rpoS mutant at the at the exponential and stationary phase in LB.

first: Sabrina

last: Nabti

first: Valérie

last: Jooste

first: Hervé

last: Mignot

first: Josette

last: Rouviere-Yaniv


title: MicroRNA expression profiling in diabetic GK rat model

city: shanghai

first: huang

last: bing

state: shanghai

address: yueyang road 320

department: chemistry

institute: Chinese Academy of Sciences

summary: MicroRNAs (miRNAs), which are a newly identified class of small single-stranded non-coding RNAs, regulate their target genes via post-transcriptional pathway. It has been proved that miRNAs play important roles in many biological processes. To better understand miRNA function with type 2 diabetes, we have used an oligonucleotide microarray to monitor miRNA expression profiles of GK and Wistar rats’ muscle. We found 7 miRNAs were down-expressed and 2 were over-expressed in the muscle of GK rats. Among them, miR-24 showed the most prominent change. P38 MAPK, which is a direct target of miR-24 also showed expression difference. All the data give a clue that miR-24 might be associated with diabetes through down regulation of p38 MAPK.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study we used male GK rats, which were established by selectively breeding of normal Wistar rats with signs of impaired glucose tolerance, as type 2 diabetes model and male Wistar rats as control. Rats were housed in a temperature-controlled room and were given free access to water and standard laboratory chow during the 14 weeks. The blood glucose levels of the rats were measured each other day up to 4 times before being killed. We used microarray to monitor rat miRNA expression profile in the course of diabetic. For each sample, two independent small RNA libraries (biological replications) were generated and two independent reverse transcriptions/amplifications/hybridizations (technical replications) were performed for each library.

first: Botao

last: Zhao

first: Ruqiang

last: Liang

first: Kangcheng

last: Ruan

first: Youxin

last: Jin


title: Microarray-based Analysis of Polyamine Transport and Metabolism in the Model Marine Bacterium Silicibacter pomeroyi

city: Kent

first: Xiaozhen

last: Mou

state: OH

address: 41 cunningham Hall, P. O. box 5190

institute: Kent State University

summary: Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton.  The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.

overall_design: Silicibacter pomeroyi DSS-3 cells were grown in chemostat in a modified marine basal medium (MBM) containing spermidine as sole carbon and nitrogen source. Serine was used as a substrate to provide comparative data for an amino acid. After reach stable condition, total RNA were extracted, mRNA were purified and aa-aRNA were amplified and fluoresently labled before hybridize on array chips. The array design is described in Burgmann et al., 2007

first: Shulei

last: Sun

first: Mary

last: Moran


title: CLF Pulldown

city: Los Angeles

first: Steve

last: Jacobsen

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

summary:
CLF binding sites
Keywords: ChIP-chip

overall_design: CLF binding sites by ChIP-chip in a CLF-GFP line using an anti-GFP antibody

first: Steven


title: Gene expression profiling in the human pathogenic dermatophyte Trichophyton rubrum during growth on proteins

city: Lausanne

first: Michel

last: Monod

address: Av. de Beaumont 29

department: Dermatology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

summary:
Dermatophytes are highly specialized filamentous fungi which cause the majority of superficial mycoses in humans and animals. The high secreted proteolytic activity of these microorganisms during growth on proteins is assumed to be linked with their particular ability to exclusively infect keratinized host structures such as skin stratum corneum, hair and nails. Individual secreted dermatophyte proteases were recently described and linked with the in vitro digestion of keratin. However, the overall adaptation and transcriptional response of dermatophytes during protein degradation is largely unknown. To address this question, we constructed a cDNA microarray for the human pathogenic dermatophyte Trichophyton rubrum, which is based on transcripts of the fungus grown on proteins. Gene expression profiling during growth of T. rubrum on soy and keratin displayed the activation of a large set of genes encoding endo- and exoproteases. In addition, other specifically induced factors with potential implication in protein utilization were identified, including heat shock proteins, transporters, metabolic enzymes, transcription factors and hypothetical proteins with unknown function. This broad-scale transcriptional analysis of dermatophytes during growth on proteins reveals new putative pathogenicity related host adaptation mechanism of these human pathogenic fungi.

Keywords: Two-condition experiment, strong proteolytic activity in the supernatant versus no proteolytic activity

overall_design: Three independently prepared T. rubrum replicates grown in each of the three media, Sabouraud, soy and keratin-soy medium (designated SabA/B/C, soyA/B/C and keratin-soyA/B/C) were used.  Pairwise transcriptional comparisons, i.e. soy versus Sabouraud, keratin-soy versus Sabouraud and keratin-soy versus soy were done. The total number of slides in this study was 9.

first: Christophe

last: Zaugg

first: Johann

last: Weber

first: Keith

last: Harshman

first: Sylvain

last: Pradervand

first: Jerome

last: Thomas

first: Manuel

last: Bueno

first: Karin

last: Giddey

first: Peter

last: Staib


title: Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response_DataSet3

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

institute: University of British Columbia

summary: We investigated the transcriptional response of hybrid poplar (Populus trichocarpa x deltoides) leaves to a variety of stress treatments (insect feeding by Malacosoma disstria larvae, mechanical wounding, wounding plus the application of insect oral secretions, and methyl jasmonate spray) over a 24 hour time course. Experiments were conducted using clonal trees under greenhouse conditions at the University of British Columbia. We used the 15.5K poplar cDNA microarray platform previously described by Ralph et al. (Molecular Ecology 2006, 15:1275-1297). Differentially expressed genes were determined using three criteria: fold-change between treated and untreated control leaves > 1.5-fold, P value < 0.05 and Q value < 0.05. This study identified > 1,000 differentially expressed genes in response to insect feeding and/or treatments that mimic insect feeding damage.

