title: The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability

status: Public on Dec 31 2013

first: Benjamin

middle: M.

last: Nitsche

address: Sylviusweg 72

department: Institute of Biology

summary: The Tup1-Cyc8 (Ssn6) complex is a well characterized and conserved general transcriptional repressor complex in eukaryotic cells. Here, we report the identification of the Tup1 (TupA) homolog in the filamentous fungus Aspergillus niger in a genetic screen for mutants with a constitutive expression of the agsA gene. The agsA gene encodes a putative alpha-glucan synthase, which is induced in response to cell wall stress in A niger. Apart from the constitutive expression of agsA, the selected mutant was also found to produce an unknown pigment at high temperatures. Complementation analysis with a genomic library showed that the tupA gene could complement the phenotypes of the mutant. Screening of a collection of 240 mutants with constitutive expression of agsA identified sixteen additional pigment-secreting mutants, which were all mutated in the tupA gene. The phenotypes of the tupA mutants were very similar to the phenotypes of a tupA deletion strain. Further analysis of the tupA-17 mutant and the ΔtupA mutant revealed that TupA is also required for normal growth and morphogenesis. The production of the pigment at 37ºC is nitrogen source-dependent and repressed by ammonium. Genome-wide expression analysis of the tupA mutant during exponential growth revealed derepression of a large group of diverse genes, including genes related to development and cell wall biosynthesis, and also protease-encoding genes that are normally repressed by ammonium. Comparison of the transcriptome of up-regulated genes in the tupA mutant showed limited overlap with the transcriptome of caspofungin-induced cell wall stress-related genes, suggesting that TupA is not a general suppressor of cell wall stress-induced genes. We propose that TupA is an important repressor of genes related to development and nitrogen metabolism.

overall_design: This data set consists of 4 microarrays (biological duplictates) corresponding to the following two experimental conditions: Aspergillus niger wild-type strain N402 and Aspergillus niger UV-mutant RD15.8#36 (TupA mutant) were cultivated under controlled conditions in 5L bioreactors in ammonium-based minimal medium (pH3) with glucose as the sole growth-limiting nutrient. Mycelium for RNA extraction was harvested after approximately 75% of the carbon source was consumed.

first: Doreen

last: Schachtschabel

first: Mark

last: Arentshorst

first: Sam

last: Morris

first: KristianF

last: Nielsen

first: Cees

last: van den Hondel

first: Frans

last: Klis

first: Arthur

middle: F

last: Ram


title: Effect of Etanercept on Active Pulmonary Tuberculosis in Rabbits

status: Public on Jan 28 2014

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

country: USA

institute: PHRI, NJMS, Rutgers the State University of NJ

summary:
Treatment of chronic inflammatory diseases with tumor necrosis factor alpha antagonists has been associated with increased risk of tuberculosis (TB). We examined the usefulness of the rabbit model of active pulmonary TB for studying the impact of the human immune modulatory reagent etanercept on the host immune response. Control of Mycobacterium tuberculosis (Mtb) infection, disease pathology and the global transcriptional response in Mtb-infected lungs of rabbits were studied.  Etanercept treatment exacerbated disease pathology and reduced bacillary control in the lungs, compared to infected untreated animals.
The microarray experiments involves comparison of changes in gene expression between Mtb-HN878 infected and Etanercept treated and untreated rabbit lungs at 4 and 8 weeks post-treatment, starting at 4 weeks post-infection.

overall_design: New Zealand White rabbits were infected with Mtb HN878 at about 3.2log10 (on day 0).  One group of rabbits were treated with Etanercept, starting at 4 weeks post-infection, for 4 or 8 weeks.  Total RNA from lung tissues of treated and untreated animals were isolated at 4 and 8 weeks post treatment and used for microarray gene expression analysis.

first: Gilla

last: Kaplan


title: Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits

status: Public on Aug 17 2013

summary:
In our rabbit model of pulmonary tuberculosis, infection with Mtb HN878, a hyper-virulent W-Beijing strain, results in progressive cavitary disease.  However, infection of rabbit lungs with Mtb CDC1551, a hyper-immunogenic strain is effectively controlled overtime, establishing latent Mtb infection.  Using these two Mtb strains, we tested the hypothesis that the initial host response in the lungs within hours of infection determines later outcome.
The microarray experiments was performed to identify gene expression changes in the Mtb-HN878 or CDC1551- infected rabbit lungs at 3 hours post infection, compared to uninfected naïve rabbit lungs.

overall_design: New Zealand White rabbits were infected with Mtb HN878 or CDC1551 at ~3.5log10.   At 3 hours post infection, lung tissue from Mtb-infected and uninfected rabbits were isolated and used for total RNA extraction. Total rabbit lung RNA was used for microarray analysis to determine infection induced changes in host gene expression.


title: De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish (array)

status: Public on Oct 01 2013

city: Shanghai

first: Guang

last: Li

address: 320 Yueyang Lu

country: China

institute: PICB

summary:
Cell cycle and metabolism are two major outputs controlled by circadian rhythm in many organisms. Here we show that the three processes were linked through inosine 5'-phosphate dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis. We using adult zebrafish as a model system,we applied a genome-wide transcriptome approach that allowed us to investigate circadian gene expression. The whole-genome transcriptome profiles of adult brain in time-series were assayed on Agilent zebrafish microarrays. We used a similar statistical method to identify zebrafish circadian genes (ZCOG) as our previous study in larval zebrafish. Three isoforms of impdh show strong circadian oscillations in different tissues of zebrafish. impdh1a contributes to the ocular development and pigment synthesis, impdh2 promotes and impdh1b delays the development.
By limiting the GTP required by DNA synthesis, impdh2 contributes to the daily rhythm of S phase in cell cycle. Multiple enzymes in the de novo purine synthesis pathway show the same circadian oscillations with peaks similar to impdh2. The circadian expression of this pathway is conserved in mouse liver. In summary, we show that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is critical for gating cell cycle in circadian rhythm.

overall_design: Adult zebrafish were sacrificed and dissected at 4h intervals starting at CT0 in both LD and DD conditions for 12 time points. Total RNA of individual zebrafish brain was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction. Microarrays were manufactured by Agilent Technologies (Agilent Technologies, Palo Alto, CA), containing 43,603 probes for zebrafish whole-genome transcriptional profiling.

first: Y

first: G

first: J

last: Du

last: Yan


title: Transcription profile of dormant and germinating Aspergillus niger conidia

status: Public on May 01 2013

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Biology

country: United Kingdom

institute: Nottingham University

summary:
Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes.
The transcriptome of dormant conidia was shown to be highly differentiated from that of germinating conidia and major changes in response to environmental shift occurred within the first hour of germination. The breaking of dormancy was associated with increased transcript levels of genes involved in the biosynthesis of proteins, RNA turnover and respiratory metabolism. Increased transcript levels of genes involved in metabolism of nitrate and proline at the onset of germination implies their use as sources of nitrogen. Dormant conidia contained transcripts of genes involved in fermentation, gluconeogenesis and the glyoxylate cycle. The presence of such transcripts in dormant conidia may indicate the generation of energy from non-carbohydrate substrates during starvation-induced conidiation or for maintenance purposes during dormancy. The immediate onset of metabolism of internal storage compounds after the onset of germination, and the presence of transcripts of relevant genes, suggest that conidia are primed for the onset of germination.

overall_design: one biological replicate for each sample, each sample contained pooled RNA from three independent replicates

first: Michaela

last: Novodvorska

first: Kimran

last: Hayer

first: Steven

middle: T

last: Pullan

first: Raymond

last: Wilson

first: Martin

middle: J

last: Blythe

first: Hein

last: Stam

first: Malcolm

last: Stratford

middle: B


title: Expression data from GGF2-treated post-MI swine

status: Public on Jun 21 2014

city: Nashvile

first: Cristi

middle: Lara

last: Galindo

state: Tennessee

address: 2220 Pierce Avenue, Room 359 PRB

department: Cardiovascular Medicine

institute: Vanderbilt University Medical Center

summary:
Neuregulin-1 (NRG-1) is a paracrine factor critical for cardiac development.  We have been examining whether the recombinant NRG-1β isoform known as glial growth factor 2 (GGF2) has therapeutic potential for heart failure. In both small and large animals after experimental myocardial infarction (MI) we have found that GGF2 treatment improves myocardial function and limits progressive myocardial remodeling.  To understand potential mechanisms for this effect, we compared gene expression in swine by microarray analysis.
We used microarrays to compared th the global gene expression underlying the efficacy of GGF2 treatment for heart injury.

