title: Gene expression profiling of gastroesophageal adenocarcinoma

status: Public on May 29 2010

city: Lund

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

institute: Clinical Sciences

summary: We aimed to genetically characterize adenocarcinomas in the gastroesophagel junction in relation to cancers in the esophagus and the stomach. In total 27 tumors was genetically profiled using gene expression array. Adenocarcinomas located in the gastroesophageal junction showed strong similarites with tumors in the distal esophagus, whereas different profiles were generated for tumors in the proximal stomach.

overall_design: Three types of gastroesophageal adenocarcinomas; 10 distal esophageal (EA) tumors, 9 junctional (JA) and 8 proximal stomach cancers (GA) was undergone differentially analysis based on gene expression profiles. One replicate of tumor ID 27_JA (replicate ID 27_JA_2) and one replicate of tumor ID 3-GA (replicate ID 3-GA-2). Reference samples consist of the Stratagene Universal Reference (10 cellines), commercially obtained from Stratagene, La Jolla, CA, USA.


title: Analysis of cardiac gene expression in response to isoproterenol-induced heart failure (part 1)

status: Public on May 31 2010

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

summary:
Myoglobin knockout mice (myo-/-) adapt to the loss of myoglobin by the activation of a variety of compensatory mechanisms on the structural and functional level. In order to analyze to what extent myo-/- mice would tolerate cardiac stress we used the model of chronic isoproterenol application to induce cardiac hypertrophy in myo-/- mice and wild type (WT) controls. After 14 d of isoproterenol infusion cardiac hypertrophy in WT and myo-/- mice reached a similar level. WT mice developed lung oedema and left ventricular dilatation indicating the development of heart failure. In contrast, myo-/- mice displayed conserved cardiac function and no signs of heart failure. Analysis of the cardiac gene expression profile using 40 k mouse oligonucleotide arrays showed that isoproterenol affected the expression of 180 genes in WT but only 92 genes of myo-/- hearts.
Only 40 of these genes were regulated in WT and myo-/- hearts. Whereas in WT hearts a prononced induction of genes of the extracellular matrix occurred suggesting a higher level of remodelling, in myo-/- hearts genes of carbon metabolism and genes linked to inhibition of apoptosis and muscular repair were altered. Interestingly, a subset of genes which was altered in myo-/- mice already under basal conditions was differentially expressed in WT hearts under isoproterenol treatment. In summary, our data show, that the genetic background (WT, myo-/-) has a major impact on cardiac gene expression even in the context of an aggressive hypertrophy model such as chronic isoproterenol stimulation.

Keywords: gene expression profiling of isoproterenol induced heart failure in WT and myo-/- mice

overall_design: We analysed the cardiac gene expression profiles in a total of 32 hearts subdivided into 4 groups (8 WT vehicle, 8 WT ISO, 8 myo-/- vehicle, 8 myo-/- ISO).

first: Andrei

last: Molojavyi

first: Claudia

last: Kessels

first: Sarah

last: Kocks

first: Karl

last: Köhrer

first: Axel

last: Gödecke


title: Effect of rbf1 deletion during controlled expression of Ustilago maydis b-mating type locus genes bE1 and bW2

status: Public on Jun 01 2010

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: In the phytopathogenic Basidiomcete Ustilago maydis, sexual and pathogenic development are tightly connected and controlled via the b-mating type locus. The b-mating type locus encodes two homeodomain transcription factors, bE and bW, which form an active heterodimeric complex when they are derived from different b-alleles. Rbf1 encodes a zinc-finger transcription factor that is expressed upon formation of an active bE/bW heterodimer. To analyse the dependency of b and rbf1, changes in gene expression were monitored in strain AB31 (Brachmann et al., 2001, Mol Microbiol 42, 1047-1063) and in the derivative AB31Δrbf1 in which rbf1 was deleted. AB31 harbours the active combination bE1 and bW2 under the control of the arabinose-inducible crg1 promoter. Samples were taken 3h, 5h and 12h after induction of bE/bW gene expression. Strain AB32, which harbors the incompatible bE2 and bW2 combination, was used as control.

overall_design: Strains were grown to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25% (w/v) salt solution, 30 mM L-glutamine, 1% (w/v) glucose, pH 7.0 (filter-sterilized). For induction of the bE and bW genes, cells were inoculated in liquid array medium containing 1% (w/v) arabinose instead of glucose as a carbon source. For induction, cells were washed once with inducing medium; time point 0 h of the time course experiments corresponds to the first contact with inducing medium. Experiments were performed in two biological replicates for each time point.

first: Mario

last: Scherer


title: Telomere dysfunction and fusion during the progression of chronic lymphocytic leukaemia: evidence for a telomere crisis

status: Public on May 28 2010

city: Cardiff

first: Duncan

last: Baird

address: Heath Park

department: School of Medicine

country: United Kingdom

institute: Cardiff University

type: Genome variation profiling by genome tiling array

summary: We performed single-molecule telomere length and telomere fusion analysis in patients at different stages of chronic lymphocytic leukaemia (CLL). Our work identified the shortest telomeres ever recorded in primary human tissue reinforcing the concept that there is significant cell division in CLL. Furthermore, we provide direct evidence that critical telomere shortening, dysfunction and fusion contribute to disease progression. The frequency of short telomeres and fusion events increased with advanced disease, but importantly these were also found in a subset of early-stage patient samples indicating that these events can precede disease progression. Sequence analysis of fusion events isolated from individuals with the shortest telomeres revealed limited numbers of repeats at the breakpoint, sub-telomeric deletion and microhomology. Array-CGH analysis of individuals displaying evidence of telomere dysfunction revealed large-scale genomic rearrangements that were concentrated in the telomeric regions; this was not observed in samples with longer telomeres.

overall_design: Array CGH was undertaken on six individuals (five CLL stage C and one stage A) that displayed evidence of telomere dysfunction, and four (three CLL stage A and one stage B) that displayed longer and apparently stable telomeres.

middle: M


title: Drought response in Piriqueta caroliniana hybrid and parental morphotypes

status: Public on May 27 2010

city: Portland

first: Heather

last: Machado

state: OR

address: 1719 SW 10th Avenue, SB2 Room 246

department: Biology

country: USA

institute: Portland State University

summary: Closely related lineages can possess phenotypic variation important for adaptation and the evolution of new species; a phenomenon that can be more clearly elucidated by studying hybrid generations.  We compare variation in gene expression in response to drought for two taxa and advanced-generation hybrids of the Piriqueta cistoides ssp. caroliniana complex that differ in their levels of tolerance to water limitation.  Drought treatments lasted 36 days, through four cycles of drought.  Gene expression in drought and control treatments was assessed using heterologous hybridization to a Glycine max microarray.  There was a predominance of down-regulated genes in response to sustained drought in all morphotypes.  This pattern was more pronounced in the hybrids, which can exhibit greater drought tolerance under field and greenhouse conditions than the parental morphotypes.  Expression response profiles were more similar between the hybrid and the drought-tolerant parental morphotype than they were between the hybrid and the parental morphotype that occurs in more mesic habitats.  Predominant down-regulation of gene expression contrasts with studies of response to short-term drought and with studies of drought-response in annual and non-drought-tolerant model species, and supports the results of a growing number of studies with other drought-tolerant perennial plants under prolonged drought.

overall_design: A total of 18 array hyridizations. Two conditions (drought and control), three morphotypes (caroliniana, viridis, and hybrid), for a total of 6 morphotype/treatment combinations. Three samples of each morphotypes/treatment combination were hybridized twice in dye swap in a loop design.

middle: E


title: cDNA expression profiles of +7 DPA wild-type upland cotton (Gossypium hirsutum cv. Xuzhou142) ovules over the one-year cycle

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

summary: A cDNA library from 0-10 day post anthesis cotton ovules was established to study genes expressed in cotton ovule during initiation and quickly elongation period. We randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 28000 high-quality cotton cDNAs (with average length>750bp) and external controls. To study the different growth potential of cotton fibers in a one-year cycle, we then hybridized the array with RNA samples derived from +7 DPA wild-type upland cotton fibers in four different seasons, respectively.

overall_design:
Data for 8 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: spring-Cy5 common_reference-Cy3
Set 1 (dye swap): common_reference-Cy5 spring-Cy3
Set 2: spring-Cy5 common_reference-Cy3
Set 2 (dye swap): common_reference-Cy5 spring-Cy3
Set 3: spring-Cy5 common_reference-Cy3
Set 3 (dye swap): common_reference-Cy5 spring-Cy3
Set 4: spring-Cy5 common_reference-Cy3
Set 4 (dye swap): common_reference-Cy5 spring-Cy3

GSM419228, GSM419333, GSM419334, GSM419335, GSM419336, GSM419337, GSM419338, GSM419340

Data for 8 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: summer-Cy5 common_reference-Cy3
Set 1 (dye swap): common_reference-Cy5 summer-Cy3
Set 2: summer-Cy5 common_reference-Cy3
Set 2 (dye swap): common_reference-Cy5 summer-Cy3
Set 3: summer-Cy5 common_reference-Cy3
Set 3 (dye swap): common_reference-Cy5 summer-Cy3
Set 4: summer-Cy5 common_reference-Cy3
Set 4 (dye swap): common_reference-Cy5 summer-Cy3

