title: Evaluating the restoration of DNA derived from archival formalin-fixed paraffin embedded tissues for genomic profiling by SNP-CGH analysis

status: Public on Jul 01 2013

city: Brisbane

first: Peter

last: Simpson

address: Royal Brisbane & Women's Hospital

department: UQ Centre for Clinical Research

institute: The University of Queensland

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin embedded (FFPE) tissue samples. Due to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromised, meaning obtaining informative data regarding epigenetic, genomic and expression alterations can be challenging. Here we have investigated the utility of repairing damaged DNA derived from FFPE tumours prior to single nucleotide polymorphism (SNP) arrays for whole genome DNA copy number analysis.

overall_design: To investigate whether repairing the DNA might improve performance in SNP array assay, we used the DNA Restore protocol from Illumina as a pre-treatment step prior to applying the DNA to the Infinium assay using the Human CytoSNP FFPE-12v2.1 arrays. DNA was extracted from FFPE samples spanning five decades involving tumor material obtained from surgical specimens and post-mortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR in predicting sample success and the effect of DNA restoration on assay performance, data quality and the prediction of copy number aberrations (CNAs). In total 8 cases were analysed in this experiment, involving 43 SNP arrays of tumour and matched normal DNA samples, replicates and other control arrays.

first: Abdel

last: Hosein

last: Song

first: Amy

last: McCart Reed

first: Janani

last: Jayanthan

first: Lynne

last: Reid

first: Jamie

middle: R

last: Kutasovic

first: Margaret

last: Cummings

first: Nic

last: Waddell

first: Sunil

last: Lakhani

first: Georgia

last: Chenevix-Trench


title: Host and pathogen interaction: time course

status: Public on Aug 26 2013

city: Hsin-chu

first: Yan-Yu

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: NTHU

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

sample_organism:
Candida albicans
Danio rerio

platform_organism:
Candida albicans
Danio rerio

overall_design: Refer to individual Series

first: Yung-Jen

last: Chuang

first: Chung-Yu

last: Lan

first: Bor-Sen

first: Wen-Ping

last: Hsieh

first: David

middle: S

last: Wong


title: Study of the differentially-expressed genes induced by the expession of two viral glycoproteins in muscle cells of adult zebrafish

status: Public on Aug 08 2013

city: Elche

first: Amparo

last: Estepa Perez

state: Alicante

address: Av. Ferrocarril s/n

department: Institute of Molecular and Cell Biology

country: Spain

institute: University Miguel Hernandez

summary: A genomic approach was used to indentify the differences in the gene expression profiles of adult zebrafish injected with different viral glycoproteins. This study intended to study the mechanisms of immunogenicity of each glycoprotein (gpG of VHSV and SVCV)

overall_design: Fish were injected with plasmids encoding the different glycoproteins and muscle samples at the site of injection were compared to control samples at three days post-immunisation.

first: A

last: Estepa


title: A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Dark Induced Senescence).

status: Public on Apr 23 2013

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

summary:
A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis.  ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes.
Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes.

overall_design: To assess mutant response to Dark Induced Senescence (DIS), leaf5 from transplanted rosettes, subjected to dark conditions, from Col-0, myb2 (genotype IM24) and myb108 (genotype BOS1) knockout plants, were photographically assessed for red/green ratio. When the average ratio for Col-0 samples was >0.8, leaf 5 for Col-0, myb2 and myb108 lines was harvested (4 biological replicates). The same sampling procedure was then performed on consecutive days to sample as senescence progressed. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).


title: A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Botrytis cinerea infection).

overall_design: To assess mutant response to Botrytis cinerea infection, Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10μl droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).