overall_design: Left ventricular tissue remote from the site of infarct was collected from each of 8 animals (3 untreated controls, 3 low dose GGF2-treated and 2 high dose GGF2-treated) and processed for gene expression microarray analysis using Affymetrix porcine genome GeneChips.

first: Douglas

last: Sawyer

middle: L


title: Effects of methylmercury on genome-wide gene expression in the liver of Atlantic cod (Gadus morhua)

status: Public on Jan 22 2013

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

summary:
Methylmercury (MeHg) is a highly toxic environmental pollutant. To understand the mechanisms of toxicity of the compound and possibly to discover new biomarkers for environmental monitoring, we have conducted toxicogenomics studies.
We designed 126k-cod-oligonucleotide arrays and performed genome-wide gene expression assays in liver samples from juvenile cod treated with MeHg (0.5 and 2 mg/kg body weight). Microarray analysis showed MeHg differentially regulated hundreds of genes. Gene Ontology and pathway analyses of differentially regulated genes revealed that MeHg modulated mainly genes involved in immune response, oxidative stress response, tissue remodelling, and energy pathways such as lipid, carbohydrate and amino acid metabolism. The results provide insights into the mechanisms of toxicity of MeHg and provide candidate biomarkers of exposure to MeHg for further evaluation.

overall_design: Analyzed 5 samples from each of 3 groups: control, 0.5 mg/BW MeHg treated, and 2 mg/BW MeHg treated. Liver total RNA was reverse transcribed, Cy3-labeled, and hybridized (one-color hybridzation).

first: Odd-Andre

last: Karlsen

first: Karin

last: Berg

first: Anders

last: Lanzén

first: Pål

last: Puntervoll

last: Olsvik

first: Christer

last: Hogstrand

last: Goksøyr


title: Transcriptome analysis of Arthrobacter in the phyllosphere

status: Public on Jun 21 2013

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.

overall_design: We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.

first: Tanja

middle: R

last: Scheublin

middle: K

first: Jan

last: van der Meer

first: Johan

middle: H

last: Leveau


title: Direct comparison of effects of slow-freezing and vitrification procedures on rabbit late blastocyst transcriptome

status: Public on Sep 19 2013

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

summary: Nowadays there is a need to improve cryopreservation protocols in both human assisted reproduction and domestic animal field. We wanted to compare the transcriptomic changes induced by two commonly used cryopreservation procedures (slow freezing and vitrification) on rabbit late blastocyst before the onset of implantation. We recovered rabbit morulae at day 3 of development, freezing or vitrified and transferred them into recipient maternal tracts till day 6 of development. In this way, we wanted to analyse if different cryopreservation techniques produce different effects on gene expression that embryos are unable to get over after three days of in vivo development.

overall_design: After artificially insemination morulae were recovered at day 3 of development, frozen or vitrified, and then transferred to recipient does. To assess gene expression differences between frozen and vitrified the recipients were slaughtered three days after the transfer, at day 6.

first: M

middle: D

first: J

middle: S

last: Vicente

first: F

last: Marco-Jimenez


title: Interleukin 1 receptor regulates miRNA-135b expression in a negative feedback mechanism during cigarette smoke-induced inflammation

status: Public on Jan 31 2013

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada

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

overall_design: Refer to individual Series


title: The transcriptomic signature of RacA activation and inactivation provides new insights into the morphogenetic network of Aspergillus niger

status: Public on Aug 25 2013

city: Leiden

first: Benjamin

last: Nitsche

state: The Netherlands

country: Netherlands

institute: Leiden University

summary: RacA is the main Rho GTPase in Aspergillus niger regulating polarity maintenance via controlling actin dynamics. We have previously shown that both deletion and dominant activation of RacA (RacG18V) provoke an actin localization defect and thereby loss of polarized tip extension. This loss of apical dominance results in frequent dichotomous branching in the racA deletion strain and an apolar growing phenotype for RacG18V. In the current study we investigated the transcriptomics and physiological consequences of these morphological changes and compared the data with our previously established morphogenetic network model for the dichotomous branching mutant ramosa-1. This integrated approach revealed that polar tip growth is most likely orchestrated by the concerted activities of phospholipid signaling, sphingolipid signaling, TORC2 signaling, calcium signaling and CWI signaling pathways. The transcriptomic signatures and the reconstructed network model for all three morphology mutants imply that these pathways become integrated to bring about different physiological adaptations including changes in sterol, zinc and amino acid metabolism and changes in ion transport and protein trafficking. We furthermore followed that fate of exocytotic (SncA) and endocytotic (AbpA, SlaB) markers in the dichotomous branching racA deletion mutant, and provide data demonstrating that hyperbranching does not per se result in increased protein secretion.

overall_design: This data set consists of 14 samples in total and covers the genome-wide transcriptional responses of Aspergillus niger towards deletion of racA and expression of a dominant active racA allele (G18V). The genome-wide transcriptional effect of deleting racA was monitored by comparison with the A. niger wild type. For both, the racA deletion mutant and the wild type, samples consist of biological triplicates (6 in total). The genome-wide transcriptional effect of expressing the dominant active racA mutant allele was monitored by sampling 2 and 4 hours after induction with maltose. For comparison, the racA wild type allele was induced and expressed similarly and samples were taken at corresponding time points. The experimental setup for the dominant active racA expression consisted of biological triplicates (8 in total).

first: Min

last: Kwon

middle: M

first: Mark

last: Arentshorst

first: Thomas

last: Jørgensen

first: Arthur

last: Ram

first: Vera

last: Meyer


title: The galactose regulator GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger.

status: Public on Sep 20 2012

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

summary: Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger,  it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger .

overall_design: We aim to discover differentially expressed genes in A.niger wild type strain N402 and ΔgalX mutant while growing on galactose as carbon source. Biological duplicates were made for both strains. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.

first: Birgit

last: Gruben

first: Miaomiao

first: Ronald

middle: P

last: de Vries


title: Polyol stress: time course

status: Public on May 31 2014

city: Gothenburg

first: Abraham

last: Ericsson

address: Medicinaregatan 9C

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

summary: It is unclear how the amount of active nuclear MAPK over time quantitatively affects transcription. Here, we seek to address this issue by studying signal transduction and transcriptional response in a system that separates signalling from adaptation and hence signal strength from signal duration. The system is based on Saccharomyces cerevisiae osmoadaptation and allows modulation of the period of HOG-dependent responses without changing the initial stress intensity. The conditional osmotic stress system includes (i) a yeast mutant (gpd1 gpd2) unable to produce its main osmolyte glycerol, subsequently stressed with (ii) a stress inductor (polyols of different sizes) and allowed to adapt by (iii) expression of polyol flux-mediating aquaglyceroporin (rat AQP9). As there is no endogenous glycerol production, the osmoadaptation rate depends only on the size dependent equilibration rate over the plasma membrane of the polyol used as both stress inductor and compatible solute. Hence, we apply initially identical stresses but with differential durations, and determine the global transcriptional response.

overall_design: Saccharomyces cerevisiae W303-1A (MATa leu2-3/112 ura3-1 trp1-1 his3-11/15 gpd1::TRP1  gpd2::URA3)  osmotically stressed with 1M of glycerol, erythritol, xylitol or sorbitol. Samples are taken in triplicates (except for sorbitol 20 an 90 min and 20 min xylitol were duplicates were taken) in time course series after stress application. Total of 45 samples. RNA from from cultures of gpd1 gpd2 cells expressing rAQP9 prior to polyol exposure was used as reference RNA for all microarrays.