GSM419341, GSM419343, GSM419345, GSM419346, GSM419348, GSM419349, GSM419351, GSM419352

Data for 8 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: autumn-Cy5 common_reference-Cy3
Set 1 (dye swap): common_reference-Cy5 autumn-Cy3
Set 2: autumn-Cy5 common_reference-Cy3
Set 2 (dye swap): common_reference-Cy5 autumn-Cy3
Set 3: autumn-Cy5 common_reference-Cy3
Set 3 (dye swap): common_reference-Cy5 autumn-Cy3
Set 4: autumn-Cy5 common_reference-Cy3
Set 4 (dye swap): common_reference-Cy5 autumn-Cy3

GSM419428, GSM419429, GSM419430, GSM419431, GSM419432, GSM419433, GSM419434, GSM419435

Data for 8 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: winter-Cy5 common_reference-Cy3
Set 1 (dye swap): common_reference-Cy5 winter-Cy3
Set 2: winter-Cy5 common_reference-Cy3
Set 2 (dye swap): common_reference-Cy5 winter-Cy3
Set 3: winter-Cy5 common_reference-Cy3
Set 3 (dye swap): common_reference-Cy5 winter-Cy3
Set 4: winter-Cy5 common_reference-Cy3
Set 4 (dye swap): common_reference-Cy5 winter-Cy3

GSM419436, GSM419437, GSM419438, GSM419439, GSM419440, GSM419441, GSM419442, GSM419443

first: Xiang

last: Jin

first: Liang

last: Zhang

first: Jing

last: Cheng

first: Yuxian


title: Mouse Cells Time of Replication (ToR)

status: Public on May 25 2010

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

department: Molecular Biology

country: Israel

institute: The Hebrew university

summary: Measurment of the ToR by comapring the DNA content of the S phase and the DNA content of the G1 phase, the method is based on the method used in the paper - Replication timing of the human genome by Woodfine et al. that was published in Hum. Mol. Genet. 2004. Briefly, after staining with Propidium Iodide,  cells in G1 and S phase of the cell cycle are sorted by FACS sorter (ARIA or Vantage), DNA is then extracted from the fractions and differentially labeled with dUTP-Cy3 or dUTP-Cy5 using direct labeling (Agilent labeling kit). The labeled DNA is cohybridized to the array. Early replicating sequences correspond to the spots with high S/G1 ratio and late replicating sequences correspond to the spots with low S/G1 ratio.

overall_design: four mouse tissues were measured (MEF, L1210, ES-stem cell, and NPC-neuronal progenitor cells derived from the same ES line), 2 replicates for each sample

first: Simon

last: Itamar

first: Farkash

last: Shlomit


title: Gene expression patterns in Schistosoma mansoni larvae and eggs

city: Sao Carlos

first: Ricardo

last: DeMarco

state: Sao Paulo

address: Av trabalhador Sao Carlense 400

country: Brazil

institute: Universidade de Sao Paulo

summary:
Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts.

The infective schistosome cercaria develops from an undifferentiated germ ball within the daughter sporocyst in the molluscan host, during which considerable morphological development and synthesis of proteins essential for infection occurs. The free-living, non-feeding cercaria is notable for its swimming and host location behaviour. On contact with host skin it rapidly penetrates, replaces its tegument surface membranes, and begins body remodelling, before crossing the dermis to exit the skin via a blood vessel. Such a ‘violent’ transition from snail to fresh water to mammalian host should be accompanied by remarkable changes in the patterns of gene expression.  All gene models from version E of the S. mansoni genome (www.GeneDB.org) were incorporated into a 350K feature Roche-NimbleGen, high-density oligonucleotide array. From a map-ordered list, every 13th 50mer was chosen as a probe. Double-stranded cDNA from three biological replicates each of germ balls, cercariae, and day 3 schistosomula was hybridised to the array without amplification. Statistical analysis was carried out using programmes from the Bioconductor suite (Gentleman et al. 2004 Genome Biol 5(10):R80). More than 1000 loci were shown to be differentially expressed in each of the comparisons between the three life cycle stages. Gene ontology (GO) analysis was then carried out to discover the categories enriched in each stage. In addition custom categories based on biological function (e.g. stress response) or parasite tissue (e.g. tegument) were analysed.

sample_organism:
Schistosoma mansoni
Biomphalaria glabrata

overall_design: Three biological replicates each of germ balls, cercariae, day 3 in vitro cultured schistosomula, and eggs were used. No technical replicates were included. This is the first genome-wide microarray platform for S. mansoni. It was used to investigate the gene expression patterns of the above lifecycle stages. The first three are the stages before, during and after penetration of mammalian host skin.

first: William

last: Mathieson

first: Sophia

middle: J

last: Manuel

first: Gary

middle: P

last: Dillon

first: Rachel

middle: S

last: Curwen

first: Peter

middle: D

last: Ashton

first: Alasdair

middle: C

last: Ivens

first: Matthew

last: Berriman

first: Sergio

last: Verjovski-Almeida

first: R

middle: A

last: Wilson.


title: NF1 microdeletions characterization by custom high-resolution array CGH

status: Public on May 26 2010

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

summary:
To allow accute charaterization of NF1 locus constitutional microdeletion in 70 NF1 patients, a custom array CGH was developped. Goal was to obtain genomic rearrangements fine characterization in order to perform genotype-phenotype correlation in NF1 microdeleted patients.

To serve as a reference group in our genotype-phenotype correlation study in NF1 microdeletion patients, non-deleted NF1 patients (i.e. patients with an intragenic NF1 mutation) were also selected from our database. A total of 389 NF1 patients were included in the reference group of non-deleted patients. Multiple logistic regression was performed to test the association of each clinical feature individually with the type of constitutional NF1 mutation (intragenic mutation vs. microdeletion). The phenotypic traits of the 389 reference patients are available in the "GSE19730_control_patient_characteristics.txt" supplementary file on the Series record.

overall_design: NF1 locus microdeletions characterization vs reference sample (pool of six normal control DNAs)

first: Audrey

last: Sabbagh

first: Ingrid

last: Laurendeau

first: Pierre

last: Wolkenstein

first: Ivan

last: Bièche

first: Béatrice

last: Parfait

first: Michel

last: Vidaud

first: Meena

last: Upadhyaya

first: Dominique


title: Human Cells Time of Replication (ToR)

first: Itamar

last: Simon

overall_design: two human tissues were measured (MOLT4 and FFT-foreskin fibroblasts), 2 replicates for each sample

first: Simon

last: Itamar

first: Farkash

last: Shlomit


title: Multi-transcript expression patterns in the gastrolith disk and the hypodermis of Cherax quadricarinatus at premolt

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

institute: Israel Oceanographic and Limnological Research

summary: Variations in Gastrolith disk and hypodermis transcript expression paterrns related to induced molt cycle were identified in male Cherax quadricarinatus using a cDNA microarray estimated to contain 2180 unique sequences. Molt induction was performed by repeated alpha-ecdysone injections. Manipulated males were sacrificed at late premolt and reference populations included intact intermolt and sham-injected intermolt individuals. Isolated gastrolith disk and hypodermis cDNAs of premolted male crayfish were hybridized onto the microarray against the sham-injected male reference. A putative effect of the injection procedure was also tested by hybridizing gastrolith disks cDNAs of sham-injected males vs. intact intermolt males. Differentially-expressed genes were identified, sequenced, and annotated. The sham injections had almost no effect on the gene expression patterns. The late premolt stage was characterized by a dramatic up-regulation of the genes in the gastrolith disk and milder but definite down-regulation in the hypodermis. The induced gastrolith genes included structural genes of the gastrolith and genes related to protein synthesis, energy provision and cell proliferation. Many other genes revealed no resemblance to known protein or nucleotide sequences, and their functions are yet to be uncovered. It is hypothesized that some of these genes are related to the calcium carbonate transportation and gastrolith deposition machinery.

overall_design:
The experiment submitted in this series includes male Cherax quadricarinatus in three experimental conditions. Individual variability was integrated into the hybridization design by using RNA populations of 4 (gastrolith disk) or 5 (hypodermis) individual crayfish males for each of three experimental conditions: injected-premolted, sham-injected and intact intermolted males. Four or five hybridization sets which are biological replicates, each composed of 3 slides, were carried out. In each set, one individual from each experimental group, the premolted, sham-injected and intact was hybridized vs. the other two cDNAs in a loop design, totaling 3 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides (see graphic presentation of the hybridization design in the supplementary file GSE16866_Cq-Hybridization_design.pdf). Each of the 12 or 15 slide sets were analyzed as one integrative experiment, resulting in three binary comparisons among experimental conditions as follows: injected-premolted vs. sham-injected, sham-injected vs. intact intermolt reference, and injected-premolted vs. intact intermolt reference. Only the former two comparisons were deposited as samples.

Data analysis was conducted generally according to: Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A. & Tom, M. (2007). Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle. Insect Mol. Biol. 16, 661-674.

Briefly, analysis was accomplished using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, G.K. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3. http//www.bepress.com/sagmb/vol3/iss1/art3).