overall_design: For each stress treatment, we compared RNA from leaves of four individual treated trees versus four individual control trees, with dye balance, using a total of 16 slides for the four treatments examined.  Based on an earlier study using pooled biological replicates (90 trees) to examine a large combination of 18 treatments and time points, we selected the peak response time point for each treatment for further investigation using individual tree replicates.  The time points and treatments examined were as follows: 24 hours for insect feeding, 6 hours for mechanical wounding, and 2 hours for both wouding plus oral secretions and methyl jasmonate.  In the original experiment, leaves were harvested 2, 6 or 24 hours after the initiation of each treatment.  For each tree, the lowest five mature leaves were caged in nylon mesh bags, treated or left untreated as a control.  As a control for methyl jasmonate treatments, we used a tween solvent.

middle: G

last: Ralph

first: Ryan

middle: N

last: Philippe


title: Transcriptional profiles of msg5 mutants and msg5 mutants in the presence/absence of alpha factor

city: Madrid

first: Maria

last: Molina

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia II Fcc Farmacia

country: Spain

institute: Universidad Complutense de Madrid

summary:
GSM306248: S. cerevisiae was grown on YEPD. Wild type and msg5 yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 4hours. After  4 hours of growth cells were collected, frozen at -80 °C and processed for RNA extraction.

GSM306249: msg5 yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 4hours. After 4 hours the culture was divided into two parts. One was treated with alpha factor and the other part was allow to grow without any treatment. After 90 minutes of treatment, both cultures of cells were collected, frozen at -80 °C and processed for RNA extraction.

overall_design:
GSM306248: Four microarrays were utilized to analyze each condition (coming from two different biological samples labeled using dye swapping strategy). Data processing involves condensing the results from the four microarrays.

GSM306249: Four microarrays were utilized to analyze each condition (coming from two different biological samples labeled using dye swapping strategy). Data processing involves condensing the results from the four microarrays.

middle: J

last: Marín

first: Marta

last: Flández

first: Clara

last: Bermejo

first: Javier

last: Arroyo

first: Humberto

last: Martín

first: María


title: Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response_DataSet2

summary: We investigated the transcriptional response of hybrid poplar (Populus trichocarpa x deltoides) leaves to methyl jasmonate treatment over a 24 hour time course.  Experiments were conducted using clonal trees under greenhouse conditions at the University of British Columbia.  We used the 15.5K poplar cDNA microarray platform previously described by Ralph et al. (Molecular Ecology 2006, 15:1275-1297).  Differentially expressed genes were determined using three criteria: fold-change between methyl jasmonate-treated and tween-treated control leaves > 1.5-fold, P value < 0.05 and Q value < 0.05.  This study identified > 1,000 differentially expressed genes in response to methyl jasmonate treatment.

overall_design: A factorial hybridization design was chosen to assess gene expression between tween-treated control leaves, and leaves subjected to methyl jasmonate treatment.  For each tree, all but the lowest five mature leaves were covered with a light-weight plastic bag and then sprayed with either methyl jasmonate or tween, the solvent control.  Leaves were harvested 2, 6 or 24 hours after the initiation of each treatment and total RNA was individually isolated from each tree.  For each treatment and time point, equal amounts of total RNA were combined from each of the five biological replicate trees prior to cDNA microarray analysis.  A total of 18 hybridizations were performed to directly compare total RNA from methyl jasmonate-treated and tween-treated control leaves at each time point, as well as among methyl jasmonate-treated leaves across time points, with dye balance.

first: Steven


title: microRNA expression profiling in neural stem cells differentiated from mouse embryonic carcinoma P19 cells

first: huang

last: bing

summary:
microRNAs (or miRNAs) are small noncoding RNAs (21 to 25 nucleotides) that are processed from longer hairpin RNA precursors and are believed to be involved in a wide range of developmental and cellular processes, by either repressing translation or triggering mRNA degradation (RNA interference). Expression analysis of miRNAs is necessary to understand their complex role in the regulation of gene expression during the development, differentiation and proliferation of cells. Here we report on the expression profile analysis of miRNAs in mouse P19 embryonic carcinoma (EC) cell，which were used to get efficient derivation of a high percentage (∼95%) of neural stem cells from in N2B27 serum-free medium, in vitro simulated the process in vivo neural induction.The data presented here indicate marked changes in the expression of miRNAs between the P19 EC cell and the neural stem cells derived from them. Among ~160 mouse miRNAs, 37 miRNAs are increased (2.0-fold up-regulated) and 41 miRNAs are decreased (2.0-fold down-regulated) in their expression level after the differentiation. MiR-124a is dramatically up-regulated (above 20-fold). However, miR-302 cluster and miR290-295 cluster are down-regulated strongly. Further analyses show that some important factors, such as Oct4 and Sox2, are involved in the regulation system of these miRNAs. In brief, our results might contribute to a greater understanding of the many biological events in neural induction of early mouse embryos regulated by miRNAs.
Keywords: microRNA, mouse, neural differentiation

overall_design: we employed a method established by Xia et al. to get a high percentage (~95%) of efficient derivation of neural stem cells from P19 EC cell in N2B27 serum-free medium by in vitro simulating the process of in vivo neural induction.We used microarray to monitor mouse miRNA expression profile in the course of their neuronal differentiation.For each sample, two independent small RNA libraries (biological replications) were generated and two independent reverse transcriptions/amplifications/hybridizations (technical replications) were performed for each library. undifferentitated P19 replicate three times while differentitated P19 replicate twice.

first: Zhao

last: botao

first: Liang

last: ruqiang

first: Ruan

last: kangcheng

first: Jin

last: youxin


title: Pearl millet seedlings treated with methyl jasmonate (MeJA)

first: Bridget

last: Crampton

summary:
Transcriptional profiling of MeJA-treated pearl millet seedlings over time [0, 12, 24 and 48 hours post treatment (hpt)].