first: Cecilia

last: Geijer

first: Dagmara

last: Medrala-Klein

first: Elzbieta

last: Petelenz-Kurdziel

first: Maria

last: Smedh

first: Marcus

last: Krantz

first: Mattias

last: Goksör

first: Bodil

last: Nordlander

first: Stefan

last: Hohmann


title: Maternal slimming reprograms metabolic gene expression in mice offspring (NimbleGen expression)

status: Public on Aug 30 2012

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Slimming is globally prevalent especially in young women, and it may contribute to the metabolic health of their offspring. Whereas some Lamarckian ideas about environmental inheritance have been dismissed, increasing evidence suggest that certain acquired traits can be transmitted to the next generation. It is therefore of great interest to determine how and to what extent a maternal lifestyle change contributes to their offspring. Here we show that enriched environment (EE) induced maternal slimming improves general health and reprograms metabolic gene expression in mice offspring. EE in mothers induced decreased body weight, adiposity, and improved glucose tolerance and insulin sensitivity. Relative to controls, their offspring exhibited improved general health such as reduced fat accumulation, enhanced metabolic parameters as well as glucose tolerance and insulin sensitivity. Maternal slimming altered the expression of 1,732 genes in the liver of offspring, with coherent downregulation of genes involved in lipid and cholesterol biosynthesis. Epigenomic profiling in offspring revealed numerous changes in cytosine methylation depending on maternal slimming, including hypermethylation of several genes involved in lipid biosynthesis, correlated with the downregulation of these genes. Maternal slimming also altered overall transcriptome patterns in mature oocytes, which contributes largely to the metabolic health and gene expression patterns in offspring. Overall, our studies suggest that maternal slimming have a beneficial role in regulating metabolic profiles in offspring, implying that it might be considered as a potential strategy to reverse the global prevalence of obesity and related metabolic syndromes.

overall_design: Female F0 founders were raised on a standard diet in a normal cage until 12 weeks of age, at which point they were placed into the enriched environmental cage or stayed in the normal cage (chosen at random) for 4 weeks. Males were always raised on a standard diet in the standard cage. At 16 weeks, female F0 founders were mated with males in standard conditions. After 1 or 2 days, males were removed, and pregnant females were left alone with a standard diet in the standard cage until their litters were 3 weeks of age. Note that we always used virgin males to avoid confounding effects brought about by the males. Moreover, males mated with two female groups did not differ in phenotypic data (body weight, adiposity, fasting blood glucose and insulin levels). At 3 weeks of age, partial offspring were sacrificed and the median lobe of liver was rapidly dissected out and flash-frozen in liquid N2, each from an independent mother. Samples from five control and four slimming offspring, each from different mothers, were chosen for microarray analysis.

first: Yanchang

last: Wei

first: Qing

middle: Y

last: Sun


title: Hematopoietic database: including HSCs, progenitors and effector cells

status: Public on Mar 03 2015

city: Be'er-Sheva

first: Roi

last: Gazit

address: POB 653

department: Shraga Segal dept of Microbiology Immunology and Genetics

country: Israel

institute: Ben-Gurion University of the Negev

type:
Expression profiling by array
Third-party reanalysis

summary:
Collection of adult mouse expression profiling covering main types of hematopoietic cells
Aiming to identify HSC-specific genes, we have compiled 131 affymetrix MG430 2.0 arrays and re-processed data of third-party that were curated and quality-assured. This collection was built to include numerous progenitors’ subpopulations and balanced representation of major myeloid- and lymphoid cells. Result provided validated identification of genes that are highly specific to HSCs within the hematopoietic system. This dataset also enable direct identification of specific-genes for the other cell types represented.

overall_design:
Gene expression profiling of covering major hematoppietic and immune cells in the C57Bl/6 mouse. This dataset include 131 arrays that include 34 distinct populations (some with both naïve and activated states). We have included many progenitors subtypes and kept a balance between the myeloid and the lymphoid branches of the hematopoietic system (while there is an access of published arrays on lymphoid subtypes).

The 131 Samples below are 131 third-party reanalyzed data from the following studies, available in the GEO database as;
GSE4142, GSE6506, GSE6681, GSE6875, GSE7302, GSE7764, GSE8407, GSE9717, GSE9810, GSE9954, GSE10246, GSE10627, GSE11110, GSE11982, GSE12001, GSE12075, GSE12581, GSE20244, GSE34723
All were compiled together and we have normalized them to obtain a balanced-representation.

*The complete dataset representing 131 third-party reanalyzed samples (re-processed using gcRMA), is linked below as a supplementary file.

first: Derrick

last: Rossi


title: Gene expression profiling in left cardiac ventricles of C57Bl/6J and C57Bl/6N male mice treated for 48 h with angiotensin II 500 ng/kg/min.

status: Public on Dec 12 2014

city: Montreal

first: Sophie

last: Cardin

state: Qc

address: 110, Pine west

department: Experimental medecine

institute: IRCM

summary: Analysis of angiotensin II effect on left ventricle at gene expression level. The hypothesis tested in the present study was that angiotensin II treatment may affect gene expression in left ventricle in a strain specific manner. Results provide important information about which genes respond to angiotensin II in C57Bl/6N male mice compared to their C57Bl/6J counterparts.

overall_design: Total RNA obtained from isolated left ventricles from C57Bl/6J and C57Bl/6N mice subjected to 48 hours of angiotensin II infusion, via osmotic mini-pumps (500ng/kg/h) implanted sub-cutaneously, compared to sham operated controls.

first: Marie-Pier

last: Scott-Boyer

first: Christian

last: Deschepper


title: Expression data from dormant and germinating conidia from Aspergillus niger.

status: Public on Mar 13 2012

first: Martin

middle: Richard

last: van Leeuwen

department: Applied and Industrial Mycology

institute: CBS-KNAW/Fungal Biodiversity Centre

summary: Conidia of Aspergillus niger are characterized by a dormant state and are moderate stress-resistant. Upon contact with a moist substrate, germination of conidia occurs by changing from a dormant stabilized state towards a growing vegetative cell. The RNA expression levels of dormant conidia and conidia that were in various stages of germination were studied. The RNA composition of dormant conidia was substantially different than all the subsequent stages of germination. This indicates that the distinct morphological changes that occur during germination are not correlated with the highest change in the transcriptome.

overall_design: Samples of germinating conidia of Aspergillus niger N402 were taken in triple at 0h (dormant), 2h, 4h, 6h and 8h after inoculation in CM.

first: Pauline

last: Krijgsheld

first: Robert

last: Bleichrodt

first: Hildegard

last: Menke

first: Hein

last: Stam

first: Jacques

last: Stark

first: Han

middle: A

last: Wösten

first: Jan

last: Dijksterhuis


title: Fission yeast Cdk7 controls gene expression through both its CAK and CTD kinase activities

status: Public on Feb 19 2012

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: Cyclin dependent kinases activation and RNA polymerase II transcription are linked by the Cdk7 kinase that phosphorylates Cdks as a trimeric CAK complex, and serine 5 within the PolII C-terminal domain (CTD) as TFIIH bound CAK. However, the physiological importance of integrating these processes is not understood. Beside the Cdk7 ortholog Mcs6, fission yeast possesses a second CAK, Csk1. Both enzymes were proposed to act redundantly to activate Cdc2. Using an improved analogue sensitive Mcs6-as kinase, we show that Csk1 is not a relevant CAK for Cdc2. Further analyses revealed that Csk1 lacks a 20 amino acid sequence required for its budding yeast counterpart, Cak1, to bind Cdc2. Transcriptome profiling of the Mcs6-as mutant in the presence or absence of the budding yeast Cak1 kinase, in order to uncouple the CTD kinase and CAK activities of Mcs6, revealed an unanticipated role of the CAK branch in the transcriptional control of the cluster of genes implicated in ribosome biogenesis and cell growth. The analysis of a Cdc2 CAK site mutant confirmed these data. Our data show that the Cdk7 kinase modulates transcription through both its well-described RNA Polymerase II CTD kinase activity, but also through the Cdc2 activating kinase activity.

overall_design: Total RNA was isolated from two biological replicates for all conditions, and each biological replicate was hybridized in duplicate on Agilent arrays (dye-swap).

first: Maxime

last: Devos

first: Elise

last: Mommaerts

first: Valerie

last: Migeot

last: van Bakel

first: Damien

last: Hermand


title: Expression data from Aspergillus niger comparing aerial structures with vegetative mycelium

status: Public on Feb 24 2012

first: R

address: Padualaan 8

institute: Utrecht University

summary:
A. niger undergoes dramatic changes during asexual development. We tried to identify the differences in RNA expression levels that are important for this development.
We used micro-arrays to determine which genes were up- or down-regulated in the aerial structures, the part of the colony that is formed during asexual development.