The Cy5 and Cy3 intensities within each slide were normalized using global Loess method, and background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5/Cy3); Cy5/Cy3 calculated using the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA>9 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to the p-value, derived from a moderated t-statistic after multiple testing correction. All these parameters are found in the sample data table.

first: Yana

last: Yudkovski

first: Lilah

last: Glazer

first: Assaf

last: Shechter

first: Richard

last: Reinhardt

first: Vered

last: Chalifa-Caspi

first: Amir

last: Sagi


title: Gene expression profiling of tumor stroma of MCF7 breast cancer xenografts overexpressing podoplanin (mouse array)

city: Zurich

first: Leah

middle: N

last: Cueni

address: Wolfgang Pauli-Str. 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary:
Expression of the membrane glycoprotein podoplanin is upregulated in several human cancers and might be associated with their malignant progression. The exact biological function and molecular targets of cancer cell-expressed podoplanin have remained unclear, however. Here, we ectopically overexpressed podoplanin in a human breast carcinoma xenograft model to study its role in cancer progression. To identify potential molecular mediators of podoplanin-induced effects in the murine tumor stroma we compared transcriptional profiles of podoplanin-overexpressing and control tumors using mouse microarrays.

Keywords: comparative transcriptional profiling

sample_organism:
Homo sapiens
Mus musculus

overall_design: MCF7 human breast carcinoma cells were stably transfected with the pTet-Off-regulator plasmid and the pTRE2hyg response plasmid, comprising or not full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474). Three podoplanin-overexpressing and three control clones were isolated and each of them was injected bilaterally into the mammary fat pads of five female nude mice. Tumors were harvested after 24 days of growth and RNA was extracted from each of them. RNA of the 10 tumors derived from the same cell clone was pooled to give a total of six samples for microarray analysis (3x podoplanin-overexpressing, 3x control).

first: Michael

last: Detmar


title: Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

city: Arlington

first: Jeff

last: Demuth

email: jpdemuth@uta.edu, eprince@uta.edu

state: TX

address: Box 19498 501 S. Nedderman Dr

institute: The University of Texas at Arlington

overall_design: Four biological replicates for male and female beetles with 20 individuals per replicate. Two technical replicates, one replicate per sex. 16,434 genes/expressed non-coding regions represented twice on each array. Three 60 mer probes for most exons/expressed non-coding regions. 167,538 unique genomic probes replicated twice per array.

first: Jeffery

first: Eldon

middle: G

last: Prince


title: Gene expression profiling of 22 inbred parental strains

city: Seattle

first: Wan-Lin

last: Su

state: WA

address: 401 Terry Ave N

institute: Rosetta Inpharmatics (a wholly owned subsidiary of Merck & Co., Inc.)

summary: The remarkable success observed in using genome-wide association (GWA) mapping in human cohorts to identify multiple genes linked to a wide number of traits related to complex diseases has renewed interest in applying genome-wide association mapping techniques to model organisms such as inbred laboratory mice.  However, unlike humans, the limited genetic diversity present in the ancestry of laboratory mice combined with intense selection pressure over the past decades have yielded an intricate population structure within the genomes of laboratory mouse that could potentially complicate the results obtained from such a study.  We sought to empirically assess the viability of genome-wide association studies in inbred mice using hundreds of expression traits where the true location of the eQTL is known a priori.  Using data from a previously published experimental mouse cross (C57BL/6J x C3H/HeJ), we selected over a thousand of the strongest cis-acting expression QTLs and measured transcript abundance levels of the associated expression traits in 16 classical and 3 wild-derived inbred strains. We next perform a genome-wide association scan demonstrating the low statistical power of such studies and show empirically the large extent to which high allelic association gives rise to spurious associations.  Moreover, we provide evidence illustrating that in a large fraction of cases, the marker with the most significant p-values fails to map to the location of the true eQTL; hence, as a result, selecting the most significant marker may lead to spurious findings.  Finally, we demonstrate that combining linkage analysis with association mapping provides significant increases in statistical power over a stand-alone GWA study as well as significantly higher mapping resolution than either study alone.

overall_design: RNA preparation and array hybridizations were performed at Rosetta Inpharmatics.  The custom ink-jet microarrays were manufactured by Agilent Technologies (Palo Alto, CA).  A custom array was designed for this study and consisted of 39,280 non-control oligonuceotides extracted from the mouse Unigene clusters and combined with RefSeq sequences and RIKEN full-length cDNA clones.  Mouse liver tissues were homogenized and total RNA extracted using Trizol reagent (Invitrogen, CA) according to manufacturer’s protocol.  Three µg of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome.  Labeled complementary RNA (cRNA) from each animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from representative animals for each strain. The hybridizations were performed in fluor reversal for 24 hours in a hybridization chamber, washed, and scanned using a confocal laser scanner.  Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance23 (type I error).

first: Robert

middle: R

last: Kleinhanz

first: Eric

last: Schadt


title: Controlled expression of compatible and incompatible combinations of Ustilago maydis b-mating type locus genes bE and bW

first: Jörg

last: Kämper

summary: In the phytopathogenic Basidiomcete Ustilago maydis, sexual and pathogenic development are tightly connected and controlled via the b-mating type locus. The b-mating type locus encodes two homeodomain transcription factors, bE and bW, which form an active heterodimeric complex when they are derived from different b-alleles. To identify genes regulated by the bE/bW transcription factor, changes in gene expression were monitored during a 12-h time course (0h, 1h, 2h, 3h, 5h, 12h) in strains AB31 and AB33 that harbor the active combination bE1 and bW2 under the control of the arabinose-inducible crg1 promoter and the nitrate-inducible nar1 promoter, respectively (Brachmann et al., 2001, Mol Microbiol 42, 1047-1063). Induction of bE1/bW2 in these strains results in a filament that resembles the infectious dikaryotic hypha formed after fusion of compatible sporidia. Strains AB32 and AB34, which harbor the incompatible bE2 and bW2 combination, were used as controls.

overall_design: Strains were grown to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25% (w/v) salt solution, 30 mM L-glutamine, 1% (w/v) glucose, pH 7.0 (filter-sterilized). For induction of genes under control of the crg1 promoter (strains AB31 and AB32) cells were inoculated in liquid array medium containing 1% (w/v) arabinose instead of glucose as a carbon source. For induction of the nar1-promoter glutamine was exchanged by nitrate (3g KNO3/l) as the sole nitrogen source. For induction, cells were washed once with inducing medium; time point 0 h of the timecourse experiments corresponds to the first contact with inducing medium. Experiments were performed in two biological replicates for each time point.

first: Mario

last: Scherer

first: Chetsada

last: Pothiratana


title: Transcriptional profiling of E. coli after addition of peroxynitrite or hydrogen peroxide to aerobically growing cells

status: Public on May 24 2010

city: Sheffield

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

summary: Peroxynitrite is formed in macrophages by the diffusion-limited reaction of superoxide and nitric oxide. This highly reactive species is capable of causing both oxidative and nitrosative stress in Escherichia coli. Previous studies have focused on the reactions of peroxynitrite with specific proteins or the effects of peroxynitrite on the growth and viability of whole cells. This work shows for the first time the transcriptomic response of E. coli to peroxynitrite, highlighting specific areas targeted by the stress. Upregulation of the cysteine biosynthesis pathway and subsequent identification of an increase in S-nitrosothiol levels suggests S-nitrosylation as a consequence of peroxynitrite exposure. Genes involved in the assembly / repair of iron-sulfur clusters also show enhanced transcription identifying another target of this reactive species. Unexpectedly arginine biosynthesis gene transcription levels were also elevated after treatment with peroxynitrite. Analysis of the negative regulator for these genes, ArgR, showed that the post-translational nitration of tyrosine residues within this protein is responsible for its degradation in vitro. Further upregulation is seen in oxidative stress response genes including katG and ahpCF. Probabilistic modelling of this data identified 5 altered transcription factors in response to peroxynitrite exposure including OxyR and ArgR. Hydrogen peroxide can be present as a contaminant in commercially available peroxynitrite preparations. Transcriptomic analysis of cells treated with hydrogen peroxide also showed an upregulation of oxidative stress response genes; however it did not show increased transcription of many other genes which are upregulated by peroxynitrite suggesting that cellular responses to peroxynitrite and hydrogen peroxide are distinct.

overall_design:
Biological experiments (i.e. a comparison of control and plus peroxynitrite cells) were carried out three times, and a dye swap performed for each experiment, providing two technical repeats for each of the three biological repeats.  Data from the independent experiments were combined. Genes that were differentially expressed ≥ twofold and displayed and P value of < 0.05 (as determined by a t test) were defined as being statistically significantly differentially transcribed.
Additional biological experiments (i.e. a comparison of control and plus hydrogen peroxide cells) were carried out three times, and a dye swap performed for each experiment, providing two technical repeats for each of the three biological repeats.  Data from the independent experiments were combined. Genes that were differentially expressed ≥ twofold and displayed and P value of < 0.05 (as determined by a t test) were defined as being statistically significantly differentially transcribed.

first: Samantha

last: McLean

first: Lesley

last: Bowman

middle: K


title: Integrated Network and Microarray Analysis to Identify New Biomarkers in Ischemic Heart Disease

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: A significant proportion of acute myocardial infarction (MI) patients develop heart failure (HF). Early identification of patients at risk of developing HF after MI would be a major breakthrough. An approach combining the power of biological information networks and the precision of microarray analysis was undertaken to identify biomarkers of HF. A set of three new biomarkers of HF was identified and provided significantly improved prediction accuracy than microarray or network analysis alone. These three biomarkers, Vascular Endothelial Growth Factor B, thrombospondin-1 and placental growth factor are all related to angiogenesis, a natural process that favors the revascularization of the heart after MI and prevents the occurrence of HF. Therefore, combined network and microarray analysis allows a systematic and less biased approach to biomarker discovery.