first: Richard

last: Hickman

first: Claire

last: Hill

first: Christopher

middle: A

last: Penfold

first: Emily

last: Breeze

first: Laura

last: Bowden

first: Peijun

last: Zhang

first: Alison

last: Jackson

first: Emma

last: Cooke

first: Findlay

last: Bewicke-Copley

middle: D

first: Andrew

last: Mead

first: Jim

last: Beynon

middle: L

last: Wild

first: Katherine

last: Denby

first: Sascha

last: Ott

first: Vicky

last: Buchanan-Wollaston


title: Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (gene expression)

status: Public on Apr 01 2013

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

institute: INIBIC

summary:
The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples.
A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array
This represents the gene expression component of the study only

overall_design: OA gene expression profiling was performed with Affymetrix Human Gene 1.1 st array was performed in and independent cohort of 23 OA patients

first: Francisco

middle: J

last: Blanco

first: Ignacio

last: Rego-Perez

last: Fernández-Tajes


title: A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (expression between lines at timepoints).

first: Jonathan

last: Moore

overall_design: Leaf 7 from the anac019 (genotype 9C11) and anac055 (genotype IM4) mutants and their WT controls, Col-5 and Col-0 respectively, was tagged with cotton 18 days after sowing (DAS) and harvested from five randomly selected plants (biological replicates), 8 h into the light period, at 23, 29, 31, 33 and 35 DAS (full senescence). Variance in expression between lines at timepoints was analysed using a local adaptation of the MAANOVA package as previously described (Breeze et al., Plant Cell 2011 Mar;23(3):873-94. PMID: 21447789) using a loop design including dye swaps.  Genotype DM (double mutant cross between IM4 and 9C11) was also included in the experiment, and was part of the loop design. Results for DM are included here in so far as they played a role in the ANOVA definition of values, but are not discussed in the paper.

first: Richard

last: Hickman

last: Hill

last: Penfold

first: David


title: Transcriptome during autoregulation of mycorrhization in soybean

status: Public on May 09 2013

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

summary: The autoregulation of mycorrhization (AOM) describes a plant regulatory mechanism that limits the number of infection events by arbuscular mycorrhizal fungi. The key signal mediator is a receptor kinase (GmNARK) that acts in the shoots. Early signals of the mycorrhizal symbiosis induce a root-derived signal that activates GmNARK in the shoot finally leading to a systemic repression of subsequent infections in the root. So far, less is known about the signals down-stream of GmNARK.  To find genes regulated by GmNARK in a mycorrhiza-dependent as well as in a mycorrhiza-independent manner, we used the Affymetrix GeneChip for soybean.    In general, mycorrhizal root systems consist of both colonized and non-colonized, but autoregulated roots. To physically separate those two root types for transcript analysis of specifically regulated genes, we used the split-root system.   Transcript profiling during AOM was done with material of Bragg wild-type and of the nark mutant nts1007, either non-inoculated or partially inoculated with the mycorrhizal fungus Rhizophagus irregularis (formerly Glomus intraradices). Wild-type and nark mutants were inoculated with R. irregularis on one half of the root-systems (root-parts "A") only. The remaining half of the root-systems stayed non-infected (root-parts "B"). Corresponding controls stayed completely non-infected. Gene expression was analyzed in inoculated root-parts, non-inoculated root-parts and shoots of three individual plants per treatment.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Sara Schaarschmidt.  The equivalent experiment is GM53 at PLEXdb.]

overall_design:
genotype: Bragg wt - inoculation: - - tissue type name: root-parts A&B(3-replications);
genotype: Bragg wt - inoculation: - - tissue type name: shoot(3-replications);
genotype: Bragg wt - inoculation: + - tissue type name: root-part A (myc)(3-replications);
genotype: Bragg wt - inoculation: + - tissue type name: root-part B (non-myc)(3-replications);
genotype: Bragg wt - inoculation: + - tissue type name: shoot(3-replications);
genotype: nts1007 - inoculation: - - tissue type name: root-parts A&B(3-replications);
genotype: nts1007 - inoculation: - - tissue type name: shoot(3-replications);
genotype: nts1007 - inoculation: + - tissue type name: root-part A (myc)(3-replications);
genotype: nts1007 - inoculation: + - tissue type name: root-part B (non-myc)(3-replications);
genotype: nts1007 - inoculation: + - tissue type name: shoot(3-replications)

first: Sara

last: Schaarschmidt

first: Florian

last: Wagner


title: Effects of maternal Cd on the female reproductive functions, gametes development and genes expression of zebrafish