Keywords: Time course, Stress response

overall_design: Loop design.  All time points compared with time = 0 h in data analysis.  Two biological replicates per sample, and one technical dye swap replicate.

first: Ingo

last: Hein

first: Dave

last: Berger


title: Differential expression in lung and lymph node of pigs with high and low responses to infection with PRRSV

city: Lincoln

first: Rodger

last: Johnson

state: NE

address: University of Nebraska East Campus Loop Animal Science Bldg. A218i

department: Animal Science

institute: University of Nebraska

summary: One hundred Hampshire by Duroc crossbred pigs (HD) and 100 NE Index line pigs (I) were infected with porcine reproductive and respiratory syndrome virus (PRRSV) and evaluated for resistance/susceptibility. Controls (100/line) were uninfected littermates to infected pigs. Viremia (V), weight change (WTΔ), and rectal temperature at 0, 4, 7, and 14 days post-infection (dpi) were recorded. Lung, bronchial lymph node (BLN), and blood tissue were collected at necropsy (14 dpi).  Infected pigs were classified as low or high responders to PRRSV based on the first principal component (PC) from principal component analyses of all variables. Low responders to PRRSV (low PRRSV burden) and their uninfected littermates were assigned to low (L) class.  High responders to PRRSV (high PRRSV burden) and their uninfected littermates were assigned to high (H) class.  Infected pigs in the L-class had high WTΔ, low V, and few lung lesions; H-class pigs had low WTΔ, high V, and many lung lesions. RNA was extracted from lung and BLN tissue of the seven highest and seven lowest responders per line and from each of their control littermates. A control reference design was used and cDNA from each reference sample tissue was prepared from pooled RNA extracted from two control pigs from each line whose infected littermates had a PC value of 0. Design variables in data analyses were line (I vs HD), class (H vs L), treatment (infected vs uninfected controls), and slide/pig as error.

overall_design:
A gene expression study was conducted with 56 pigs from a PRRSV-infection experiment involving a total of 400 pigs. Two hundred pigs from the NE Index line (I), selected 20 generations for increased litter size, and 200 pigs from a commercial Hampshire x Duroc (HD) cross selected for lean growth, were used. Two pigs of the same sex from each available litter, representing 83 sires and 163 dams, were selected at random for the experiment. A total of 200 pigs were infected with PRRSV and 200 uninfected littermates served as controls. The experiment was conducted in two replicates within each of two seasons with 50 pigs per breed in each year/season/replicate.

Pigs were housed in two isolation rooms at the University of Nebraska Animal Research Facility of the Veterinary and Biomedical Sciences Department. Each room contained two pens of 12-13 pigs per pen, with Line I pigs in one pen and Line HD pigs in the other pen.  One room was randomly assigned for treatment and pigs in it were inoculated intranasally with 105 CCID50 of PRRSV strain 97-7985.  Application rate was 1cc per nostril.  Littermates, serving as controls to the infected pigs, were placed in the second room.

Phenotypic data included viremia (V) from serum samples collected at 4, 7, and 14 days post-infection (dpi), changes in weight (WTΔ) and rectal temperature from 0 to 4, 4 to 7, and 7 to 14 dpi, lung and bronchial lymph node viremia from tissue collected at necropsy at day 14, and severity of lung lesions. Blood serum at day 0 before infection was collected and stored.  Samples were collected at 4, 7, and 14 dpi to monitor changes during and shortly after the acute phase of viral infection.

Uninfected HD pigs gained more and had higher rectal temperature from 0 to 14 dpi than uninfected I pigs, whereas infected I pigs gained more and had lower temperature than infected HD pigs. Viremia (CCID50/mL, cell culture infectious dose 50%/mL) was also greater in HD than I pigs at 4, 7, and 14 dpi. Genetic line differences in lung and lymph viremia levels were not significant, but tended to be greater in HD than I pigs. Based on these results, the current microarray experiment was designed to determine whether expression of genes differed between pigs in the tails of the PRRSV response distribution.

Phenotypic data for infected pigs were subjected to principal component (PC) multivariate procedures to identify 28 pigs, seven pigs within each line in the outermost tails of the distributions of viral response variables. The first PC eigenvector, which accounted for 27% of the variation, was used to rank pigs. The 28 control littermates to each of these pigs were also selected, resulting in 56 pigs used in the gene expression experiment. Infected pigs in the right tail of the PC distribution were considered to be susceptible to PRRSV. Those pigs and their control littermates formed the H class (high PRRSV burden). Pigs in the left tail were considered to be tolerant or resistant. They and their control littermates formed the L class (low PRRSV burden).