overall_design:
The 32 patients of this study were divided in 2 groups corresponding to the extreme quartiles of FE values. The first group are the patients with low Ejection fraction and the second group are the patients with high ejection fraction.
Blood  sample: 2.5 mL harvested in PAXgene® Blood RNA tubes (PreAnalytix)
RNA extraction: PAXgene® Blood RNA kit (Qiagen)
We used a Universel Reference RNA (Stratagene)
RNA amplification and labelling: kit Amino Allyl MessageAmp II (Ambion)
We hybridized 4 microarrays per patient using pangenomic microarrays from the "Réseau National des Génopôles" (Illkirch, France). 2 slides were hybridized with reference RNA labelled Cy3 and patient RNA labelled Cy5, and 2 slides were hybridized with reference RNA labelled Cy5 and patient RNA labelled Cy3.
Hybridation : Agilent protocol with few modifications : 750 ng of each labelled RNA were hubriddized at 60°C during 17 hours in an Aglient hybridization oven.
After washings, Slides were scanned with a GenePix 4000B scanner (Molecular Devices). Image intensity data were extracted with GenePix Pro 6.0 analysis software.
Quantification of Cy3 and Cy5 and selection of good spots were performed using the MAIA software (Novikov E and Barillot E. Software package for automatic microarray image analysis (MAIA).
Bioinformatics. 2007 Mar 1;23(5):639-40.
The ACUITY software was then used to normalize log ratios Cy3/Cy5 with Lowess non linear normalization, to filter out genes not present in at least 3 slides out of 4, to evaluate the reproducibility of the 4 microarrays of each patient (hierarchical clustering, Self Organizing Maps). Statistical analyses to insure reproducibility was performed using Excel (correlation coefficients, ANOVA). Only slides that passed all reprocubility tests were validated.


title: HBX-HepG2 versus Control-HepG2 (no UV)

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Mature microRNA expression profiling of HBx-expressing HepG2 cells versus Control cells. Free of UV sensitization.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The mature microRNA expression profile of HBx-expressing HepG2 cells versus control cells in three independent biological repeated experiments (no UV).  This study focuses only on human sequences. The complete data matrix is linked below as a supplementary file.

first: Caroline

last: Lee


title: Viral Microarray - Cultured Virus Set

city: New York

first: Omar

last: Jabado

state: NY

address: 722 W 168 Street 17th Fl

department: Epidemiology

institute: Columbia University

summary: Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.  Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful.   Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.

sample_organism: Influenza A virus (A/Texas/36/1991(H1N1))

overall_design: A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.

first: W

middle: I

last: Lipkin


title: Viral Microarray - Control Set

sample_organism:
Homo sapiens
West Nile virus
artificial sequences

overall_design: A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.


title: Peptide alarmone signalling triggers an auto-active bacteriocin necessary for genetic competence

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary: The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co-ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress-induced expression of the peptide pheromone competence-stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP-induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the ‘death effector’. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness-enhancing genes in the oral biofilm.

overall_design: Streptococcus mutans UA159 were grown with 2 uM CSP or without (uninduced control) to mid-log phase. Total RNA was extracted as described above. The cDNAs were prepared for hybridization using the PFGRC protocol. Microarray chips were scanned using a Gene Pix 4000B (Axon) and analyzed using the TM4 Microarray Software Suite (http://www.tm4.org/). Transcript levels were measured by cDNA hybridized to a fourfold redundant S. mutans microarray and averaged for three replicated hybridizations. Differential gene expression was based on a post-normalization cut-off of ±> twofold.

first: Julie

last: Perry

first: Marcus

middle: B

last: Jones

first: Scott

last: Peterson

first: Dennis

last: Cvitkovitch

first: Céline

last: Lévesque


title: Oenococcus oeni CGH 11strains vs AWRIB515

city: Urrbrae

first: Anthony

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

summary: CGH analysis of copy number variation in 11 strains of Oenococcus oeni compared to strain AWRIB515.

overall_design: strain vs AWRIB515. One replicate per strain.

first: Eveline

last: Bartowsky

first: Jane

last: McCarthy

first: Paul

last: Chambers


title: Gene expression profile of an ldhA-pflB- double knockout strain of E. coli BW25113 relative to wild-type

city: Boulder

first: Amar

last: Singh

state: CO

address: 1111 Engineering Drive, UCB 424

department: Chemical & Biological Engineering

institute: University of Colorado

summary: Comparison of gene expression profile in E. coli BW25113 wild type and ldhA-pflB- double mutant growing microaerobically in M9 media containing 10 g/L Glucose

overall_design: two samples: wild type and mutant

first: Amarjeet

first: Anis

last: Karimpour-fard

first: Ryan

middle: T

last: Gill


title: Transcriptional regulation of metabolism associated with desiccation resistance of the cactophilic Drosophila mojavensis

status: Public on May 21 2010

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

summary:
In Drosophila, adaptation to xeric environments presents many challenges, greatest among them the maintenance of water balance.  Drosophila mojavensis, a cactophilic species from the deserts of North America, is one of the most desiccation-resistant in the genus, surviving low humidity primarily by reducing its metabolic rate.   Genetic control of reduced metabolic rate, however, has yet to be elucidated.  We utilized the recently sequenced genome of D. mojavensis to create an oligonucleotide microarray in order to pursue the identities of the genes involved in metabolic regulation during desiccation.  We observed large differences in gene expression between male and female D. mojavensis as well as both quantitative and qualitative sex differences in their ability to survive xeric conditions.  As expected, genes associated with metabolic regulation and carbohydrate metabolism were differentially regulated between stress treatments. Most importantly, we identified four points in central metabolism (Glyceraldehyde 3-phosphate dehydrogenase, transaldolase, alcohol dehydrogenase and phosphoenolpyruvate carboxykinase) that indicate the potential mechanisms controlling metabolic rate reduction associated with desiccation resistance.  Furthermore, a large number of genes associated with vision pathways also were differentially expressed between stress treatments, especially in females, that may underlie the initial detection of stressful environments and trigger subsequent metabolic changes.
Dataset from Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis Matzkin,LM and Markow, MA, Genetics.

overall_design: The stock used in this study (15081-1352.22) was the same one utilized for the recently published D. mojavensis genome sequence.  Flies were reared using standard Tucson Drosophila Stock Center banana/Opuntia media.  The experimental design consisted of two mating status treatments (virgin and mated) and two stress treatments (desiccation and food) for both sexes.  There were two replicates per mating status/stress/sex treatment (16 total hybridizations)

first: Therese

last: Markow


title: MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

institute: SA Pathology

summary:
This Series reports results of miRNA profiling of estrogen-receptor-positive (MCF7) and estrogen-receptor-negative (MDA-MB-231) cells.
Retinoic Acid (RA) induces mir-21 in MCF-7 but not in MDA-MB-231 cells.
MCF-7 and MDA-MB-231 cells were treated (or not) with retinoic acid (RA) and grown for either 6 hours or 48 hours.

platform_organism:
Arabidopsis thaliana
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Gallus gallus
Macaca mulatta
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus

overall_design: miRNA profiling: Factorial design 2x2x2 'cube'; main factors: RA, cells, time; interactions: RA.cells, RA.time, cells.time, RA.cells.time.

first: Mineko

last: Terao

first: Maddalena

last: Fratelli

first: Gregory

last: Goodall

first: Enrico

last: Garattini


title: Sinorhizobium meliloti cells: untreated 1021 wild type strain vs. RD64 strain

status: Public on May 20 2010

city: Napoli

first: Carmen

last: Bianco

address: Via p. Castellino 111

country: Italy

institute: IGB-CNR

summary: Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P minimizing chemical fertilizers dependence.    It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. We present here data showing that RD64 is also highly effective in mobilizing P from insoluble sources such as phosphate rock (PR). Under P-limiting conditions, the higher P-mobilizing activity of RD64, as compared to 1021 wild type strain, is connected with the up-regulation of genes coding for the high-affinity P transport system, the induction of acid phosphatase activity and the increased secretion into the growth media of malic, succinic and fumaric acids. Medicago truncatula plants nodulated by RD64 (Mt-RD64), when grown under P deficient conditions, released higher amounts of another P-solubilizing organic acid, the 2-hydroxyglutaric acid, as compared to the plants nodulated by the wild-type strain (Mt-1021).   It has already been shown that Mt-RD64 plants exhibited a higher dry weight production as compared to Mt-1021 plants. Here we report that also P-starved Mt-RD64 plants show a significant increase both in shoot and root fresh weight when compared to P-starved Mt-1021 plants.   We discuss how, in a rhizobium-legume model system, a balanced interplay of different factors linked to the bacterial IAA over-production rather than IAA production per se stimulates plant growth under stressful environmental conditions, and in particular, under P-starvation.

overall_design: Two-conditions experiment: untreated 1021 vs. untreated RD64 cells. Biological replicates: 6 untreated control strain, 6 untreated IAA-overproducing strain, independently grown and harvested. One replicate per array.