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

country: Japan

institute: Acdemia Sinica

summary: The impacts of maternal Cd on zebrafish from female to embryo which included fecundity, gametes development, growth, other reproductive functions, and gene expression of 5hpf embryo were up and down regulated after female pretreated with Cd. The mating rate decreased by 30 %. It can be observed in growth delay during 6-somite stage. The ceratohyal head angle of larvae is widest upon 35.6 μM maternal Cd treatment and it was showed a dose response. Besides, pericardial edema occurred in some 96hpf larvae. There were showed 33 and 37 target genes appeared significantly down and up regulation after microarray assay, respectively. The major effect on gene up regulation was showed at the functional of transcription (occupied 18.9%) and down regulation at the functional of protein biosynthesis (occupied 33.3%). These results demonstrated that maternal Cd influenced the reproduction ability of female and causes development abnormal of embryo.

overall_design:
Sexually mature zebrafish (D. rerio) of both sexes, obtained from the Institute of Cellular and Organismic Biology, Academia Sinica (Taipei, Taiwan), were kept in an aquarium supplied with dechlorinated, circulated, aerated local tap water at 28 °C with a 14: 10-h light/dark cycle, and were fed Daphnia and shrimp. Fertilized eggs were incubated in “zebrafish solution“ (E3 solution) which contained 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, and 1 ppm methylene blue (pH 7.2). Developing embryos of 5 h post-fertilization (hpf) were collected for total RNA extraction, and process of microarray assay. The number of hatched zebrafish larvae at 48 and 72 hpf were recorded. The larvae of 72 hpf larvae were collected for cartilage stain in order to observe the development of pharyngeal arch.
Nguyen and Janssen (2001) reported that the LC50 at 96 h of Cd was 0.62~1.33 μM for 12-dpf stage zebrafish, and our previous study showed that the zebrafish embryo could induced physiological response with 0.89 μM Cd exposure (Wu et al., 2008). Hence, a 10× (8.9 μM)  , 20× (17.8 μM) and 40× (35.6 μM) dose of 0.89 μM was used in female zebrafish. The Cd medium was prepared using completely dried CdCl2 (Sigma, St. Louis, MO) dissolved in 1 mL concentrated HCl; double-deionized water was used to prepare the 10 mg/L Cd stock solution, which was then diluted with zebrafish solution before being used in the exposure experiments. During all experiments, the test containers were cleaned with HNO3 and thoroughly rinsed with double-deionized water before use.

first: Ming-Yi

first: Sumei

last: Wu


title: A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves


title: Expression data from HT-29, a human colonic epithelial cell line

status: Public on Mar 16 2013

city: Dhaka

first: Protim

last: Sarker

address: Mohakhali

country: Bangladesh

institute: icddr,b

summary: Gene(s) in epithelial cells can be upregulated or downregulated by different stimuli in a tissue-specific manner. We used genome-wide microarray analysis to profile the expression of genes in HT-29 cells that are upregulated after stimulation with sodium butyrate (NaB) and subsequently downregulated by the addition of ciprofloxacin antibiotic. The specific aim was to evaluate genes that are associated with mucosal immunity.

overall_design: HT-29 cells were stimulated with sodium butyrate (NaB) (n=3), NaB and ciprofloxacin (n=3) or culture media (unstimulated control, n=3) for 24 hours. RNA extracted from these cells were hybridized on Affymetrix microarrays.


title: Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colonocytes by selective PPARγ modulation

status: Public on Mar 11 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Angiopoietin-like protein 4 (ANGPTL4, also referred to as Fiaf) has been proposed as a circulating mediator between the gut microbiota and fat storage in adipose tissue. Very little is known about the mechanisms of regulation of ANGPTL4 in the colon. Here we show that transcription and subsequent secretion of ANGPTL4 in human T84 and HT-29 colonocytes is highly induced by physiological concentrations of products of bacterial fermentation, the short-chain fatty acids. Short-chain fatty acids induce ANGPTL4 by activating the nuclear receptor PPARγ, as shown by microarray, transactivation assays, coactivator peptide recruitment assay, and use of PPARγ antagonist. At concentrations required for PPARγ activation and ANGPTL4 induction in colonocytes, SCFA do not stimulate PPARγ in mouse 3T3-L1 and human SGBS adipocytes, suggesting that SCFA act as selective PPARγ modulators (SPPARM), which is supported by coactivator peptide recruitment assay and structural modelling. It can be concluded that 1) SCFA potently stimulate ANGPTL4 synthesis in human colonocytes, and 2) SCFA transactivate and bind to PPARγ by serving as selective PPAR modulators. Our data point to activation of PPARγ as a novel mechanism of gene regulation by SCFA in the colon.