A 2x2x2 factorial treatment design was utilized for the gene expression experiment. Design effects included class (H and L), line (I and HD), and treatment (infected and uninfected), with seven pigs in each of the eight categories.

first: Jared

middle: S

last: Bates

first: Derek

middle: B

last: Petry

first: James

last: Eudy

first: Lisa

last: Bough


title: Calorie Restriction Feminizes Liver Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways

first: preston

middle: w

last: estep

address: PO Box 53

institute: Longenity Inc.

summary:
Background: Calorie restriction (CR) is the only intervention known to extend lifespan in a wide range of organisms, including mammals. However, the mechanisms by which it regulates mammalian aging remain largely unknown and the involvement of the TOR and Sirtuin pathways (which regulate aging in lower organisms) remain controversial. Femaleness is a second phenotype generally associated with longevity but the relationship between sex-biased and CR-induced gene expression remains undetermined.    Methodology/Principal Findings: We generated microarray gene expression data from livers of male mice fed high calorie or CR diets, and we find that CR significantly changes the expression of over 3,000 genes, many between 10- and 50-fold. We compare our data to the GenAge database of known aging-related genes and to prior microarray expression data of genes expressed differently between male and female mice. CR generally feminizes gene expression and many of the most significantly changed individual genes are involved in aging, hormone signaling, and p53-associated regulation of the cell cycle and apoptosis. Among the genes showing the largest and most statistically significant CR-induced expression differences are Ddit4, a key regulator of the TOR pathway, and Nnmt, a regulator of lifespan linked to the Sirtuin pathway. Using Western analyses, we confirmed post-translational inhibition of the TOR pathway.    Conclusions: Our data show that CR induces widespread gene expression changes and acts through highly evolutionarily conserved pathways, from microorganisms to mammals, and that its life-extension effects might arise partly from a shift toward a gene expression profile more typical of the longer-lived female sex.
Keywords: Two-class gene expression comparison. Calorie restriction (CR) versus HIGH CALORIE feeding.

overall_design: Design of the experiment is a two-class paired design in which the two classes are HIGH CALORIE and CALORIE RESTRICTION (CR) dietary regimens fed to mice, resulting in 15 HIGH CALORIE microarrays and 8 CR microarrays; 23 total microarrays. Four HIGH CALORIE and 2 CR microarrays were produced using pools of 3 RNA samples for each microarray (6 pools of 3, plus 17 individual samples = 35 individual mouse liver samples, 23 microarrays). Total liver RNA was labeled directly. Reference RNA: Stratagene Universal Mouse Reference RNA.

first: Preston

middle: W

last: Estep III

first: Jason

last: Warner

first: Martha

middle: L

last: Bulyk


title: MicroRNAs expression profile in human hepatocellular carcinoma

city: Shanghai

first: JIANREN

last: GU

address: No.25/Ln.2200, Xietu Road,

department: State Key Laboratory of Oncogenes and Related Genes

institute: Shanghai Cancer Institute, Shanghai Jiao Tong University

summary:
Liver cancer tissue could be indentified from corresponding non-cancerous tissues and normal liver tissue with a microRNA expression profile including 69 microRNAs.Besides, one single microRNA could be used to predict the outcome of liver cancer patients.
Keywords: molecular marker, predict prognosis

overall_design: In this study, the microRNAs expression profile in liver cancer tissue  and corresponding non-cancerous tissues of 78 HCC cases followed up for up to 68 month, and in 10 normal liver tissue were analyzed by using microarray probed with 509 miRNAs. The analysis suggested one profile including 69 microRNAs expressed differentially between liver cancer tissues and noncacerous tissue, and some of micRNAs related to clinical factor, especially one single could be used to predict the prognosis of liver cancer patients.

first: Wenxi

last: Li

first: Jianren

last: Gu


title: Microarray analysis of gene expression in acaricide exposed Rhipicephalus (Boophilus) microplus.

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

state: TX

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

summary:
A R. microplus microarray was used to study differential gene expression in acaricide exposed larvae from an amitraz-resistant strain.  The acaricide treatments were: organophosphate (OP), pyrethroid, ivermectin, and amitraz.  The microarrays contained over 13,000 probes corresponding to each member of R. microplus gene index ESTs previously described (http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=b_microplus).  Serial analysis of gene expression (SAGE) data from the OP treated R. microplus was used to verify the OP microarray data.  The expression profiles of selected transcripts were verified by real time PCR.  Among the significantly differentially expressed genes, were a tick legumain, involved in blood digestion, gluthathione S-transferase (GST), a detoxification enzyme involved in pesticide resistance, acyltransferase, several putative salivary sulfotransferases, and a glutamate receptor.
**Note: contact person:  Felix D. Guerrero   email:  felix.guerrero@ars.usda.gov
Keywords: Rhipicephalus (Boophilus) microplus, acaricide resistance genes, organophosphates OP, microarrays, detoxification enzymes.

overall_design: In the study presented here, 10 hybridizations were preformed.  Two technical replicates for each treatment.   There were no biological replicates included in this study due to limitations on biomaterials.   Expression profiles for 13601 unique ESTs were analyzed.

first: Felix

middle: D

last: Guerrero

first: Kelly

last: Brayton


title: Gene expression profiling in peanut using oligonucleotide microarrays

city: Lubbock

first: Kameswara Rao

last: Kottapalli

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

summary:
Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently have moderately significant number of ESTs has been released into the public domain. Utilization of these ESTs for the oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology. We have developed a high-density oligonucleotide microarray for peanut using approximately 47,767 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and investigate the utility of this array, we compared transcript levels in pod to peg, leaf, stem, and root tissues. Results from this experiment showed a number of putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to either peg, leaf, or stem.
Keywords: Peanut tissue-specific gene expression

overall_design: We used Agilent peanut gene chips (017430) to identify putative tissue-specific genes and investigate the utility of the array for expression profiling of various peanut tissues. Pod, leaf, stem, peg and root tissues of the peanut genotype Flavrunner 458 were used in the study. Field grown plants under normal irrigation were used for sample collection. Three replications of microarray experiments were carried out by hybridizing the cRNA from pod tissue and cRNA from leaf, stem, peg and root tissues on the same dual color oligonucleotide arrays.