overall_design: A. niger was grown as a sandwiched culture (Wösten et al., 1991,Journal of General Microbiology 137: 2017–2023) in a 0.25 mm layer of 0.6 % agarose between two porous polycarbonate membranes (diameter 76 mm, pore size 0.1 µm; Profiltra; www.profiltra.nl). After six days of growth, the top membrane of the sandwich was replaced by a membrane with pores of 10 µm (Profiltra), allowing formation of aerial hyphae and conidiophores for 24 h. Vegetative mycelium and aerial structures of 7-day-old maltose-grown cultures of A. niger were harvested from 3 and 5 sandwiched colonies, respectively. The aerial structures were scraped from the top membrane of the sandwiched culture with a razor blade. From other colonies, vegetative mycelium was harvested by flipping over the top membrane and scraping it off with a razor blade.

first: Robert-Jan

first: M

last: Grijpstra


title: The carbon starvation response of Aspergillus niger during submerged cultivation

status: Public on Aug 13 2012

first: Benjamin

middle: M.

last: Nitsche

summary: Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential genes expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.

overall_design: for each post-exponential time point (Day1, Day3 and Day6 post-carbon depletion), biological duplicates were performed.

first: Thomas

last: Jørgensen

first: Michiel

last: Akeroyd

first: Vera

last: Meyer

first: Arthur

middle: F

last: Ram


title: Maternal slimming reprograms metabolic gene expression in mice offspring (NimbleGen methylation)

first: yanchang

last: wei

type: Methylation profiling by genome tiling array

overall_design: Female F0 founders were raised on a standard diet in a normal cage until 12 weeks of age, at which point they were placed into the enriched environmental cage or stayed in the normal cage (chosen at random) for 4 weeks. Males were always raised on a standard diet in the standard cage. At 16 weeks, female F0 founders were mated with males in standard conditions. After 1 or 2 days, males were removed, and pregnant females were left alone with a standard diet in the standard cage until their litters were 3 weeks of age. Note that we always used virgin males to avoid confounding effects brought about by the males. Moreover, males mated with two female groups did not differ in phenotypic data (body weight, adiposity, fasting blood glucose and insulin levels). At 3 weeks of age, partial offspring were sacrificed and the median lobe of liver was rapidly dissected out and flash-frozen in liquid N2, each from an independent mother. Samples from five control and four slimming offspring, each from different mothers, were used for DNA extraction. The samples of DNA from the control or slimming group were pooled, and the pools were used for microarray analysis.

first: Yanchang

last: Wei

first: Qing

last: Sun


title: Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger

status: Public on Aug 07 2012

summary:
Background: HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the present study, we replaced the endogenous hacA gene of an Aspergillus niger strain with a gene encoding a constitutively active form of the HacA transcription factor (HacACA). The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes.
Results: Transcription profiles for the wild-type strain (HacAWT) and the HacACA strain were obtained using Affymetrix GeneChip analysis of three replicate batch cultures of each strain. In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant. Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription. A remarkable transcriptional response in the HacACA strain was the down-regulation of the AmyR transcription factor and its target genes.
Conclusions: The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.

overall_design: The transcriptomic data set comprises 12 arrays representing independent triplicates for each of the following four conditions: HacAWT, HacAMT-T1, HacAMT-T2 and HacAMT-T3. Using the robust multi-array analysis (RMA) Bioconductor package, RMA expression values were computed from the perfect match probes only. Background correction, normalization and probe summarization steps were performed according to the default settings of the RMA package.

first: Neuza

last: Carvalho

first: Mark

last: Arentshorst

first: Cees

last: van den Hondel

first: David

last: Archer


title: The knockdown of maternal glucocorticoid receptor mRNA alters embryo development in zebrafish

status: Public on Nov 16 2011

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

country: Italy

institute: University of Padua

summary: In zebrafish, ovulated oocytes contain both cortisol deposited from the maternal circulation and maternal mRNA for the glucocorticoid receptor (gr mRNA), which is spread as granular structures throughout the central ooplasm. At the 1-cell stage (0.2 hpf), this transcript is relocated by streamers in the blastodisc area and equally partitioned among blastomeres. At 15 hpf, it is replaced by the zygotic transcript. Morpholino knockdown was applied to block translation (grATG1MO or MO2-nr3c1 and grATG2MO or MO3-nr3c1) of both maternal and zygotic gr transcripts, while a missplicing morpholino (grmismMO or MO4-nr3c1) was used to block post-transcriptionally the zygotic transcript alone. MO2-nr3c1 and MO3-nr3c1 (but not MO4-nr3c1) treatment produced craniofacial and caudal malformations in 1-dpf embryos and 5-dpf larvae, which were also affected by pericardial oedema, persistent yolk sac, reduced subintestinal veins, altered neurogenesis and uninflated swim bladder. Such effects were rescued with trout gr2 mRNA. Pangenomic microarray analysis revealed that 114 and 37 highly expressed transcripts were up- and down-regulated, respectively, by maternal GR protein deficiency in 5-hpf embryos. Similar alterations were found at 10 hpf. These effects were confirmed by real-time PCR of 2 up- (casp8, grp1 and igf2a) and 1 down-regulated transcripts (mcm6) evaluated at 4, 8 and 12 hpf. As the contents of transcripts were modified already at 4 hpf, it seems that the lack of GR affects both ways the molecular machinery for the degradation of maternal mRNAs. These results indicate that the maternal gr transcript participates in the maternal programming of zebrafish development.

overall_design: MO2-nr3c1 morphants were compared with MO2-nr3c1-5m morphants at 5 hpf and 10 hpf. MO2-nr3c1 morphants were compared with wild type (WT) at 5 hpf and 10 hpf.  MO2-nr3c1 is a morpholino selected to knockdown translation of gr mRNA. MO2-nr3c1-5m is a specific control morpholino.

first: Surachai

last: Pikulkaew

first: Benato

last: Francesca

first: Chiara

last: Zucal

first: Tatjana

last: Skobo

first: Lorenzo

last: Colombo

first: Luisa

last: Dalla Valle


title: Comparative transcriptomics of wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strains (UCD 543) of Nostoc punctiforme ATCC 29133

status: Public on Jan 01 2013

city: Davis

first: Douglas

last: Risser

state: California

address: One Shields Ave

department: Microbiology

institute: UC Davis

summary:
Change in gene expression for a wild-type (Nostoc punctiforme ATCC 29133) and hmpD-deletion strain (UCD 543) of Nostoc punctiforme ATCC 29133 over the time course of hormogonium  development
This study is further descirbed in Risser, D.D. and Meeks, J.C. 2013. Comparative transcriptomics with a motility deficient mutant leads to identification of a novel polysaccharide secretion system in Nostoc punctiforme. Molecular Microbiology

overall_design: Total RNA from 3 biological replicates at each time point from 0 to 24 hours after hormogonium induction was converted to cDNA, dye-labled and hybridized to nimblegen 12x135k array slides

first: John

middle: C

last: Meeks


title: Deep Sequencing Identifies IDH1 R132S Mutation in Adult Medulloblastoma (CGH)

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

summary:
Here we present the case of adult medulloblastoma with minimal chromosomal rearrangements.
Data presented here are aCGH analyses of two biopsies of adult patient with a medulloblastoma which was classified as a Shh subgroup.

overall_design:
Analyses were performed on 2 archival specimens of medulloblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital from 2007.
This Series represents the CGH part of the study.