overall_design: T84 human colonic carcinoma epithelial cells were treated with rosiglitazone (0.1 uM) or butyrate (1mM, 8mM) for 24hrs, whereafter gene expression was profiled.

first: Sheril

last: Alex

first: Katja

last: Lange

first: Tom

last: Amolo

first: Jeffrey

last: Grinstead

first: Ewa

last: Szalowska

first: Arjen

last: Koppen

first: Karin

last: Mudde

first: Danielle

last: Haenen

first: Sa'ad

last: Al-Lahham

first: Han

last: Roelofsen

first: René

last: Houtman

first: Bart

last: van den Burg

first: Alexandre

middle: M

last: Bonvin

first: Eric

last: Kalkhoven

first: Michael

last: Muller

first: Sander

last: Kersten


title: Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients

first: Juan

last: Fernandez Tajes

type:
Expression profiling by array
Methylation profiling by array


title: Estrogen receptor dynamics in diverse patient-derived luminal breast cancer xenografts

status: Public on Feb 24 2013

city: Aurora

first: peter

last: kabos

address: 12801 E. 17th Avenue

department: Medicine

institute: University of Colorado Denver

summary: Primary breast cancer xenografts

overall_design: Two primary xenografts with different treatments

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Transcriptional response of Streptococcus pneumoniae D39 to Cellobiose at time point T2

status: Public on Feb 20 2013

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium+ 0.5 % (w/v) Cellobiose (CM17) to grown in M17 medium + 0.5 % (w/v) Glucose (GM17) hervasted at time point T2.

overall_design: Two conditions design comparison of one strain including a dye swap.

first: Tomas

middle: G

last: Kloosterman

first: Oscar

middle: P

last: Kuipers


title: Impact of bguR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔbguR to D39 wild-type grown in M17 medium + 0.5% glucose (GM17).

overall_design: One condition design, comparison of two strains including a dye swap


title: Cellobiose-mediated gene expression in Streptococcus pneumoniae and the repressor function of the novel GntR-type regulator BguR

summary:
The human pathogen Streptococcus pneumoniae has the ability to use the carbon- and energy source cellobiose due to the presence of a cellobiose-utilizing gene cluster (cel locus) in its genome. This system is regulated by the cellobiose-dependent transcriptional activator CelR, which has been previously shown to contribute to pneumococcal virulence. To get a broader understanding of the response of S. pneumoniae to cellobiose, we compared the pneumococcal transcriptome during growth on glucose as the main carbon source to that with cellobiose as the main carbon source. The expression of various carbon metabolic genes was altered, including a PTS operon (which we here denote as the bgu operon) that has high similarity with the cel locus. In contrast to the cel locus, the bgu operon is conserved in all sequenced strains of S. pneumoniae, indicating an important physiological function in the lifestyle of pneumococci. We next characterized the transcriptional regulation of the bgu operon in more detail. Its expression was increased in the presence of cellobiose, and decreased in the presence of glucose. A novel GntR-type transcriptional regulator (which we here denote as BguR) was shown to act as a transcriptional repressor of the bgu operon and its repressive effect was relieved in the presence of cellobiose. BguR-dependent repression was demonstrated to be mediated by a 20-bp DNA operator site (5’-AAAAATGTCTAGACAAATTT-3’) present in PbguA as verified by promoter truncation experiments. In conclusion, we have identified a new cellobiose-responsive PTS operon, together with its transcriptional regulator in S. pneumoniae.