first: Paxton

last: Payton

first: KameswaraRao


title: Gene expression induced by localized nitrate in a split-root system

city: Beijing

first: Guohua

last: Mi

address: Yuan-Ming-Yuan West Rd 2

department: Plant Nutrition

institute: China Agricultural University

summary: Arable soils are extremely heterogeneous in spatial nutrient distribution. It is well documented that lateral roots (LRs) proliferate in nitrate-rich patch. Yet less information is available as to which genes are involved in this process, in particular in cereals. To understand the molecular mechanism for local nitrate induced LR growth in maize (Zea mays L.), we analyzed the gene expression profiling in maize root in early response (1 hour) to local nitrate stimulation by using Maize Oligonucleotide Array (http://www.maizearray.org) and a split-root system. Selected differentially expressed genes were further confirmed by semi-quantitative RT-PCR. The results showed that reception and/or transduction of local NO3- signal involve some important protein kinases and protein phosphatases (histidine kinases, serine/threonine kinases, protein phosphatase 2A etc.) and transcription factors (F-box, Zinc finger, Myb and bZIP transcription factors and response regulator). Increasing expression of genes encoding auxin response factor 7b, ethylene receptor, and cytokinin oxidase suggests strong interaction among hormonal pathways and local NO3- signaling pathways. Genes involving NO3- uptake and assimilation (NRT2.1, NR, etc.), sugar transport (a sugar transporter) and utilization (a sucrose synthase) were enhanced in the N-fed root. Furthermore, local NO3- induces rapid expression of genes related to cell division and expansion such as alpha-expansin, celluose synthase, kinesin, plasma membrane and tonoplast aquaporins. Based on the differentially expressed genes, a putative model which combines both the 'NO3- signal' and 'metabolic sink' theories is proposed to explain the molecular mechanism controlling local nitrate induced LR elongation in maize.

overall_design: plants were pre-cultured in solution containing 0.5 mmol L-1 NO3- for 6 days and then transferred to N-free solution to grow for another 2 days. Then these plants were transferred to a two-compartment split-root system with only half root supplied with 1.0 mmol L-1 NO3-. Supply of Ca2+ in the N-free half was compensated by adding 1.0 mmol L-1 CaCl2. One hour after the local nitrate treatment, root segments (15cm from root tip to lateral root elongation zone) were sampled for RNA extraction. Two biological replicates were performed for each treatment.

first: Jinxin

last: Liu

first: Lili

last: Han

first: Fanjun

last: Chen

first: Juan

last: Bao

first: Fusuo

last: Zhang


title: Control vs hyper; 25 mM glucose_Filtered fb-bg

city: Ede

first: Arno

last: Wegkamp

address: Kernhemseweg 2

institute: NIZO food research

summary:
Transcriptional analysis upon the overexpression of the folate gene cluster on a high copy plasmid when compared to an empty vector in the lactic acid bacterium L. plantarum. The transcriptional response was determined for both strains in continuous culture in the presence of glucose thereby using the hybridisation sceme as described in the data processing section.
Keywords: comparative genomic hybridization

first: Astrid

last: Mars

first: Magda

last: Faijes

first: Douwe

last: Molenaar

first: Ric

last: de Vos

first: Sebastian

last: Klaus

first: Andrew

last: Hanson

first: Willem

first: Eddy

last: Smid


title: Effects of intermittent and chronic hypoxia on HAEC

city: Baltimore

first: Dmitry

last: Grigoryev

state: MD

institute: JHU

summary:
Intermittent hypoxia (IH) in HeLa cell culture activates proinflammatory transcription factor NFκB, whereas chronic hypoxia (CH) does not.  In order to determine whether IH may be linked to vascular inflammation, we developed a novel IH cell culture system and exposed HAEC (human aortic endothelial cells) to IH or CH.
Keywords: Human Artery Endothelial Cells (HAEC)

overall_design: HAEC were gassed with: 1) 16% O2, 5%CO2, balanced N2 (control); 2) 4%O2, 5%CO2, balanced N2 (continuous hypoxia) or 3) 5 minutes of 16% O2, 5%CO2, balanced N2 alternating with 5 minutes of 0% O2, 5%CO2, balanced N2 (intermittent hypoxia). After 8 hours cells were quickly harvested for RNA extraction by the Trizol methods with subsequent RNEasy clean up. Gene microarrays were performed using Illumina’s Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA) n=4 for each condition.


title: Identification of discriminant genes and gene networks involved in pig ovarian follicular atresia

city: Castanet-Tolosan Cedex

first: Agnes

last: Bonnet

address: Chemin de Borde-Rouge  BP 52627

institute: INRA

summary:
Folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration (a process called atresia). Even if atresia involves an apoptosis process, this mechanism is not well understood. The objective of this experiment was : 1) to analyse gene expression in pig granulosa cells of ovarian follicles during atresia using transcriptome analysis with a 9 024 cDNAs microarray, 2) the identification of gene networks involved in pig ovarian follicular atresia. Granulosa cells were isolated from atretic follicles (small, medium or large). Gene expression was analysed by hybridization of nylon cDNA microarrays.  The images were quantified using Bzscan software and the data were managed with BASE software. Statistical analysis was performed using R software.
Keywords: pig ovary, folliculogenesis, atresia, gene expression, cDNA microarray, bio-analysis