title: PDE-4 inhibition alters gene expression and improves INH-mediated clearance of Mtb in rabbit lungs

status: Public on Mar 16 2011

city: Newark

first: Selvakumar

last: Subbian

address: 225 Warren Street

institute: Public Health Research Institute at UMDNJ

summary:
Tuberculosis kills nearly 2 million people through out the world, every year.  The outcome of M. tuberculosis infection is determined by the host and bacterial factors.  A strong host immune response controls the growth of the bacilli effectively.  However, in a host with suboptimal immune response, the bacilli grows and mounts disease.  Activation of immune response following M. tuberculosis infection affects the expression of many host genes that are involved in the production of immune system molecules such as cytokines, chemokines, surface receptors and transcriptional regulators that manifest in the change of subsequent cellular events, including chemotaxis and proliferation of effector cells. The infecting bacilli counteracts the bactericidal activities of the host immune cells, primarily by modifying their gene expression. However, the specific nature of the host-pathogen interactions and the outcome of Mtb infection are not fully understood.  Tumor necrosis factor-alpha (TNF-a), produced by the immune cells, is an important cytokine in protecting the host against Mtb infection. However, excessive TNF-a production leads to severe inflammation and host cell destruction. In fact, pharmacologic inhibition of TNF-a production has been considered as a therapeutic modality in inflammatory diseases.  Interestingly, inhibitors of host phosphodiesterase-4 (PDE4) have been shown to reduce TNF-a production and dampen inflammation without complete immune suppression of the host.  In this study, we have explored the use of one of the PDE4 inhibitors, CC-3052, as an adjunct immune modulatory drug, in combination with isoniazid (INH) treatment in rabbit pulmonary tuberculosis. We hypothesize that reducing TNF-a levels during Mtb infection would reduce the environmental pressure on the bacteria, rendering them more amenable to killing by INH.  Mtb infected rabbits were treated with CC-3052 or INH or both and the lung tissue were harvested after 4 and 8 weeks of treatment.  Lung bacterial load, histologic changes and host and bacterial gene expression were determined  for each timepoint and compared between various treatment groups. The results of our study provides data to support the idea that combining anti-TB drugs with an adjunctive immune modulator may enhance the efficacy of current TB therapy regimens and shorten the duration of treatment if applied appropriately to humans.
The microarray experiments involves 2 comparison groups. 1) Changes in rabbit gene expression between Mtb infected and uninfected animals; 2). Changes in rabbit gene expression between CC-3052 treated and untreated animals during Mtb infection at 4,8 and 12 weeks post infection.

overall_design:
New Zealand White rabbits were infected with Mtb HN878 at 3.2log10 (on day 0).   At 4 weeks post infection, one group of infected rabbits were treated with a phosphodiesterase-4 (PDE4) inhibitor, CC-3052, and the treatment was continued up to 12 weeks post infection. The compound was used at 25mg/kg body weight, dissolved in distilled water and administered through gavage five days a weeks. Lung tissue from Uninfected, Mtb-infected and Untreated or CC-3052 treated rabbits were isolated at Day0, 4,8 and 12 weeks post infection and used for total RNA extraction.
Only the 8 and 12 week timepoints correspond to the associated publication.

first: Gilla

last: Kaplan


title: Streptomyces griseus transcriptome analysis in delta sigD, encoding an ECF-sigma factor

status: Public on Feb 23 2011

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

country: Japan

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

summary: To identify genes regulated by SigD, transcriptome profiles between wild type strain and sigD mutant with pI486-sigD, in which sigD level is low compared to wild type strain, were analyzed.

overall_design: Analysis used wild type strain steady state RNA as control samples for comparison to the sigD mutant.

first: Akiyoshi

last: Higo

first: Hirochi

last: Ohtani


title: Transcriptome profiling of Pythium graminicola-inoculated rice roots.

status: Public on Oct 04 2011

city: Gent

last: De Vleesschauwer

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: Ghent University

summary: Contrary to the relative wealth of information regarding pathogen defense responses in aboveground plant parts, little is known about the mechanistic basis and regulation of plant immunity in root tissues. Aiming to further our fundamental understanding of root immune responses, we have investigated the interaction between rice and one of its major root pathogens, the oomycete Pythium graminicola. The specificic objectives of this study were twofold: i) to disentangle the molecular and genetic basis of the rice-Pythium interaction by comparing the transcriptome of rice roots at different times after inoculation with a highly virulent Pythium strains, and ii) to offer fundamental insights into the genetic architecture and regulation of rice disease resistance pathways operative in root tissue and to identify the molecular players controlling the possible nodes of convergence between these resistance conduits

overall_design: Comparison between P. graminicola- and mock-infected rice roots. Two treatments (infected and non-infected) x three timepoints (1, 2 and 4 days post inoculation) x three biological replicates

first: Monica

last: Höfte


title: ROR1 Is Expressed In Human Breast Cancer And Associated With Enhanced Tumor-cell Growth

status: Public on Feb 01 2012

city: La Jolla

first: suping

last: zhang

state: CA

address: 8955 health science Dr

department: Medical school

institute: UCSD

summary: Receptor-tyrosine-kinase-like orphan receptor 1 (ROR1) is expressed during embryogenesis and by certain leukemias, but not by tissues of healthy adults.  Here we show that the neoplastic cells of many human breast cancers express the ROR1 protein and high-level expression of ROR1 in breast adenocarcinoma was associated with aggressive disease.

overall_design: Total mRNA from Ct-shRNA MDA-MB-231 stable cell line and ROR1-shRNA MDA-MB-231 stable cell line were labeled with Cy5, hybridized to a human Oligo Microarray (Phalanx Human Whole Genome OneArrayTM, Phalanx Biotech) according to the manufacturer’s protocol.  Arrays in duplicates were then scanned using GenePix 4000B scanner (Molecular Devices) and the probe intensities were extracted and processed using the GenePix Pro 6.0 software (Molecular Devices).  After removing experimental control probes, the intensities of 30968 probes were quantile normalized to have similar distributions across all 4 arrays. The normalized intensity of probes derived from the same gene was collapsed into a single NCBI Entrez gene by the maximal value in each sample (mapping information is obtained from Phalanx’s probe annotation table). In total, 15598 genes were measured at transcription level.  Differential expression of genes was quantified using fold enrichment. Gene functional annotation regarding cell proliferation, cell apoptosis,  CREB signaling, breast cancer signature was downloaded from MSigDB database. Gene set enrichment analysis was described by Mootha.

first: Suping

last: Zhang

first: Liguang

last: Chen

first: Bing

last: Cui

first: Han-Yu

last: Chuang

first: Jianqiang

last: Yu

first: Jessica

last: Wang-Rodriguez

first: Li

last: Tang

first: George

first: Grzegorz

middle: W

last: Basak

first: Wendy

last: Frankel

first: Thomas

middle: J

last: Kipps


title: Kinetics of progressive pulmonary cavitary TB disease in rabbits

status: Public on Dec 07 2011

first: Selvakumar

last: Subbian

department: Medicine

summary:
Every year, tuberculosis kills nearly 1.8 million people through out the world.  Though  outcome of M. tuberculosis infection into active disease is determined by the host and bacterial factors, a strong host immune response controls the growth of the bacilli effectively.  However, in a host with suboptimal immune response, the bacilli grows and mounts active disease.  Activation of immune response following M. tuberculosis infection affects the expression of many host genes that are involved in the production of immune system molecules such as cytokines, chemokines, surface receptors and transcriptional regulators that manifest in the change of subsequent cellular events, including activation, maturation, chemotaxis and proliferation of effector cells. However, the specific nature of the host-pathogen interactions and the outcome of Mtb infection are not fully understood.   In this study, we have analysed the systematic changes in the global host gene expression profile in the lungs of Mtb infected rabbits at various stages of infection.  Mtb infected rabbit lung tissues were isolated at T=0,2, 4 and 16 weeks post-infection.  Lung bacterial load, histologic changes and host and bacterial gene expression were determined  for each timepoint and compared . Our data suggests a strong correlation between the significant changes in the global transcriptome of infected rabbits and the progression of Mtb infection into a chronic, cavitary TB disease.
The microarray experiments involves comparison of: 1) Changes in rabbit gene expression between Mtb-HN878 infected and uninfected animals at 2,4 and 16 weeks post infection.

overall_design: New Zealand White rabbits were infected with Mtb HN878 at 3.2log10 (on day 0).   Lung tissue from Mtb-infected rabbits were isolated at Day0, 2, 4 and 16 weeks post infection and used for total RNA extraction.