This SuperSeries is composed of the SubSeries listed below.


title: Transcriptional response of Streptococcus pneumoniae D39 to Cellobiose at time point T1

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium+ 0.5 % (w/v) Cellobiose (CM17) to grown in M17 medium + 0.5 % (w/v) Glucose (GM17) hervasted at time point T1.


title: Sediment Series Upper Danube River (Sediment Extract and Freeze-Dried)

status: Public on Dec 31 2012

city: Karlsruhe

first: Jens

middle: C

last: Otte

address: Postfach 3640

department: Institute of Toxicology and Genetics

country: Germany

institute: Karlsruhe Institute of Technology

summary: The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in freeze-dried whole sediment samples and their corresponding organic extracts in parallel. To this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerable extent be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Additionally, different gene expression was shown to be less influenced by the sampling site than by the method of exposure, which could be attributed to differential bioavailability of contaminants.

overall_design: Microarray analyses were performed with early life stages of zebrafish exposed to sediment extracts or freeze-dried sediment from three sampling sites (Ehingen, Lauchert, Sigmaringen) along the Upper part of the Danube River, Germany. The expression profiles were compared within the sampling sites, between the exposure scheme and to the expression pattern of model toxicants, such as 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, mechanism-specific bioassays and chemical analysis of the sediments have been combined and compared to the present gene expression data.

first: Kerstin

last: Bluhm

first: Lixin

last: Yang

first: Christian

last: Zinsmeister

first: Jessica

last: Legradi

first: Steffen

last: Keiter

first: Thomas

last: Kosmehl

last: Braunbeck

first: Uwe

last: Strähle

first: Henner

last: Hollert


title: Environmentally relevant concentrations of the flame retardant BDE-209 in sediment cause minimal effects on Zebrafish embryos.

status: Public on Jan 01 2013

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects.

overall_design: Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer. Total RNA was stored at -80oC until analyzed with oligonucleotide microarrays. Zebrafish 44,000 gene arrays (Agilent Single Color 19161, Platform number GPL6457) were purchased from Agilent (Sta. Clara, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations. Four controls and four treated samples were analyzed, each sample consisting of a pool of  embryos. One ug of total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA). An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA) was used to scan microarray images at 5 μm resolution.  Data were resolved from microarray images using Agilent Feature Extraction software and analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA).

first: Lynn

last: Escalon

first: Eva

last: Prats

first: Patrick

last: Babin

first: Edward

last: Perkins

first: Demetrio

last: Raldua


title: Human inflammatory dendritic cells induce Th17 differentiation

status: Public on Nov 01 2012

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

country: France

institute: Institut Curie

summary: Transcriptome analysis of five population of Antigen Presenting Cells: inflammatory macrophages, Inflammatory dendritic cells, Cd14+CD16- monocytes, CD14 dim Cd16+ monocytes and BDCA1+ Dendritic cells.

overall_design: We analyzed transcriptomic profiles from 5 differents DC populations: inflammatory DC  and macrophages form inflammatory ascites (ovarian cancer, 4 different donors); CD14+CD16- monocytes, CD14dim CD16+ monocytes and BDCA1+ DC (from 3 different healthy donors) using the Affymetrix Human Gene 1.1 ST platform.

first: Elodie

last: Segura

first: Armelle

last: Bohineust

first: Antonio

last: Cappucio

first: Anne

last: Hosmalin

first: Marc

last: Dalod

first: Vassili

last: Soumelis

first: Sebastian

last: Amigorena


title: Genome wide expression profiling during spinal cord regeneration identifies comprehensive cellular responses in zebrafish