overall_design: Calibrated follicles were isolated from porcine ovaries after ovariectomy (24h ou 96h after the end of progestagen treatment: Regumate 18 days, 20 mg/days). The follicular status was determined by histological criteria using Feulgen coloration (Monget et al. 1993, Besnard et al. 1996).  Healthy follicle is characterized by frequent mitosis and pyknosis absence in granulosa cells. Presence of frequent pyknotic bodies in granulosa cells and no mitosis were allocated to atretic cells. Two cross-classified biological factors of pig ovarian follicles are considered : 1) the stage of development of the follicular growth : small (1-2 mm of diameter), medium (3 mm) and large (>5 mm) follicles; 2) the follicular status: healthy (S1) vs beginning (A2) or advanced (A3) atresia. Gene expression was analysed by hybridization of nylon cDNA microarrays (GPL3729). After hybridisation the data analysis using BASE software and statistical analysis was performed to identify regulated genes. For each of three follicle class and three follicle status combination 4 biological replicates were considered. Total 36 membranes were first hybridized with a vector oligonucleotide labeled (T7 probe 5'-taatacgactcactataggga-3') with gamma33P ATP at 42°C during 12h to determine the quality of the spotting process. After being washed, the arrays were exposed 6 or 24 hours to radioisotopic-sensitive imaging plates (BAS-2025, Fujifilm, Raytest France S.A.R.L., Courbevoie, France). The imaging plates were scanned thereafter with a phosphor imaging system at a 25 Âµm resolution (BAS-5000, Fujifilm, Raytest France S.A.R.L., Courbevoie, France). Data were acquired with help of a microarray image processing software - AGScan (Cathelin, 2006, http://mulcyber.toulouse.inra.fr/projects/agscan/). Fixed circle segmentation, i.e. a grid process with a fixed spot diameter was applied. The hybridization images were quantified by the extraction of the intensity for each spot. Arrays images and data were stored using BASE software (Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, and Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 3: SOFTWARE0003, 2002) adapted by Sigenae (http://www.sigenae.org) for analysis and storage of radioactitive microarray data


title: mRNA expression in TTHA0118 deletion mutant of Thermus thermophilus HB8 strain grown on minimum essential medium

city: Toyonaka

first: Taisuke

last: Wakamatsu

state: Osaka

address: Machikaneyama 1-1

department: Department of Biology

country: Japan

institute: Osaka University

summary:
We compared the expression profile of TTHA0118 deletion mutant strain of Thermus thermophils HB8 with that of wild-type. The mutant strain grown in minimum essential medium (CS medium) exhibited growth retardation. In early log phase, 29 genes were suppressed and 25 genes were activated for the mutant strain. The suppressed genes included genes of electron transport, and cell growth and division. The activated genes included genes of stress response. We suggested that these transcriptional alterations in the mutant cell were induced by the pAp accumulation and mononucleotides starvation. Keywords: cell type comparison

Keywords: cell type comparison

overall_design: Wild-type and the mutant strains were precultured in rich medium (TT medium) for two times at 70 oC and then subcultured to minimum essential medium (CS medium). These cells were harvested at 7 × 10^8 cells/ml. Total RNA were extracted from each strain and used for the cDNA synthesis. For the biological replication, above experiments were performed four times independently. The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions. The 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix). The Probe Array was scanned with a GeneArray Scanner (Affymetrix), and then, the image data was scaled to the target intensity by one-step Tukey's biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix). The data analysis was performed by using GeneSpring GX (Agilent Tech.). The genes which had detection call of 'presence' more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student's t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.

first: T

first: N

last: Nakagawa

first: R

last: Masui

first: S

last: Kuramitsu


title: JM43 cells grown aerobically in galactose and treated with Antimycin A

city: Urbana

first: Kurt

last: Kwast

state: IL

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary:
In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium.  Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand.  A similar pattern of gene expression is seen when cells encounter other “environmentally stressful” conditions.  However, cells shifted to anaerobiosis on glucose, in which no catabolic rearrangement is required nor change in growth rate observed, do not exhibit this pattern, suggesting the “stress” encountered is one associated with the abrupt cessation of galactose-dependent respiration and slowing of growth, not oxygen deprivation per se.  In order to test this hypothesis, we conducted this genomic study using the respiratory inhibitor, antimycin A, under aerobiosis, which mimicked the retooling of metabolism from respiro-fermentative to strictly fermentative growth.
Keywords: time course

overall_design: Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) for six generations of preconditioning.  When cell density was ≈1 Klett unit, Antimycin A (1 μM) was added into medium.  Samples were harvested after 0 (control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of aerobic growth in the presence of Antimycin A.  Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5).  The full time series was repeated in triplicate.

first: Liang-Chuan

last: Lai

first: Matthew

middle: T

last: Kissinger

first: Patricia

middle: V

last: Burke


title: Synergy between plasminogen activator inhibitor-1 and Snail in tumoral migration

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

summary:
Snail, a family of transcriptional repressors implicated in cell movement, has been correlated with tumour invasivity. The Plasminogen Activation system (PAs), including urokinase (uPA), its receptor (uPAR), and its inhibitor (PAI-1), also plays a key role in cancer invasion and metastasis, either through proteolytic degradation or by non proteolytic modulation of cell adhesion and migration. Thus, Snail and PAs both influence those processes and are over-expressed in cancers. In this study we aimed to determine first whether Snail activity is correlated with PAs components expression and second how this correlation can influence tumoral cell migration.
Keywords: Tumoral migration

overall_design: Comparison the invasive breast cancer cell-line MDA-MB-231 expressing Snail (MDA-Neo) with its derived clone expressing a dominant negative form of Snail (Snail-DN). Expression of PAs mRNAs was performed by cDNA microarrays and real time quantitative RT-PCR. Wound healing assay was used to determine cell migration. PAI-1’s distribution was assessed by immunostaining.