first: Gilla

last: Kaplan


title: Submerged differentiation of Aspergillus niger in carbon-limited cultures approaching zero specific growth rate

status: Public on Jul 07 2010

first: Benjamin

last: Nitsche

address: Sylviusweg 72

department: Institute of Biology

summary: This work presents an exploration of submerged differentiation of the ubiquitous saprophyte and industrially important fungus, Aspergillus niger, in response to a limited availability of a sole carbon and energy source, maltose. In aspergilli and other mold fungi, asexual reproduction through formation of elaborate conidiogenic structures normally requires an aerial interface. This requirement is bypassed in submerged culture in response to severe nutrient limitation. Continuous cultures with cell retention (retentostat cultures) were applied to generate a fundamental physiological state, where the specific growth rate approaches zero, as the density of the cell population adapts to the supply of the limiting energy source. Temporal differentiation of mycelium structure and commitment to asexual reproduction were major phenomena, apparent on biochemical, morphological, physiological, and transcriptomic level. The severe substrate limitation had a rapid negative impact on cytoplasmic processes, and promoted endo- and exogenous nutrient mobilization, and hyphal compartmentalisation. The first conidiogenic structures appeared after one day with little additional differentiation until Day 4 to 6, where a transition to full commitment to reproductive growth took place. Submerged conidiation in A. niger involved transcriptional regulation of homologs of the regulatory pathway, centered around the Bristle gene (brlA), and structural genes previously described in other aspergilli. Comparison of transcriptomes, revealed a number of co-regulated gene clusters, which appear to encode secondary metabolite biosynthetic potential. We discuss the concept of maintenance energy in the context of differentiation, a possible physiological trigger for sporulation and the special physiological adaptations of the starved mycelium. We also present a simple and efficient method for in situ retention of filamentous organisms.

overall_design: The dataset consists of 9 Affymetrix arrays derived from defined growth conditions of lab-scale bioreactor cultures (5L). Total RNA was extracted from biomass harvested at three different growth phases: exponential growth phase, 2 and 8 days of retentostat  cultivation. For each of the phases, the data is derived from three biological replicates.

last: Jørgensen

first: Gerda

middle: E

last: Lamers

first: Mark

last: Arentshorst

first: Cees

last: Hondel

first: Arthur

last: Ram


title: The transcriptional response of bioreactor-grown Aspergillus niger cultures towards three oils

status: Public on Sep 01 2009

city: Wageningen

first: Leo

last: De Graaff

address: Dreijenplein 10

institute: Wageningen University and Research Centre

summary:
The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, for which it is equipped with a range of enzyme systems. A significant proportion of plant material are lipids that might be available either as for energy storage or as membrane building blocks. With 63 potential lipase-encoding genes in its genome, A. niger has the tools to degrade these extracellular lipids. In contrast to polysaccharide-degrading enzyme networks not much is known about the signalling and regulatory processes that control lipase expression and activity in fungi both under laboratory and natural occurring conditions.
A pulse of 1 mM of various oils was applied to four bioreactor-grown A. niger cultures to examine (i) whether A. niger responds at the level of gene transcription, (ii) at what time point this effect is detected most accurately, and (iii) whether differences between the response towards oils are observed. The triglyceride olive oil induces genes encoding peroxins and enzymes of fatty acid metabolism. A complex oil mixture extracted from wheat gluten, which is enriched for digalactosyl-diglycerides, induces genes encoding peroxins as well as enzymes of fatty acid metabolism, but with different expression profile when compared to olive oil. Pure digalactosyldiglyceride, a proxy for plant membrane lipids, does not trigger a transcriptional response.

Keywords: time course; induction experiment

overall_design: In one week, 4 fermentor cultures were run in 2.2-liter batch fermentors in which A. niger was grown on 100 mM sorbitol. At 14 hours after oxygen supply had switched from headspace to sparger-inlet each fermentor was induced with 22 mL medium which contained 100 mM (final concentration in fermentor: 1 mM) of either olive oil, a complex oil mixture extracted from wheat gluten, pure wheat digalactosyldiglycerides, or was induced with a solution of minimal medium containing only 0.2% (in fermentor, final concentration 0.002%) triton X-100 which served as emulsifier agent. For each fermentor vessel, a sample of 10 mL was taken prior to induction (T=0), or 30 minutes, 1 hour, or 2 hours after induction. Every sample was hybridized onto a single microarray, yielding in total 16 DNA microarrays.

first: Douwe

last: van der Veen

first: Willy

last: Van den Berg


title: Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics

status: Public on Sep 17 2009

institute: Leiden University

summary: Reconstruction of signaling networks regulating fungal morphogenesis by the expression profiling of wild-type and the temperature sensitive morphological ramosa-1 mutant.

overall_design: Aspergillus niger wildtype versus Ramosa mutant for 1h at 37 under controlled growth condition in 5L bioreactor

first: Vera

last: Meyer

first: Simon

last: Flitter

first: MinJin

last: Kwon

first: Cristina

last: Reynaga-Pena

first: Salomon

last: Bartnicki-Garcia


title: Yeast response to the DNA damaging beta-lapachone

status: Public on Dec 31 2011

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: β-lapachone (b-lap) is an anticancer agent that selectively induces cell death in human cancer cells. A mechanism for b-lap cytotoxicity was shown to be mediated by the NQO1 NAD(P)H dehydrogenase and radical oxygen species (ROS) generation in several tumour cells.  To further characterise the molecular effects of b-lap action, we compared the gene expression profile of yeast cells treated or not with b-lap using cDNA microarrays. Genes involved in tolerance to oxidative stress were enriched in the set of differentially expressed genes.  Accordingly, b-lap treatment generated reactive oxygen species (ROS), which were efficiently blocked by dicoumarol, and inhibitor of NADH dehydrogenases (NADH-DH). In addition, a mutant defective in the mitocondrial NADH dehydrogenase Nde2p was found to be resistant to b-lap treatment, thus resembling tumour cell responses to b-lap exposure. However, b-lap treatment elicited similar ROS production in WT and nde2 cells, and dicoumarol did not affect cell viability in b-lap treated yeasts. Most interestingly, DNA damage responses triggered by b-lap were abolished in the nde2 mutant. Furthermore, the nde2 mutant was sensitive to DNA damaging agents other than b-lap. These data indicated that ROS production did not mediate b-lap cytotoxicity and highlighted a role of Nde2p in DNA damage checkpoints. Amino acid biosynthesis genes were also differentially expressed in b-lap treated cells, suggesting that b-lap exposure somehow triggered the General Control of Nutrients (GCN) pathway. Supporting this, b-lap treatment increased phosphorylation of eIF2 alpha in a Gcn2p-dependent manner. eIF2alpha phosphorylation required Gcn1p and Gcn20p and surprisingly Nde2p. Gcn2p was also shown to be required for the G1 checkpoint triggered by b-lap and for cell survival.  Remarkably, b-lap treatment also increased phosphorylation of eIF2 alpha in breast tumour cells, which was partially dependent on the Nde2p orthologue AMID. These findings i) suggest that Gcn2p and Nde2p are key determinants of b-lap toxicity in yeast and human cells, ii) uncover a new functional connection between Nde2p, Gcn2p and DNA damage checkpoints conserved throughout evolution and iii) suggest that pharmacological modulation of Gcn2p could provide an effective strategy for  antitumour drug discovery.

overall_design: Direct comparison between wt samples and b-lapachone treated-wt samples. Four biological replicates. Dye was swapped in two of them

first: Mauricio

last: Menacho-Marquez

first: Jorge

last: Perez-Valle

first: Joaquin

last: Ariño

middle: R

last: Murguia


title: Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis [methylation profiling]

status: Public on Jun 10 2011

city: Daejeon

first: Mirang

last: Kim

address: 52 Eoeun-dong

department: human genome center

country: South Korea

institute: KRIBB

summary: Hepatocytes that have differentiated from human embryonic stem cells have great potential for the treatment of liver disease as well as for drug testing. Moreover, in vitro hepatogenesis is a powerful model system for studying the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism that influences differential gene expression during embryonic development. We profiled gene expression and DNA methylation of three cell states of in vitro hepatogenesis—human embryonic stem cells, endoderm progenitors, and mature hepatocytes—using microarray analysis. Among 525 state-specific expressed genes, 67 showed significant negative correlation between gene expression and DNA methylation. State-specific expression and methylation of target genes were validated by quantitative reverse transcription–PCR and pyrosequencing, respectively. To elucidate genome-scale methylation changes beyond the promoter, we also performed high-throughput sequencing of methylated DNA captured by MBD2 protein [see SRA link below]. We found dynamic methylation changes in intergenic regions of the human genome during differentiation. Conclusion: This study provides valuable methylation markers for the lineage commitment of in vitro hepatogenesis and should help elucidate the molecular mechanisms underlying stem cell differentiation and liver development.

overall_design: ES, EP, and MH methylation assays were run in triplicate. Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research, Orange, CA), and 200 ng of the converted DNA was used for amplification. Amplified DNA was hybridized to the Infinium HumanMethylation27 BeadChip (Illumina), which analyzes the methylation status of 27,578 CpG sites selected from more than 14,495 well-annotated genes. The arrays were imaged using the BeadArray Reader, and image processing and extraction of intensity data were performed according to Illumina’s instructions. Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines).