status: Public on Dec 01 2012

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: Among the vertebrates, teleost and urodele amphibians are capable of regenerating their central nervous system. We have used crush injury method on zebrafish spinal cord, which is a common mammalian mode of injury in spinal cord. To identify the molecular mechanisms of the underlying cellular events during regeneration of zebrafish spinal cord, we have employed high density oligonucleotide microarrays and profiled the temporal transcriptome dynamics during the entire phenomenon. A total of 3842 genes expressed differentially with significant fold changes during spinal cord regeneration. Cluster analysis revealed event specific dynamic expression of genes related to inflammation, cell death, cell migration, cell proliferation, neurogenesis, neural patterning and axonal regrowth. We have also validated the expression pattern of 14 genes (which include inflammatory regulators, cell cycle regulators, pattern forming genes and signaling molecules) by different methodologies. Spatio-temporal analysis of STAT3 expression suggested its possible function in controlling inflammation and cell proliferation.  Genes involved in the proliferating neural progenitors and their dorso-ventral patterning (sox2 and dbx2) are differentially expressed. Injury induced cell proliferation is controlled by many cell cycle regulators and some of them also show their common expression in other regenerating systems like fin, heart and retina. We also reported unusual expression pattern of certain pathway genes like one carbon folate metabolism and N-glycan biosynthesis which have not been reported during regeneration of spinal cord. Genes like stat3, socs3, atf3, mmp9 and sox11, which are known to control peripheral nervous system (PNS) regeneration in mammals, are also upregulated in zebrafish spinal cord injury (SCI) thus creating PNS like environment after injury. Our study provides a comprehensive genetic blue print of diverse cellular response(s) during regeneration of zebrafish spinal cord that could be used to induce successful regeneration in mammals.

overall_design: The spinal cord has been injured by crushing dorso-ventrally for 1 sec with a number 5 Dumont forceps at the level of 15th/16th vertebrae. Later the wound were sealed by placing a suture. Both spinal cord injured and sham operated fish were allowed to regenerate and the progress of regeneration was observed after 1, 3, 7, 10 and 15 days of injury. Zebrafishes were anesthetized deeply for 5 minutes in 0.1% tricaine (MS222; Sigma, USA) and approximately 1mm length of spinal cord both rostrally and caudally from injury epicenter were dissected out from 50-60 fishes in each batch and pooled for RNA extraction.

first: Subhra

last: Hui

first: Dhriti

last: Sengupta

first: Triparna

last: Sen

first: Sudip

last: Kundu

first: Sinnakaruppan

last: Mathavan

first: Sukla

last: Ghosh


title: A global transcriptome analysis of keratinocytes upon suppression of endogenous microRNA-31

status: Public on Oct 30 2012

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

summary: MiR-31 is one of the most highly overexpressed miRNAs in psoriasis skin; however, its biological role in the disease has not been studied. Here we show that miR-31 is markedly overexpressed in psoriasis keratinocytes. To study the biological role of miR-31 in keratinocytes, we transfected miR-31 hairpin inhibitor (anti-miR-31) into primary human keratinocytes to inhibit endogenous miR-31. We performed a global transcriptome analysis of keratinocytes upon suppression of endogenous miR-31 using Affymetrix arrays.

overall_design: Expression profiling of primary human keratinocytes transfected with 10nM miR-31 hairpin inhibitor (anti-miR-31) or control hairpin RNA (anti-miR-Ctrl) for 48 hours (biological triplicates in each group) was performed using the Affymetrix GeneTitan system.

first: Florian

last: Meisgen

first: Lynn

last: Butler

first: Gangwen

last: Han

first: Xiao

last: Wang

first: Cecilia

last: Söderberg-Nauclér

first: Mona

last: Ståhle

first: Andor

last: Pivarcsi

first: Enikö

last: Sonkoly


title: Grapevine response to Planococcus ficus feeding

city: Geisenheim

first: Alicia

middle: Eva

last: Timm

address: Vone-Lade-Str 1

department: Phytomedicine

institute: Forschungsanstalt Geisenheim

summary: Plant response to insect feeding appears to be highly specific with regard to the organisms in the system.  Here, we report on the interaction between grapevine Vitis vinifera plants and a phloem-feeding insect pest, the vine mealybug Planococcus ficus.  Plants were exposed to P. ficus for periods of 6 hours and 96 hours, after which they were analysed for gene expression levels using microarrays and quantitative real-time PCR (qPCR).  Both methods showed that grapevine displayed only a minimal response to mealybug feeding at the transcript level at both time periods.  Intermediate grapevine exposure times (24, 48 and 72 hours) to P. ficus feeding were investigated using qPCR analysis of ten additional genes associated with known plant defense responses.  Results showed that only a single gene, pathogenesis-related protein 1, was differentially expressed after 48 hours of mealybug feeding.  During the course of mealybug feeding, however, a number of other genes were significantly up- or down-regulated at certain time points. Thus, it appears as if grapevine responds minimally to feeding by P. ficus as well as within a very narrow time period.  The relative lack of grapevine plant defense mechanisms may be a result of the feeding strategies of mealybugs.