first: Elizabeth

last: Fabre-Guillevin

last: Peinado

first: Gema

last: Moreno

first: Jose

last: Palacios

first: Amparo

last: Cano

first: Cécile

last: Charrière-Bertrand


title: JM43_Galactose_N2_AntimycinA

middle: E

summary:
In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium.  Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand.  A similar pattern of gene expression is seen when cells encounter other “environmentally stressful” conditions.  However, cells shifted to anaerobiosis on glucose, in which no catabolic rearrangement is required nor change in growth rate observed, do not exhibit this pattern, suggesting the “stress” encountered is one associated with the abrupt cessation of galactose-dependent respiration and slowing of growth, not oxygen deprivation per se.  In order to test this hypothesis, we added the respiratory inhibitor, antimycin A, under aerobiosis for three generations then shifted to anaerobiosis, which no catabolic rearrangement is required.
Keywords: time course

overall_design: Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) in the presence of Antimycin A for three generations.  After three generations, the sparge gas was switched from air to O2-free N2 and samples were harvested after 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of anaerobic growth in the presence of Antimycin A.  Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5).  The full time series was repeated in triplicate.


title: Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response_DataSet1

first: Joerg

last: Bohlmann

summary: We investigated the transcriptional response of hybrid poplar (Populus trichocarpa x deltoides) leaves to a variety of stress treatments (insect feeding by Malacosoma disstria larvae, mechanical wounding, and wounding plus the application of insect oral secretions) over a 24 hour time course.  Experiments were conducted using clonal trees under greenhouse conditions at the University of British Columbia.  We used the 15.5K poplar cDNA microarray platform previously described by Ralph et al. (Molecular Ecology 2006, 15:1275-1297).  Differentially expressed genes were determined using three criteria: fold-change between treated and untreated control leaves > 1.5-fold, P value < 0.05 and Q value < 0.05.  This study identified > 1,000 differentially expressed genes in response to insect feeding and/or treatments that mimic insect feeding damage.

overall_design: A factorial hybridization design was chosen to assess gene expression among the untreated control leaves, and leaves subjected to one of three stress treatments: forest tent caterpillar (Malacosoma disstria) feeding, mechanical wounding, and mechanical wounding plus the application of forest tent caterpillar oral secretions.  For each tree, the lowest five mature leaves were caged in nylon mesh bags, treated or left untreated as a control.  Leaves were harvested 2, 6 or 24 hours after the initiation of each treatment and total RNA was individually isolated from each tree.  For each treatment and time point, equal amounts of total RNA were combined from each of the five biological replicate trees prior to cDNA microarray analysis.  For the herbivory, mechanical wounding and oral secrection treatments, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations.

first: Steven

last: Ralph

first: Ryan

last: Philippe


title: Splicing_Arrays_2

status: Public on Dec 30 2008

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

summary:
In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down.

Keywords: Genetic modification

overall_design: This set of arrays evaluate the off target effect of the RNAi. Two differerent non-overlapping dsRNA targeting hrp36 were used to knock down its expression. The net-expression value of each splicing junction was then extracted and compare.


title: Splicing_Arrays_1

overall_design: Each individual protein (four total) were individually knock-down. RNA from biological triplicates were isolated 4 days after the initial treatment. A non-specific RNAi control was performed and the RNA isolated from multiple replicates were pooled and used as control sample in the microarray.


title: The anticancer effects of tanshinone I in human non-small-cell lung cancer

city: Taichung

first: Chen-Yu

last: Lee

address: 250, Kuo Kuang Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

summary:
Tanshinones are the major bioactive compounds of Salvia miltiorrhiza Bunge (Danshen), roots, which are used in many therapeutic remedies in Chinese traditional medicine. We investigated the anticancer effects of tanshinones on the highly invasive human lung adenocarcinoma cell line, CL1-5. Tanshinone I significantly inhibited migration, invasion, and gelatinase activity in macrophage-conditioned medium (CM)-stimulated CL1-5 cells in vitro and also reduced the tumorigenesis and metastasis in CL1-5-bearing severe combined immunodeficiency mice. Unlike tanshinone IIA, which induces cell apoptosis, tanshinone I had no significant cytotoxicity. Real-time quantitative polymerase chain reaction (RTQ-PCR), luciferase reporter assay, and an electrophoretic mobility shift assay revealed that tanshinone I reduces the transcriptional activity of interleukin-8 (IL-8), the angiogenic factor involved in cancer metastasis, by attenuating the DNA-binding activity of activator protein-1 and nuclear factor kappaB in CM-stimulated CL1-5 cells. Microarray and pathway analysis of tumor-related genes identified the differentially expressed genes responding to tanshinone I, and these results were validated by RTQ-PCR. The responsive genes included human platelet-derived growth factor beta chain, Shb, H-ras, N-Ras, mitogen-activated protein kinase kinase 3, phosphoinositide-3-kinase, CD44, Rac1, and collagen type IV; these genes may be associated with the Ras MAPK and Rac1 signaling pathways. These results suggest that tanshinone I exhibits anticancer effects both in vitro and in vivo, and that these effects are mediated at least partly through the IL-8, Ras MAPK, and Rac1 signaling pathways.
Keywords: treatment with dose respone, cDNA array

overall_design:
Five concentrations of tanshinone I in CM were used: 0, 0.01, 0.1, 1, 10 ug/mL; in addition to a control condition without CM. Thirty micrograms of total RNA derived from CL1-5 cells from each treatment described above were labeled with digoxigenin during reverse transcription. The averaged intensity for each gene (there were three copies on a chip for each gene) was used for the subsequent analyses. To reduce the variation arising from experimental results derived from different microarrays, the intensity values of the spots from each microarray were rescaled using a quantile normalization method and a housekeeping gene, GAPDH. To reduce background noise, any background intensity lower than 2,330 was assigned the value of 2,330.
Genes were clustered into groups on the basis of expression profiles by the self-organizing maps (SOMs) algorithm using the Acuity 3.0 program (Axon Instruments, Union City, CA). After cluster analysis by the SOM method, genes whose expression profiles correlated with the concentration of tanshinone I were identified.