title: Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with tryptophan (Trp)

summary: Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence.  It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. We present here data showing that RD64 is also highly effective in mobilizing P from insoluble sources such as phosphate rock (PR). Under P-limiting conditions, the higher P-mobilizing activity of RD64, as compared to the 1021 wild type strain, is connected with the up-regulation of genes coding for the high-affinity P transport system, the induction of acid phosphatase activity and the increased secretion into the growth media of malic, succinic and fumaric acids. Medicago truncatula plants nodulated by RD64 (Mt-RD64), when grown under P-deficient conditions, released higher amounts of another P-solubilizing organic acid, the 2-hydroxyglutaric acid, as compared to the plants nodulated by the wild-type strain (Mt-1021). It has already been shown that Mt-RD64 plants exhibited a higher dry weight production as compared to Mt-1021 plants. Here we report that also P-starved Mt-RD64 plants show a significant increase both in shoot and root fresh weight when compared to P-starved Mt-1021 plants. We discuss how, in a rhizobium-legume model system, a balanced interplay of different factors linked to the bacterial IAA over-production rather than IAA production per se stimulates plant growth under stressful environmental conditions, and in particular, under P-starvation.

overall_design: Two-conditions experiment: untreated vs. Trp-treated cells. Biological replicates: 6 untreated control, 6 treated samples, independently grown and harvested. One replicate per array.


title: DosS responds to a reduced electron transport system to induce the Mycobacterium tuberculosis DosR regulon

status: Public on May 22 2010

city: Aurora

middle: William

last: Honaker

department: Microbiology

institute: University of Colorado Denver

summary: The DosR regulon in Mycobacterium tuberculosis is involved in respiration-limiting conditions and its induction is controlled by two histidine kinases, DosS and DosT. Recent experimental evidence indicates DosS senses either molecular oxygen or a redox change. This report demonstrates that DosS responds to a reduced electron transport system (ETS), although this does not rule out a role for oxygen in silencing signaling. Under aerobic conditions induction of the DosR regulon by DosS but not DosT was observed after the addition of ascorbate, a powerful cytochrome c reductant, demonstrating DosS responds to a redox signal even in the presence of high oxygen tension. During hypoxic conditions regulon induction was attenuated by treatment with compounds that occluded electron flow into the menaquinone pool or decreased the size of the menaquinone pool itself. Increased regulon expression during hypoxia was observed when exogenous menaquinone was added, demonstrating the menaquinone pool is a limiting factor in regulon induction. Taken together these data indicate that a reduced menaquinone pool directly or indirectly triggers induction of the DosR regulon via DosS. Biochemical analysis of menaquinones upon entry into hypoxic/anaerobic conditions demonstrated the disappearance of the unsaturated species and low-level maintenance of the mono-saturated menaquinone. Relative to the unsaturated form, an analog of the saturated form is better able to induce signaling via DosS, rescue inhibition of menaquinone synthesis, and is less toxic. The menaquinone pool is central to the ETS and therefore provides a mechanistic link between the respiratory state of the bacilli and DosS signaling.

overall_design: Aerobically growing logarithmic phase DosS and DosT mutant strains were analyzed after treatment with the cytochrome c reductant ascorbate to examine the effect on DosR signaling caused by reducing the electron transport system. Experiments were repeated in triplicate (dosT mutant) or duplicate (dosS mutant).

middle: W

first: Rakesh

last: Dhiman

first: Prabagaran

last: Narayanasamy

first: Dean

last: Crick

first: Martin

last: Voskuil


title: Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-carboxylic acid (ICA)

overall_design: Two-conditions experiment: untreated 1021 vs. ICA-treated 1021 cells. Biological replicates: 6 untreated control, 6 treated samples, independently grown and harvested. One replicate per array.


title: Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole (IND)

overall_design: Two-conditions experiment: untreated vs. IND-treated cells. Biological replicates: 6 untreated control, 6 treated samples, independently grown and harvested. One replicate per array.


title: DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions

city: Guadalajara

first: Mario

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

summary: In this report we demonstrated that under aerobic conditions, Mycobacterium bovis BCG expressing an hsp60-driven second copy of the hypoxia-related transcriptional regulator DosR increased 2-fold or greater the expression of 38 out of the 48 genes belonging to the DosR regulon, including the latency antigens Rv1733c, Rv2029, Rv2627, and Rv2628. Expression of DosR under these conditions slightly delayed in vitro growth, but did not promote a non-replicating state as opposed to microaerobic and hypoxic adaptation. Our results suggest BCG producing DosR can be cultured under standard in vitro  conditions, allowing evaluation of this strain as a latency-specific vaccine candidate.

overall_design: Set of arrays that are part of repeated experiments

first: M

last: Flores-Valdez


title: Discovery of microRNAs and other small RNAs in solid human tumors: expression

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

institute: Rosetta Genomics

summary: MicroRNAs (miRNAs) are ~22 nucleotide-long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs from 23 breast, bladder, colon, and lung tumor samples using high-throughput sequencing. We identified 49 novel miRNA and miRNA-like small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, and normal and tumor tissue samples using two independent platforms, namely microarray and RT-PCR. Some of the novel sequences show a large difference in expression between tumor and tumor-adjacent tissues, between different tumor stages, or between different tumor types. We also report the identification of novel small RNA classes in human: highly expressed small RNA derived from Y-RNA and endogenous siRNA. Finally, we identified dozens of new miRNA sequence variants that demonstrate the existence of miRNA-related SNP or post-transcriptional modifications. Our work extends the current knowledge of the tumor small RNA transcriptome and provides novel candidates for molecular biomarkers and drug targets.

overall_design: The microarray was hybridized to 38 different samples. The samples were from 17 different tissue types and blood samples and were divided among normal (n = 8), tumor (n = 15), tumor adjacent (n = 5) and metastasis indications (n = 8).

first: Eti

last: Meiri

first: Asaf

last: Levy

first: Hila

last: Benjamin

first: Miriam

last: Ben-David

first: Lahav

last: Cohen

first: Avital

last: Dov

first: Nir

last: Dromi

first: Noga

last: Yerushalmi

first: Orit

last: Zion

first: Gila

last: Lithwick-Yanai


title: Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-acetic acid (IAA)

first: Carmen

last: Bianco

overall_design: Two-conditions experiment: untreated 1021 vs. IAA-treated 1021 cells. Biological replicates: 6 untreated controls, 6 treated samples, independently grown and harvested. One replicate per array.


title: Do different neurons age differently? Direct genome-wide analysis of aging in single identified cholinergic neurons

city: St Augustine

first: Andrea

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

institute: University of Florida

summary:
The complexity of events associated with age-related memory loss (ARML) cannot be overestimated. The problem is further complicated by the enormous diversity of neurons in the CNS and even synapses of one neuron within a neural circuit. Large-scale single-neuron analysis is not only challenging but mostly impractical for any model currently used in ARML. We simply do not know: do all neurons and synapses age differently or are some neurons (or synapses) more resistant to aging than others? What is happening in any given neuron while it undergoes “normal” aging? What are the genomic changes that make aging apparently irreversible?  What would be the balance between neuron-specific vs global genome-wide changes in aging? In the proposed paper we address these questions and develop a new model to study the entire scope of genomic and epigenomic regulation in aging at the resolution of single functionally characterized cells and even cell compartments. In particular, the mollusc Aplysia californica has been implemented as a powerful paradigm in addressing fundamental questions of the neurobiology of aging.
The proposed manuscript will consist of four parts.
First, we will provide an introduction to Aplysia as a representative of the largest superclade of bilaterian animals (Lophotrochozoa). Aplysia has a short lifespan of 220-300 days with a well-characterized life cycle and characterized phenomenology of aging. Most importantly, Aplysia possess the largest nerve cells in the entire animal kingdom (only eggs are larger); these cells can be uniquely identified and mapped in terms of their well-defined interactions with other neurons forming relatively simpler neural circuits underlying several stereotypic and learned behaviors.
Second, we have identified in Aplysia more that a hundred neurological- and age-related genes that were lost in other established invertebrate models (such as Drosophila and C. elegans). The proposed long-term regulatory age-related mechanisms include a high level of conservation among many epigenetic processes known to be lost in nematodes and flies with extremely short lifecycles and particularly derived genomes. We also identify and cloned more than 30 evolutionarily conserved homologs of genes involved in Alzheimer’s, Parkinson’s and Huntington’s diseases as well as age-related hormones.
Third, we performed genome-wide analysis of expression patterns of more than 55,000 unique transcripts by comparing two different identified cholinergic neurons (R2 and LPl1) among young and aged animals. This direct single neuron genomic analysis indicates that there are significant cell-specific changes in gene-expression profiles as a function of aging. We estimated that only ~10-20% of genes that are differently expressed in the aging brain are common for all neuronal types - the remaining 80% are neuron-specific (i.e. found in aging neurons of one but not another type). The list of “common aging genes” includes components of insulin growth factor pathways, cell bioenergetics, telomerase-associated proteins, antioxidant enzymes, water channels and estrogen receptors. The rest were neuron-specific gene products (including apoptosis-related proteins, Alzheimer-related genes, growth factors and their receptors, ionic channels, transcription factors and more than 120 identified proteins known to be involved in neurodevelopment and synaptogenesis). Surprisingly, even two different identified cholinergic motoneurons age differently  and each of them has a unique subset of genes differentially expressed in older animals.
Fourth, we showed that the activity of the entire genome and associated epigenomic modifications (e.g. DNA methylation, histone dynamics) can be efficiently monitored within a single Aplysia neuron and can be modified as a function of aging in a neuron-specific manner including selective histones and histone-modifying enzymes and DNA methylation-related enzymes.
This genome-wide analysis of aging allows us to propose novel mechanisms of active DNA demethylation and cell-specific methylation as well as regional relocation of RNAs as three key processes underlying age-related memory loss. These mechanisms tune the dynamics of long-term chromatin remodeling, control weakening and the loss of synaptic connections in aging. At the same time, our genomic tests revealed evolutionarily conserved gene clusters in the Aplysia genome associated with senescence and regeneration (e.g. apoptosis- and redox- dependent processes, insulin signaling, etc.).