overall_design: Eight samples were analysed.  Two replicates each were included for each treatment (6 hour and 96 hour feeding), resulting in four samples.  Two control replicates were included for each treatment (6 hour and 96 hour feeding controls), resulting in a further four samples.

first: Annette

last: Reineke


title: Response of Rpp4-silenced plants to soybean rust

status: Public on Oct 20 2012

first: PLEXdb Curator

summary: Experimental design:  1 genotypes: PI- (resistant USDA Plant Introduction (PI459025B) line containing SBR Rpp4 resistance gene)    2 treatments: Rub inoculation with BPMV-VIGS construct targeting the LRR region of Rpp4 candidate gene. This  BPMV construct and the plant tissue used for microarray was described in Meyer et al. (2009) Plant Physiol. 150:295-307. Control plants were inoculated with empty BPMV vector. At three weeks after BPMV inoculation, all plants were inoculated with Soybean rust (Phakopsora pachyrhizi) isolate LA04-1. LA04-1 is a single spore isolate maintained at the Foreign Disease Weed Science Research Unit.    3 replications  1 time point: 14 days after inoculation    TOTAL: 5 Affymetrix GeneChip(R) Soybean Genome Arrays    LA04-1 treatment: 500,000 spores per ml in 0.01% Tween 20   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Michelle Graham.  The equivalent experiment is GM51 at PLEXdb.]

overall_design: treatment: BPMV-LRR(2-replications);  treatment: BPMV empty vector(3-replications)

first: Michelle

last: Graham


title: Molecular characterization of the Rpp4 resistance response

status: Public on Oct 10 2012

summary: Experimental design:  2 genotypes: PI- (resistant USDA Plant Introduction (PI459025B) line containing SBR Rpp4 resistance gene) & Cultivar Williams that does not have a known SBR resistance gene  2 treatments: Soybean rust (Phakopsora pachyrhizi) isolate Hawaii 94-1 & mock infection  3 replications  6 time points: 12, 24, 72, 144, 216 and 288 hours after inoculation  TOTAL: 72 Affymetrix GeneChip(R) Soybean Genome Arrays    Mock treatment: 0.01% Tween 20  Hawaii 94-1 treatment: 500,000 spores per ml in 0.01% Tween 20   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Steve Whitham.  The equivalent experiment is GM37 at PLEXdb.]

overall_design: genotype: Williams - pathogen inoculation: Mock - time: 12 hai(3-replications);  genotype: Williams - pathogen inoculation: Mock - time: 24 hai(3-replications);  genotype: Williams - pathogen inoculation: Mock - time: 72 hai(3-replications);  genotype: Williams - pathogen inoculation: Mock - time: 144 hai(3-replications);  genotype: Williams - pathogen inoculation: Mock - time: 216 hai(3-replications);  genotype: Williams - pathogen inoculation: Mock - time: 288 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 12 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 24 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 72 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 144 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 216 hai(3-replications);  genotype: Williams - pathogen inoculation: Hawaii 94-1 - time: 288 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 12 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 24 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 72 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 144 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 216 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Mock - time: 288 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 12 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 24 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 72 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 144 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 216 hai(3-replications);  genotype: PI459025B - pathogen inoculation: Hawaii 94-1 - time: 288 hai(3-replications)

first: Steve

last: Whitham


title: Expression data from salinity treated and control soybean

status: Public on Sep 25 2012

city: Jinan

first: Yuguang

last: Song

state: Shandong

address: South Shanda Road 27

department: School of life sicense

country: China

institute: Shandong University

summary:
Soybean's productivity is significantly compromised by soil salinity, but, like most plants, it has evolved a variety of mechanisms to aid its survival under environmental stress. The expression of many plant genes is altered by salinity stress.
We used microarrays to detail the global programme of gene expression and identified distinct up or down-regulated genes between salinity stressed and non stressed soybean