first: Hui-Fang

last: Sher

last: Chen


title: RIP_Chip_analysis

overall_design: This set of arrays were used to globaly identify the location of RNP containing the four Drosophila hnRNP A/B homologues.


title: Comparative genomic analysis of 93 Bp strains using K96243 as the reference

status: Public on Dec 26 2008

city: Singapore

first: Sim

middle: Siew

last: Hoon

address: 27 Medical Drive

department: MCB

country: Singapore

institute: DSO National Laboratories

summary:
Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in 93 South East Asian clinical, environmental, and animal Bp isolates. 14% of the reference Bp K96243 genome was variably present across the strain panel, more than double previous estimates, and both hypothetical proteins and paralogous gene pairs (PGPs) were significantly over-represented in the set of strain-variable genes. Examining patterns of PGP retention and loss, we successfully sub-categorized the PGPs into non-redundant, functionally biased, and completely redundant classes. We then identified 20 novel regions (“islands”) variably present between strains previously missed by computational analysis. Three of these novel islands contained lipopolysaccharide (LPS) biosynthesis genes, and strains lacking one such LPS island demonstrated reduced virulence in mouse infection assays. Clinical isolates associated with human melioidosis were strongly associated with the presence of specific genomic islands, but a common set of virulence-related genes was present in all strains. Our results suggest that most Bp strains possess a core virulence machinery capable of causing disease, but accessory functions provided by mobile elements may predispose distinct host species and ecological niches to specific individual strains. This hierarchical model of Bp virulence reconciles previous conflicting studies comparing Bp environmental and clinical isolates, and suggests novel molecular strategies for disease surveillance and outbreak detection efforts in melioidosis.
Keywords: aCGH of 93 Bp strains

sample_organism:
Burkholderia pseudomallei
Burkholderia pseudomallei K96243

overall_design: genomic DNA of 93 Bp strains were assessed on Bp_array_v2

first: SH

last: Sim

first: YT

last: Yu

first: CH

last: Lin

first: M

middle: K

last: Krishna

first: HH

last: Chua

first: V

last: Wuthiekanun

first: C

last: Ong

first: S

last: Suppiah Paramalingam

first: G

last: Tan

first: L

last: Tang

last: Lau

first: EE

last: Ooi

first: SJ

last: Peacock

first: P


title: The effect of Wolbachia infection on Drosophila ovarian transcript levels

city: Berkeley

first: Sha

last: Sun

state: CA

address: 16 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary:
We used microarray analysis to screen the Drosophila genome for effects of Wolbachia infection on transcript levels in wildtype adult immature ovaries.
Keywords: Comparative expression analysis of infection effect

overall_design: To generate the ovaries to be compared, we first rid a wildtype Canton-S line of Drosophila of the well characterized YW strain of Wolbachia that it harbored (Bourtzis et al., 1998, Presgraves, 2000) by raising the flies for three generations on food containing tetracycline.  After the line had been raised for three more generations on food without tetracycline, we used a standard PCR assay (O'Neil et al., 1999) to confirm that the line was Wolbachia free.  Genetically matched infected and uninfected females were recovered as the daughters from two reciprocal crosses between the infected and the cured Canton-S lines.  Previtellogenic ovaries were harvested from these females 1-5 h after eclosion

first: Thomas

last: Cline


title: Gene expression change caused by CYS4 alleles

city: Dallas

first: Hyun Seok

last: Kim

address: Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Each strain was grown overnight then diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit, reverse transcribed, labeled with either Cy3 or Cy5, and hybridized to epoxy-coated slides with 6388, 70mer oligos (Qiagen-Operon). After an overnight hybridization, microarrays were scanned using a ScanArray Express laser scanner.

overall_design: Reference, a pool of total RNA from all samples, was used to contrast with each sample. Dye-swap was performed for one of the three replicates of each strain, where Cy3 instead of Cy5 was used to label the reference RNA.

first: Hyun-Seok

first: Justin

middle: C

last: Fay


title: Interactions between Yeast Proteins and Rsp5 Ubiquitin Ligase

first: Eitan

last: Halper-Stromberg

address: 733 N Broadway

institute: Johns Hopkins

summary: To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase

overall_design: We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.

first: Heng

last: Zhu

first: Joel

last: Bader


title: Progressive human proteinuric nephropathies

status: Public on Dec 24 2008

city: Innsbruck

first: Michael

last: Rudnicki

state: Tirol

address: Anichstrasse 35

department: Dept of Nephrology

institute: University of Innsbruck

summary:
We obtained gene-expression profiles of microdissected renal-tubule cells from patients with proteinuric nephropathies. Based on the renal function during follow-up, the patients were divided in stable (n=14) and progressive (n=7) subjects (table 1).
The cells of interest were laser-capture microdissected from frozen sections from archived kidney biopsy material.
Initially all samples were processed as technical duplicates (2 x 21 arrays); due to a large number of signal-negative spots several arrays were excluded leaving 36 arrays for analysis. The samples P2, P6, P7, S10, S13 and S14 were analysed as individual arrays, all other samples were analysed after combination of duplicate arrays.
Quality control: To test for reproducibility we calculated the intra-array variability of the duplicate arrays. Duplicate arrays were combined before statistical analysis where applicable.
Patient and control characteristics can be found in the manuscript and on our website
Frozen kidney biopsies were stained for alkaline phospatase, then the tubule cells were lasercapture microdissected using the PixCell II Laser Capture Microdissection System and CapSure; LCM Caps.
Set of arrays that are part of repeated experiments
Disease State: samples from patients with proteinuric nephropathy (stable or progressive)

overall_design:
Biological Replicate
Computed

first: Timothy

last: Meyer