first: Yong-Sung


title: A Metagenomics Analysis of Pandemic 2009 H1N1 Infection in Patients in North America

status: Public on Nov 01 2010

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic.

overall_design: We used metagenomics-based technologies (the Virochip microarray) and deep sequencing to analyze nasal swab samples from individuals with 2009 H1N1 infection. This Series includes the Virochip microarray data only.

first: Eunice

last: Chen


title: LNGFR- and Thy-1-based prospective isolation of human mesenchymal stem cells reveals functionally distinct subpopulations.

status: Public on Dec 22 2011

city: Tokyo

first: Yo

last: Mabuchi

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

type: Genome variation profiling by genome tiling array

summary: Human multipotent mesenchymal stem cells (MSCs), isolated based on their adherence to plastic, show poor growth and differentiation and frequently contain contaminating cells, which limits to clarify their own characteristics.  In this study, the identification of two cell surface markers, LNGFR and Thy-1, allowed the prospective isolation of highly purified clonogenic human MSCs.  Furthermore, single cell sorting assays followed by in vitro expansion revealed three distinct MSC subpopulations: rapidly-, moderately- and slowly proliferating MSC clones (RPCs, MPCs and SPCs, respectively).  While RPCs exhibited robust multilineage differentiation and self-renewal potency, MPCs and SPCs contained a majority of senescent cells and exhibited frequent genome errors.

overall_design:
Single cell sorting assays followed by in vitro expansion revealed three distinct MSC subpopulations: rapidly-, moderately- and slowly proliferating MSC clones (RPCs, MPCs and SPCs, respectively).
Sample: RPC, MPC and SPC (n=3).

first: Satoru

last: Morikawa

first: Seiko

last: Harada

first: Kunimichi

last: Niibe

first: Sadafumi

last: Suzuki

first: Francois

last: Renault-Mihara

first: Diarmaid

last: Houlihan

first: Hideyuki

last: Okano

first: Yumi

last: Matsuzaki


title: Light exposure of wild-type and kdmA deletion mutant

status: Public on Jul 31 2012

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: Transcriptional profiling of wild-type and kdmA deletion mutant in response to white light exposure, against a wild-type dark-incubated reference

overall_design: Two strains, two conditions. Two biological replicates were hybridised (as dye swaps) for each sample, with the exception of a single sample for the kdmA mutant in the dark (incidental to the main results of the study).

first: Alex

last: Andrianopoulos


title: Gene expression in Aspergillus nidulans at different developmental stages

status: Public on May 01 2008

city: Norwich

first: Andrew

last: Breakspear

address: Norwich Research Park

institute: John Innes Centre

summary:
Microarray analysis was used to compare different developmental stages of the filamentous fungus Aspergillus nidulans.  Cells were grown for various times and comparisons made between:
1. Isolated conidia (0 hours) and isotropically expanding cells (3 hours).
2. Isotropically expanding cells (3 hours) and polarly extending cells (5 hours).
3. Undifferentiated vegetative hyphae (18 hours) and synchronously conidiating cultures (42 hours).
Keywords: Developmental stage comparison

overall_design:
A total of 4 hybridizations were performed for each microarray experiment described in the summary.  The following replicates were carried out:
1. Two biological replicates were performed using cultures grown in parallel.
2. Two Technical ‘dye swap’ replicates were carried out for each biological replicate.

first: Michelle

last: Momany


title: Aspergillus niger exposed to combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH

status: Public on Apr 08 2010

city: Zeist

first: Machtelt

last: Braaksma

address: Utrechtseweg 48

institute: TNO

summary:
Microarray analysis of Aspergillus niger under conditions with differing combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH
Fermentor cultures were grown in minimal medium (MM) at a constant temperature of 30 ± 0.5 ºC and with differing combinations of carbon source (either 277.5 mM glucose or 333.0 mM xylose), nitrogen source (NH4Cl or NaNO3) and nitrogen concentration (4x: 282.4 mM; 8x: 564.8 mM), and pH (pH4 or pH5) of the medium (M. Braaksma, A.K. Smilde, M.J. van der Werf, P.J. Punt, submitted for publication). At different time points samples were collected, quenched immediately in methanol at -45 ºC and centrifuged at -20 ºC to remove supernatant. Part of the biomass was frozen into liquid nitrogen and stored at -80 ºC for microarray analysis.
For each of the 16 culture conditions one sample was selected for microarray analysis; samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion. In addition some technical duplicates were included.

overall_design: 20 samples were analyzed from 16 different fermentation conditions. The fermentation conditions were varied according to a full factorial design of four factors tested at two levels. From one fermentation two different time samples were analyzed, from another fermentation four samples, two technical replicates of two different time samples, were analyzed. Samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion.

first: Peter

last: Punt

first: Mariët

last: Van der Werf

first: Trifa

last: Omer


title: Hematopoietic stem cells treated with the Notch ligand Delta 4 HSC_notch_IGR

status: Public on Jun 29 2006

city: Villejuif

first: Cyril

last: Catelain

address: 39, rue Camille Desmoulins

country: France

institute: INSERM

summary:
The Notch pathway regulates cell-fate decisions in a wide variety of cell types, often inhibiting particular differentiation programs and permitting either self-renewal or differentiation along alternate pathways. Notch receptors and Notch ligands have been found on hematopoietic stem cells (HSC) or marrow stromal cells. In the present study, through a microarray approach, we analyzed the gene expression variations from cultured murine HSC with or without a Notch ligand Delta4 at 6 hours, 12 hours and 24 hours after the induction of the Notch pathway.
Keywords: time course

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
13 samples against a common reference.
two dye swap  for each condition.


title: Gene expression profiling in Daphnia magna, Part III: Uncovering Biomarkers for Metal and ORC exposures

status: Public on Oct 16 2008

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary:
To determine toxicant specific effects of Ordnance Related Compound (ORC) exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following different ORC exposures at the 1/10 LC50.  The gene expression profiles revealed toxicant specific gene expression profiles allowed for the identification of specific biomarkers of exposure.

Keywords: ecotoxicogenomic exposure study

overall_design: We exposed Daphnia magna the 1/10 LC50 of different Ordnance Related Compounds (Cu, Zn, Pb, WO4, RDX, TNT, 2-ADNT, 2-ADNT, TNB, DNB, 2,4-DNT,  and 2,6-DNT) for 24 hours. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total, except TNT and Cu).  All exposures were compared to a unexposed laboratory control (MHRW media).

first: Natalia

last: Garcia-Reyero

first: Alan

last: Kennedy

first: Xin

last: Guan

first: Lynn

middle: L

last: Escalon

first: Bonnie

last: Chang

first: Julia

last: Varshavsky

middle: V

last: Loguinov

first: Chris

last: Vulpe

first: Edward

last: Perkins


title: Gene expression in Entamoeba histolytica cysts and trophozoites

status: Public on Mar 01 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

summary:
We compared multiple strains of lab trophozoites to recent clinical isolates. Clinical isolates were grown in xenic media, and maintained many characteristics of the cyst stage of devlopment
Keywords: Stage conversion

overall_design: E. histolytica trophozoites of three different strains (HM1:IMSS, Rahman, and 200:NIH) and grown under multiple conditions (Long term axenic growth in TYI, Growth in low glucose media, Mouse adapted parasites and in vivo growth in a mouse model) were compared to recent clinical isolates that had grown in xenic culture for 1-8 weeks.

first: Rashidul

last: Haque

first: Jason

last: Hackney

first: Daniel

last: Eichinger

first: Upinder

last: Singh


title: Myxococcus xanthus cells: wild-type vs. EBP mutant gene expression during development

status: Public on Jan 28 2009

city: Syracuse

first: Anthony

last: Garza

address: 212 BRL,  130 College Place

institute: Syracuse University

summary: The mutants in our study carry an insertion in the nla4 (MXAN2516), nla6 (MXAN4042), nla18 (MXAN3692) or nla28 (MXAN1167) gene. (MXAN numbers are the conventional gene names; nlas are common names). Mutations in the nla genes produce strong defects in fruiting body development.  All four of the nla genes code for enhancer binding proteins (EBPs), which are transcriptional activators. In this study, we examined how the nla mutations alter gene expression patterns in developing cells.