overall_design: This is a reference design experiment with all samples being compared to one CNS from Aplysia. Two cholinergic neurons (R2 and LPl1), two ages (young and old), two arrays (AAA and DAA), three biological replicates each sample type. Two direct comparison experiments were also performed. One with young and old abdominal ganglion and the other with young and old R2.

first: Leonid

middle: L

last: Moroz


title: Response of bovine mammary tissue to experimental Staphylococcus aureus infection experiment 3.

city: St Lucia

first: Ylva

last: Strandberg-Lutzow

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

institute: CSIRO

summary:
Mastitis in dairy cattle can result from infection by a range of microorganisms but is principally caused by coliform bacteria and gram positive bacteria such as Staphylococcus aureus (S. aureus). The former species are often acquired by environmental contamination while S. aureus is particularly problematic due to its resistance to antibiotic treatments and ability to reside within mammary tissue in a chronic, subclinical state. The transcriptional and translational responses within bovine mammary epithelial tissue subjected to intramammary challenge with S. aureus are poorly characterised, particularly at the earliest stages of infection. A Bovine Innate Immune Microarray was employed to measure changes in gene expression occurring in bovine mammary tissues sampled from three dairy cows after a brief and graded intramammary challenge with a virulent strain of S. aureus.
Keywords: dose response, disease state analysis

overall_design: Animal infected with vaying doses of S. aureus in different udder locations were compared to a single control uninfected tissue and to the other 2 locations at each infective dose. Dye swaps were performed for each comparison.

last: Strandberg Lutzow

first: Laurelea

last: Donaldson

first: Christian

last: Gray

first: Tony

last: Vuocolo

first: Roger

last: Pearson

first: Antonio

last: Reverter

first: Keren

last: Byrne

first: Paul

last: Sheehy

first: Ross

last: Tellam


title: Response of bovine mammary tissue to experimental Staphylococcus aureus infection experiment 1.

overall_design: Animal infected with varying doses of S. aureus in different udder locations were compared to a single control uninfected tissue and to the other 2 locations at each infective dose. Dye swaps were performed for each comparison.


title: MSCs rescue lethally irradiated mice by differentiation-independent mechanisms

status: Public on May 18 2010

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

summary:
Overall survival after irradiation was compared between HSC after single transplantation of MSC.
Transplanted MSC did not differentiate into HSC, but salvaged endogeneous hematopoiesis.

overall_design: BM, HSC and MSC were isolated from bone marrow 7 months after transplantation with MSCs.

first: Katharina

last: Eggert

first: Bärbel

last: Brunswig-Spickenheier

first: Heike

last: Cappallo-Obermann

first: Cornelia

last: Rudolph

first: Axel

last: Zander

first: Ursula

last: Gehling

first: Claudia

last: Lange


title: Transcriptional profiling of Sarcophaga crassipalpis pupal diapause

city: Gainesville

first: Greg

last: Ragland

department: Entomology and Nematology

summary: Gene expression microarray exprement comparing differential expression between: 1) Early Diapause (ED), 2) Late Diapause (LD), 3) Non-Diapause (ND), 4) Hexane-induced diapause break (HEX).

overall_design: Four phenotypes (ED,ND,LD,HEX), four replicate pools of four individuals (four individuals in each replicate) in each phenotype, four competitve hybs comparing each phenotype to every other phenotype.

first: Gregory

middle: J

first: David

last: Denlinger

first: Daniel

last: Hahn


title: Structural and molecular basis of the role of starch and sucrose in Streptococcus mutans biofilms development

city: Rochester

first: Marlise

last: Klein

address: 601 Elmwood Ave.

department: Dentistry - Center for Oral Biology

institute: University of Rochester

summary: Transcriptional profiling to investigate the response of Streptococcus mutans biofilms to starch and sucrose.

overall_design: RNA was extracted and purified from four replicate samples of each biofilm sample of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.

first: Hyun

last: Koo


title: The response of Mycobacterium tuberculosis to reactive oxygen and nitrogen species

first: Martin

last: Voskuil

summary: The bacteriostatic and bactericidal effects and the corresponding expression profiles of Mycobacterium tuberculosis to representative oxidative and nitrosative stresses were investigated by growth and survival studies and whole genome expression analysis.  The response of M. tuberculosis to a range of hydrogen peroxide (H2O2) concentrations tended to fall into three distinct categories: (1) low level exposure resulted in induction of few H2O2 sensitive genes, (2) intermediate exposure resulted in massive transcriptional changes without an effect on growth or survival, and (3) high exposure resulted in a muted transcriptional response and eventual death. Nitric oxide (NO) exposure initiated much of the same transcriptional response as H2O2. However, unlike H2O2 exposure, NO exposure affected a dose-dependent bacteriostatic activity without killing and induction of dormancy-related genes. Included in the shared response to H2O2 and NO was the induction of genes encoding oxidative stress detoxification and iron-sulfur cluster repair functions. Expression of several key oxidative stress defense genes was constitutive, or increased moderately from an already elevated level, suggesting bacilli that are continually primed for oxidative stress defense. Deletion of the known oxidative stress responsive regulator, FurA, resulted in the constitutive expression of furA, katG, and Rv1907c; while other genes do not appear to be solely controlled by FurA. In contrast to Escherichia coli, M. tuberculosis appears highly resistant to DNA damage-dependent killing caused by low mill molar levels of H2O2. Furthermore, instead of limiting access to iron to prevent hydroxyl radical formation from H2O2 and thus DNA damage, M. tuberculosis induced iron uptake genes in response to H2O2 and NO.

overall_design:
Set of arrays that are part of repeated experiments
Compound Based Treatment: H2O2 or DETA/NO treatment

first: Kevin

last: Visconti


title: Characterization of the NifA-RpoN Regulon in Rhizobium etli CFN42 in symbiosis using whole genome transcript analysis

status: Public on May 15 2010

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

institute: Universidad Nacional Autonoma de México

summary: The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alpha-proteobacteria. Based on the complete Rhizobium etli genome sequence, we constructed the R. etli CFN42 oligonucleotide (70 mer) microarray, and utilized this tool to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain in symbiosis with Phaseolus vulgaris. As expected, the genes associated with a NifA and RpoN binding sites were downregulated in the NifA mutant strain.

overall_design: Three independent biological materials with one dyeswap were performed.

first: Emmanuel

last: Salazar

first: Javier

last: Díaz-Mejía

first: Gabriel

last: Moreno-Hagelsieb

last: Martínez-Batallar

first: Yolanda

last: Mora

first: Jaime

middle: M

last: Encarnacion


title: Pro-inflammatory rat macrophage mediators

city: Solna

first: Alan

last: Gillett

address: CMM L8:04

country: Sweden

institute: Karolinska Institutet

summary:
DA and congenic R11 macrophages were stimulated with zymosan for 1 or 24 hours and pro-inflammatory mediators measured at mRNA level
R11 macrophages had reduced pro-inflammatory mediators after stimulation

overall_design: TaqMan Low Density Array with 48 selected targets. 3 House-keeping-genes (18S, GAPDH and HPRT) included

first: Maja

last: Jagodic


title: Toxicogenomic response of Rhodospirillum rubrum S1H to the model micropollutant triclosan

status: Public on May 19 2010

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: Aiming at the development of a micropollutant biosensor in the frame of the Micro-Ecological Life Support System Alternative (MELiSSA), a pilot study was initiated to identify triclosan (TCS)-responsive biomarker genes in the MELiSSA carbon-mineralizing microorganism, Rhodospirillum rubrum S1H. TCS is a biocide, commonly found in human excrements and is considered an emerging pollutant in wastewater and the environment. Chronic exposure to MELiSSA-relevant concentrations (≥25 µg L-1) TCS caused a significant extension of the lag phase without affecting the growth rate. Analytical determination gave no indication of TCS biodegradation during the growth experiment and flow cytometric viability analyses revealed that TCS is only slightly toxic to R. rubrum. Through microarray analyses, the genetic mechanisms supporting the reversibility of TCS-induced inhibition were scrutinized. Hence, an extremely TCS-responsive cluster of four small adjacent genes was revealed, with up to 34-fold induction at 25 µg L-1. These four genes, for which the name micropollutant-upregulated factor (muf) was proposed; appear to be unique to R. rubrum and are shown for the first time to be involved in the response to stress. Moreover, numerous other systems that are associated with the proton-motive force were shown to be responsive to TCS, but never as highly upregulated as the muf genes. Hence, R. rubrum induced the phage shock protein operon (pspABC), numerous major facilitator efflux systems, cell envelope consolidation mechanisms, oxidative stress response, beta-oxidation, and carbonic anhydrase; while downregulating bacterial conjugation- and carboxysome synthesis genes. The muf genes and three efflux-related genes showed most potential as low-dose biomarkers.