overall_design: Two condition experiment, normal wild-type vs mutant

first: Nora

middle: B

last: Caberoy


title: Determination of variability of fermentor-grown Aspergillus niger

status: Public on Dec 31 2008

first: Leo

middle: H

last: De Graaff

summary:
Knowledge of the biological and technical variation for fermentor-grown Aspergillus niger cultures is needed to design DNA microarray experiments properly. We cultured A. niger in batch-operated fermentor vessels and induced with D-xylose. Transcript profiles were followed in detail by qPCR for 8 genes. A variance components analysis was performed on these data to determine the origin and magnitude of variation within each process step for this experiment.
6 Fermentor cultures were selected to determine technical and biological variation for all 14554 ORFs present on this array type.
Keywords: Validation of microarrays; variation analysis; experimental design

overall_design: For 5 weeks, 4 batch-fermentation per week were run in which A. niger was grown on 100 mM sorbitol. At 14 hours after oxygen supply had switched from headspace to sparger-inlet each fermentor was induced with either 0.1 mM D-xylose or 0.1 mM sorbitol. Samples were harvested just before induction and 1 hour after induction. Per week, 3 fermentors were induced with D-xylose and 1 fermentor was induced with sorbitol. Six samples were selected to be put on microarrays based on their biomass density, time distribution, magnitude of xylose-induced genes as measured by qPCR, fermentor vessel number.

first: Douwe

last: Van der Veen

first: Jose

middle: M

last: Oliveira

first: Willy

last: Van den Berg


title: Waldman Bladder tumors

status: Public on Jul 01 2005

first: Ekaterini

last: Blaveri

address: 2340 Sutter street

institute: UCSF Comprehensive Cancer Center

summary:
80 bladder tumors of different stages, grades and histologies
analyzed on costom made cDNA arrays with 10638 gene elements
Keywords: parallel sample


title: mRNA expression data from keratinocytes with disorganized lipid raft structures (by cholesterol depletion by methyl-beta-cyclodextrin)

status: Public on Apr 17 2010

city: Namur

first: conny

last: mathay

address: 61, rue de Bruxelles

institute: FUNDP

summary:
Lipid rafts are cholesterol-rich cell signaling platforms and their physiological role can be explored by cholesterol depletion. To dress a global picture of transcriptional changes ongoing after lipid raft disruption, we performed whole-genome expression profiling in epidermal keratinocytes, a cell type which synthesizes its cholesterol in situ.
We used microarrays to identify transcriptional changes in gene expression of cholesterol-depleted keratinocytes. Cholesterol depletion by methyl-beta-cyclodextrin disrupts the organization of lipid rafts, which are cholesterol- and sphingolipid-rich membrane microdomains.

overall_design: Transcript levels were measured in autocrine confluent cultures of normal human epidermal keratinocytes were either left untreated (Ctrl), cholesterol-depleted for 1h with 7.5mM methyl-beta-cyclodextrin (MBCD), or mock cholesterol-depleted for 1h with 7.5mM cholesterol-charged methyl-beta-cyclodextrin complexes (MBCD/chol) (Mock cholesterol depletion is a suppementary negative control as this treatment does not extract cholesterol from cell membranes). Samples are analysed either immediately after the treatment (R0h) or after recovery times of 1h (R1h) respectively 8h (R8h). in total 9 samples are analysed and no replicates are performed.

first: Conny

last: Mathay

first: Michael

last: Pierre

first: Mark

last: Pittelkow

first: Eric

last: Depiereux

first: Yves

last: Poumay


title: Revealing impaired pathways in regulatory mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.

status: Public on Feb 29 2012

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

institute: University of Verona

summary: Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida.

sample_organism:
Petunia x hybrida
Petunia axillaris
Petunia integrifolia subsp. inflata

overall_design:
The manuscript describes the creation by next generation sequencing of a large catalogue of the transcriptome of the two Petunia species, that are considered to represent the natural material from which the breeders selected their varieties.

This submission represents the transcriptome component of study. The high throughput sequencing data were submitted to SRA (accession numbers: SRA027293, SRP004866.1, SRX036999.2, SRX036998.2).

first: Nunzio

last: D’Agostino

first: Giovanni

last: Tornielli

first: Francesca

last: Quattrocchio

first: Maria

last: Chiusano

first: Ronald

last: Koes

first: Jan

last: Zethof

first: Flavia

last: Guzzo

first: Massimo

last: Delledonne

first: Luigi

last: Frusciante

first: Tom

last: Gerats

first: Mario

last: Pezzotti


title: Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome.

first: Gretchen

last: Ehrenkaufer

summary:
A genome-wide transcriptional analysis of Entamoeba histolytica was performed on trophozoites isolated from the colon of six infected mice and from in vitro culture.  Adaptation to the intestinal environment was accompanied by increases in a subset of cell signaling genes including transmembrane kinases, ras and rho family GTPases, and calcium binding proteins. Significant decreases in mRNA abundance for genes involved in glycolysis and concomitant increases in lipases were consistent with a change in energy metabolism. Defense against bacteria present in the intestine (but lacking from in vitro culture) was suggested by alterations in mRNA levels of genes similar to the AIG1 plant antibacterial proteins. Decreases in oxygen detoxification pathways were observed as expected in the anaerobic colonic lumen. Of the known virulence factors the most remarkable changes were a 20-35-fold increase in a cysteine proteinase four-like gene, and a 2-3-fold decrease in two members of the Gal/GalNAc lectin light subunit family. Control of the observed changes in mRNA abundance in the intestine might potentially rest with four related proteins with DNA binding domains that were down-regulated 6-16-fold in the intestinal environment. In conclusion, the first genome-wide analysis of the transcriptome of E. histolytica demonstrated that the vast majority of genes are transcribed in trophozoites, and that in the host intestine trophozoites altered the expression of mRNAs for genes implicated in metabolism, oxygen defense, cell signaling, virulence, antibacterial activity, and DNA binding.
Keywords: Transcritional response to in vivo growth

overall_design: An Affymetrix platform gene expression array was designed for this analysis that included probe sets for 9435 open reading frames (ORFs) and 9066 5' and 3' flanking regions. Transcripts were detected for > 80% of all ORFs. A total of 523 transcripts (5.2% of all E. histolytica genes) were significantly changed in amebae isolated from the intestine on Days 1 and 29 after infection: 326 and 109 solely on Days 1 and 29, and 88 on both days. Quantitative real-time reverse transcriptase PCR confirmed these changes in 11/12 genes tested using mRNA isolated from an additional six mice.

first: Carol

last: Gilchrist

last: Houpt

first: Nino

last: Trapaidze

first: Zhangjun

last: Fei

first: Amon

last: Asgharpour

first: Clive

last: Evans

first: Susan

last: Martino-Catt

first: Duza

last: Baba

first: Shinjiro

last: Hamano

first: Mami

last: Okada

first: Upinder

last: Singh

first: Tomoyoshi

last: Nozaki

first: Barbera

last: Mann

first: William

last: Petri


title: Genome-wide DNA methylation study in bladder cancer

status: Public on Feb 16 2012

city: ROTTERDAM

first: raju

last: kandimalla

address: DR molewaterplein 50

department: pathology

institute: erasmus mc

summary: Genome-wide DNA methylation profiles were determined on a set of fresh 44 bladder cancer tissues using normal blood as control. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Agilent Human CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of bladder cancer along with finding markers for progresssion and early diagnosis.

overall_design: 44 bladder cancer tissues were profiled against commercially available normal human genomic blood DNA (Promega, Madison, WI, USA) as a reference

first: Raju

last: Kandimalla

first: Angela

last: Van Tilborg

first: Ellen

last: Zwarthoff


title: profiling of midbrain from arthritic C57Bl/6 mice s.c. vs. control C57Bl/6 mice

status: Public on May 02 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Using microarrays we studied the gene expression profile of the midbrain in C57Bl/6 mice strain that developed collagen induced-arthritis vs control mice.
Keywords: gene expression profile of the midbrain in response to induction of arthritis.

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyze changes in gene expression profile in the midbrain of arthritic vs control mice. We performed 3 samples (biological replicates)

last: Alvarez

first: Cintia

middle: G

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando

last: Pitossi