overall_design: The two microarray experiments (10 and 25 µg l-1 Triclosan) were all performed in biological triplicate and containing three (in-slide) technical repeats. For all conditions, the Triclosan exposed sample (Cy5) was compared with the non-exposed solvent control (Cy3) to identify those genes that were differentially expressed upon Triclosan exposure.

first: Benny

last: Pycke

first: Guido

last: Vanermen

first: Pieter

last: Monsieurs

first: Heleen

last: De Wever

first: Max

last: Mergeay

first: Willy

last: Verstraete

first: Natalie

last: Leys


title: Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with 2,4-dichlorophenoxyacetic acid (2,4-D)

first: Carmen

last: Bianco

overall_design: Two-conditions experiment: untreated 1021 vs. 2,4-D-treated 1021 cells. Biological replicates: 6 untreated controls, 6 treated samples, independently grown and harvested. One replicate per array.


title: Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Nimblegen)

status: Public on May 16 2010

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

type: Genome binding/occupancy profiling by genome tiling array

summary: In higher eukaryotes, histone methylation is involved in the maintenance of cellular identity during somatic development. During spermatogenesis, most nucleosomes are replaced by protamines. Therefore, it is unclear if histone modifications function in paternal transmission of epigenetic information. Here we show that active H3K4 di-methylation (H3K4me2) and repressive H3K27 tri-methylation (H3K27me3), two modifications important for Trithorax and Polycomb-mediated gene regulation, are present in chromatin of human spermatozoa and show methylation-specific distributions at regulatory regions. H3K4me2-marked promoters control gene functions in spermatogenesis and cellular homeostasis suggesting that this mark reflects germline transcription. In contrast, H3K27me3 marks promoters of key developmental regulators in sperm as in soma.  Many H3K27me3-marked genes are never expressed in the male and female germline, and in early “totipotent” embryos, suggesting a function for Polycomb in repressing somatic determinants across generations. Targets of H3K4me2 and H3K27me3 are also modified in mouse spermatozoa, implicating an evolutionary conserved role for histone methylation in chromatin inheritance via the male germline.

overall_design: Chromatin immuno precipitation (ChIP) was performed on sperm samples obtained from 9 normospermic donors. DNA associated with H3K4me2 or H3K27me3 was precipitated using specific antibodies. Input and precipitated DNA were amplified and hybridized to a tiling microarray (NimbleGen Systems Inc.) representing 18029 promoter regions (2200bp upstream to 500bp downstream of transcription start sites) of all RefSeq annotated human genes. For each modification 3 independent ChIP experiments were performed of which one was hybridized in a dye swap configuration.

first: Urszula

last: Brykczynska

first: Mizue

last: Hisano

first: Liliana

last: Ramos

first: Edward

last: Oakeley

first: Tim

last: Roloff

first: Dirk

last: Schübeler

first: Michael

last: Stadler

middle: H


title: Expression data of Streptococcus pneumoniae against penicillin

status: Public on May 13 2010

city: WP

first: cheng foh

last: le

address: jalan universiti

department: Medical Microbiology

country: Malaysia

institute: University Malaya

summary:
The increasing rate of penicillin resistance in S. pneumoniae in the early 1970s has resulted in therapeutic challenges and has prompted the need for alternative therapy in the management of pneumococcal infections. The development of penicillin resistance has been documented to be as a result of altered penicillin binding protein which alters the binding capacity of the drug to the organism.
We used microarrays to investigate other genes  which may be involved in the development of penicillin resistance in S. pneumoniae and identified classes of genes on the surface of the organism which may contribute to resistance.

overall_design: Strains of S. pneumoniae with varying initial susceptibility to penicillin were selected. These strains were grown to the logarithmic phase before being exposed to subinhibitory concentration of penicillin. RNA was extracted before and after penicillin stress and hybridized on Affymetrix microarrays and represented as either Untreated (before penicillin stress) or treated (after penicillin stress). This was carried out for 3 representative strains; S676, I81, and R98. S, I, and R abbreviates Sensitive, Intermediate and resistant to Penicillin.

first: Navindra-Kumari

last: Palanisamy

first: Soon-Sen

last: Leow

first: Cheng-Foh

last: Le

first: Mohd-Yasim

last: Yusof

first: Shamala-Devi

last: Sekaran


title: Profile of macrophages in human abdominal aortic aneurysms: a transcriptomic, proteomic and antibody protein array study

status: Public on May 12 2010

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary: Abdominal aortic aneurysms (AAA), are defined by an increased aortic diameter and characterized by impairment of the extracellular matrix, macrophages infiltration and decreased density of smooth muscle cells. Our aim is to identify the key molecules involved in the pathogenesis of AAAs. This study investigated transcriptomic and proteomic profiles of macrophages from AAA patients (> 50 mm aortic diameter) and peripheral arterial occlusion (PAO) patients without AAA detected, who both needed a surgery.

overall_design: Transcriptomic profiling data presented here.  We tested mRNA from macrophages of 4 different AAA patients and 4 different PAO (peripheral arterial occlusion) samples. RNA sample from each AAA and PAO patients were compared each other.

first: Florence

last: Pinet

first: Emilie

last: Dubois

first: Philippe

last: Ratajczak


title: Mesenchymal stem cell labelings with ferritin

status: Public on May 17 2010

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary:
Mesenchymal stem cells (MSC) omplexed to different transfection agents (R60, R200, DOSPER, jetPei, Pulsin). Two MSC populations (h21 and h24)
and two passages (P2 and P4) were tested with different labelings. In a direct design experiment each sample was compared to its unlabeled control sample.
Keywords: Human gene expression study

overall_design: Reference design with unlabeled cells in the Cy3 reference channel, and labeled cells in the Cy5 channel.

first: Derek

last: Zieker

first: Katharina

last: Buck

first: Richard

last: Schäfer

first: Rainer

last: Kehlbach


title: Response of bovine mammary tissue to experimental Staphylococcus aureus infection experiment 2.

first: Ylva

last: Strandberg-Lutzow

middle: C

last: Strandberg Lutzow

first: Laurelea

last: Donaldson

first: Christian

middle: P

last: Gray

first: Tony

last: Vuocolo

first: Roger

middle: D

last: Pearson

first: Antonio

last: Reverter

first: Keren

last: Byrne

first: Paul

last: Sheehy

first: Ross

last: Tellam


title: Over-expression of ODDSOC2 in Golden Promise

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Comparison of wild type barley plants versus plants over-expressing ODDSOC2; a vernalization responsive MADS box gene   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Aaron Greenup.  The equivalent experiment is BB93 at PLEXdb.]

overall_design: genotype: Wild-Type(3-replications);  genotype: Over-expression(3-replications)

first: Aaron

last: Greenup


title: Characterization of the NifA-RpoN Regulon in Rhizobium etli CFN42 in Free Life using whole genome transcript analysis

status: Public on May 10 2010

first: Sergio

last: Encarnación

summary: DNA microarray technology was used to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain under microaerobic (free living) conditions. As expected, several genes associated with a NifA binding site were downregulated in the NifA mutant strain.

first: Emmanuel

last: Salazar

first: Javier

last: Díaz-Mejía

first: Gabriel

last: Moreno-Hagelsieb

last: Martínez-Batallar

first: Yolanda

last: Mora

first: Jaime


title: DNA methylation in progenitor cells: MeDIP study

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Methylation profiling by genome tiling array

summary: We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence.

overall_design: DNA was isolated from MSCs isolated from various tissues and from differentiated cells, immunoprecipitated using antibodies to 5-methylcytosine, and co-hybridized onto Nimblegen promoter arrays together with input DNA.

first: Andrew

last: Reiner


title: Age-related retinal degeneration study in mice

city: Ann Arbor

first: Jun

last: Li

state: MI

address: 5789A Medical Science II, Box 5618

institute: University of Michigan

summary:
The first goal of the study was to find the genes that explain the difference in progression of age-related retinal degeneration (ageRD) between the inbred strains C57BL/6J-c2J (B6a) and BALB/cByJ (C). The specific goal was to find the candidate genes that explain the chromosome 6 and chromosome 10 quantitative trait loci (QTL) found in a previous study.  Genes differentially expressed in retina between both strains and that map to the QTL are candidate genes.
By integrating different approaches: microarray study, knowledge-based candidate gene search and screening of genetic variants, we found 35 candidate genes for chromosome 6 QTL and 14 candidate genes for chromosome 10 QTL. Five genes for each QTL were selected for sequencing and qPCR analysis. One gene, Tnfaip3 was selected for phenotypic testing and was excluded as the quantitative trait gene for chr10 QTL.
The second goal of the study was to find biological processes and pathways associated with ageRD by Gene Ontology analysis of the microarray data. We concentrated on GO terms overrepresented in either strain at 8 months; the age when there is a difference in the phenotype (outer nuclear layer thickness). The GO analysis revealed that transcripts associated with inflammation, mitochondrial envelope, DNA repairing and oxidative stress were increased in the ageRD sensitive C strain with age (8 months). In the ageRD resistant B6a strain transcripts associated with antioxidant response, regulation of blood vessel size and growth factor activity were increased with age. Transcripts associated with cell remodeling and lipid metabolism were increased in either strain with age.
This study aims to identify gene expression differences in posterior eyecups between the strains C and B6a at 4 months and at 8 months. Twelve animals were used per strain and time point for a total of 48 mice. Total RNA for 3 animals (6 eyes) were pooled giving a total of 4 biological replicates per strain and time point.
The 4-month C samples labeled with Cy5 were hybridized with the 4-month B6a samples labeled with Cy3 (4 biological replicates); the 8-month C samples labeled with Cy5 were hybridized with the 8-month B6a samples labeled with Cy3, for 8 arrays (4 biological replicates).  A second set of eight arrays were used to analyzed the same RNA samples but with the dye orientation reversed, yielding a total of 16 arrays in the experiment.

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

first: Mitra

last: Alizadeh


title: Expression profiling of genes responding to flurbiprofen enantiomers in HaCaT cells

status: Public on May 09 2010

city: Adelaide

first: Benjamin

last: Lewis

address: Frome Road

department: Sansom Institute

institute: University of South Australia

summary:
Previous work from our laboratory has identified R-flurbiprofen as a candidate chemopreventive agent for skin cancer. Despite our findings, and the investigation of R-flurbiprofen as a chemopreventive for prostate and colon cancer by other groups, the mechanism of action remains unclear. To gain mechanistic insight into these anti-proliferative effects, we carried out microarray analysis of HaCaT cells in response to both R-flurbiprofen and S-flurbiprofen treatment. This analysis shows that both R-flurbiprofen and S-flurbiprofen produced significant changes in gene expression compared to untreated control, however, no significant differences were identified between effects induced by the individual enantiomers. Many of the genes found to be altered compared to control are implicated in cellular growth, apoptosis and metastasis, a selection of which are discussed. The altered expression of these genes may contribute to the anti-proliferative effects of R-flurbiprofen and S-flurbiprofen.

Keywords: oligonucleotide array, HaCaT, flurbiprofen, NSAID

overall_design:
The study was designed as a triangular comparison, where RNA samples from both R-flurbiprofen and S-flurbiprofen treated cells would be compared to samples from untreated control cells to identify genes which were altered by the drugs. Additionally, direct comparison between samples from R-flurbiprofen treated cells and S-flurbiprofen treated cells would be carried out to facilitate identification of genes with different regulation between the two enantiomers.

The Compugen 19k Human Oligo array was used to carry out this expression profiling. Array printing, sample labelling, hybridisation and data analysis were carried out by Adelaide Microarray Centre, where the Spot software package was used for data extraction and analysis. 3 arrays were used to compare R-flurbiprofen extracts to untreated controls, while 2 arrays each were used for comparison of S-flurbiprofen to control, and R-flurbiprofen to S-flurbiprofen.

first: Tamara

middle: A

last: Crittenden

first: Peter

last: Wigley

first: Allan

last: Evans

last: McKinnon


title: Gene Expression Profiling of C. elegans - ets-4 Mutant Animals Vs Wild-type

city: Salt Lake City

first: Bargavi

last: Thyagarajan

state: UT

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: The gene expression profile of WT (N2) C. elegans were compared to that of ets-4(ok165) and ets-4(uz1) mutant animals

overall_design: Total RNA was extracted from L4 larval stage WT, ets-4(ok165) and ets-4(uz1) worms and used to detect the differences in gene expression profiles of ets-4 mutant animals from WT


title: The actin-related protein Arp6 contributes to chromatin anchoring independently of its nucleosome remodeling activity

status: Public on May 11 2010

city: Sendai, Aoba-ku

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1

country: Japan

institute: Tohoku University

summary:
The SWR1 chromatin remodeling complex, which contains Arp6 and Swr1 as components, exchanges H2A in nucleosomes with its variant H2AZ. We have investigated the chromosome-wide dynamic distribution of Arp6 and Swr1 in budding yeast cells by chromatin immunoprecipitation analysis using a high-density genome tiling array. We found that the majority of Arp6 colocalizes with Swr1 on chromosomes and is enriched in the promoters of divergently promoters. This shows that Arp6 binds chromatin as a component of the SWR1 complex and is involved in transcriptional regulation in these regions. On the other hand, in some chromosomal regions, including telomere, centromere and ribosomal protein genes, the binding of Arp6 did not coincide with that of Swr1, and was remained in the absence of Swr1. This shows that a portion of Arp6 binds to chromosomes in Swr1-independent manner. These observations suggest that Arp6 has Swr1-dependent and –independent functions on chromosomes.
Keywords: ChIP-chip

overall_design:
･ The goal of the experiment.
Genome-wide localization of Arp6, Swr1 in Wt and Arp6 in swr1 deleted cells on chromosomes in Saccharomyces cerevisiae
･Key word
Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI), Arp6, Swr1
･Experimental factor
Distribution of Arp6 and Swr1in WT cells in random culture.
Distribution of Arp6 in swr1 delta cells in random culture.
･ Experimental design
ChIP analyses: W303 background cells expressing FLAG tagged protein were used for the ChIP using anti-FLAG M2 antibody.
ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI ) was used.

first: Takahito

last: Yoshida

first: Kenji

last: Shimada

first: Kazuto

last: Kugo

first: Kunihiro

last: Ohta

first: Hitoshi

last: Iwahashi

first: Angela

last: Taddei

first: Fabien

last: Cubizolles

first: Haico

last: Van Attikum

first: Susan

last: Gasser

first: Masahiko

last: Harata


title: Estrogen-driven Prolactin-mediated Gene Expression Networks Hormone Induced Prostatic Dysplasia

city: RTP

first: Johannes

last: Freudenberg

state: NC

address: 111 TW Alexander Dr

department: Biostatistics Branch

institute: NIEHS

summary: Emerging evidence suggests that estrogen and prolactin (PRL) play a key role in prostate cancer development, yet their relationship and molecular actions in prostate is not well understood. To address this issue, we made the first direct comparison of estrogen and PRL actions in the Noble rat (NBL) prostate dysplasia model.

overall_design: Prostatic dysplasia in lateral prostate (DLP) has been induced by elevated circulating levels of estrogen and PRL in NBL with estrogen (E2)-filled implants, while physiological level of testosterone (T) was maintained with T-filled implants. The effect of estrogen and PRL was studied by using ICI and bromocriptine (Br) as their respective blockers, both can effectively inhibited dysplasia development under T+E2 induction. Transcript expression profile of the four treatment groups (Control, T+E2, T+E2+Br, and T+E2+ICI) has been characterized in this array.

first: Neville

last: Tam

first: Carol

middle: Y

last: Szeto

first: Amy

middle: N

last: Fullenkamp

first: Mario

last: Medvedovic

first: Shuk-Mei

last: Ho


title: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis: mid versus late spermatogenesis

status: Public on May 07 2010

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

summary: The Senegalese sole (Solea senegalensis) is a marine flatfish of high economic value and a target species for aquaculture. Here, we used a transcriptomic approach to investigate changes in genes expressed in the Senegalese sole testis throughout spermatogenesis in wild-caught fish adapted to captivity. We identified approximately 400 genes that are differentially expressed during the progression of spermatogenesis and that participate in processes such as activation of the ubiquitin-proteasome system, sperm maturation and motility, cell adhesion or cytoskeletal remodeling. The results from this study contribute to our understanding of the molecular changes ocurring during spermatogenesis in the Senegalese sole.

overall_design:
This study represents spermatogenesis in Solea senegalensis: mid versus late spermatogenesis.

Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC.

first: Ignasi

last: Forné

first: Barbara

last: Castellana

first: Rubén

last: Marín-Juez

first: Joan

last: Cerdà

first: Joaquin

last: Abián


title: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis: functional mature versus late spermatogenesis

overall_design:
This study represents spermatogenesis in Solea senegalensis: functional mature versus late spermatogenesis.

Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC.


title: Global profiling of gene expression during glycerol-induced spore formation in Myxococcus xanthus

status: Public on May 06 2010

city: Marburg

first: Penelope

last: Higgs

address: Karl-von-Frisch-Str.

department: Ecophysiology

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

summary:
Myxococcus xanthus is a gram negative rod-shaped delta proteobacterium that differentiates into environmentally resistant spores in response to starvation.  Little is known about the sporulation mechanism in part because sporulation occurs in a subpopulation of cells undergoing a lenghtly complex multicellular developmental program. This developmental program requires a solid surface, motility, a minimum population density and a sophisticated network of inter and intra-cellular signals which direct some cells first to aggregate into multicellular fruiting bodies and then to sporulate exclusively within these fruiting bodies. However, it has previously been demonstrated that synchronous conversion of vegetative cells into myxospores can also be triggered in nutrient-rich liquid medium by addition of glycerol to 0.5 M. Here, we took advantage of the glycerol-induced sporulation process to gain information about the core M. xanthus sprorulation mechanism. We determined changes in the global gene expression at 0.5, 1, 2, and 4 hours after glycerol induction compared to vegetative cells (wild-type DK1622). The expression of nearly 1,500 genes was found to be significantly altered at least two-fold within four hours of glycerol-induced development. Most of the known core sporulation marker genes were up-regulated, whereas most genes required for proper aggregation and fruiting body formation were not significantly regulated.

Keywords: Time course of glycerol-induced (0.5 M final conc.) development with 4 time points referenced to vegetative cells

overall_design: 3 biological replicates each; normalized ratios to vegetative cells of  DK1622 (wt) Cy3

first: Frank

last: Müller

middle: I