overall_design: Seedlings of the soybean cultivar Williams 82 were grown in vermiculite under a 16h photoperiod at 25 ºC for 14 days. RNA were isolated from the mock (M0, M1, M3, M6, M12, M24) and salinity treated (S0, S1, S3, S6, S12, S24) seedlings. 0.5 µg RNA that extracted from each time point of the mock and salinity-stressed seedlings were mixed respectively to obtain the mock and salinity-stressed RNA pools, and then they were used to synthesize the cDNA. The cDNA was labeled with biotin, and then hybridized to an Affymetrix soybean Genome Array.

first: Dandan

last: Ji

first: Shuo

last: Li


title: Effects of acute exercise on gene expression in exercising and non-exercising human skeletal muscle

status: Public on Oct 23 2012

first: Milene

last: Catoire

address: Bomenweg 2

department: Human Nutrition

summary: Background: Exercising is know to have an effect on exercising skeletal muscle, but unkown is the effect on non-exercising skeletal muscle. Gene expression changes in the non-exercising skeletal muscle would point to a signalling role of skeletal muscle

overall_design: 9 healthy middle-aged men performed 1 hour of one-legged exercise, before and afterwards muscle biopsies were taken from both legs. Skeletal muscle biopsies were analyzed by microarray.

first: Milène

first: Marco

last: Mensink

first: Mark

middle: V

last: Boekschoten

first: Roland

last: Hangelbroek

first: Michael

last: Müller

first: Patricht

last: Schrauwen

first: Sander

last: Kersten


title: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (tga3-2 knockout data)

status: Public on Oct 03 2012

first: Jonathan

last: Moore

summary:
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified but our knowledge of how these different components interact is still rudimentary. We have generated a high-resolution time series of gene expression profiles from a single Arabidopsis leaf during infection by the necrotrophic fungal pathogen, Botrytis cinerea.

Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 hours after infection, with the majority of gene expression changes occurring before significant lesion development. We have used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions and testing of one such prediction identified a novel role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional change during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks underlying the Arabidopsis response to B. cinerea.

overall_design: Samples were compared at three time points: 16, 24 and 32 hours post infection. Time points were chosen based on the expression profile of TGA3 in the high-resolution time series also presented in this paper. Samples were collected for three different conditions: tga3-2 mock inoculated, tga3-2 infected and Col-0 infected. Four individual leaves (biological replicates) from separate plants were collected for each treatment-time point totalling 36 samples. The four biological replicates for each treatment-time point were pooled. At each time point, the expression of the 4 pooled replicates was compared between tga3-2 mock inoculated vs. tga3-2 infected and tga3-2 infected vs. Col-0 infected using four technical replicates for each comparison which included balanced dye swaps.

first: Oliver

last: Windram

first: Priyadharshini

last: Madhou

first: Stuart

last: McHattie

first: Claire

last: Hill

first: Richard

last: Hickman

first: Emma

last: Cooke

first: Dafyd

last: Jenkins

first: Christopher

last: Penfold

first: Laura

last: Baxter

first: Emily

last: Breeze

first: Steven

last: Kiddle

first: Johanna

last: Rhodes

first: Susanna

last: Atwell

first: Daniel

last: Kliebenstein

first: Youn

last: Kim

last: Stegle

first: Karsten

last: Borgwardt

first: Cunjin

last: Zhang

first: Alex

last: Tabrett

first: Roxane

last: Legaie

first: Bärbel

last: Finkenstadt

first: David

last: Wild

first: Andrew

last: Mead

last: Rand

first: Jim

last: Beynon

first: Sascha

last: Ott

first: Vicky

last: Buchanan-Wollaston

first: Katherine

last: Denby


title: Impact of rokA delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

status: Public on Oct 22 2012

first: Sulman

last: Shafeeq

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔrokA to D39 wild-type grown in M17 medium + 0.5% glucose (GM17).

overall_design: One condition design comparision of two strains including a dye swap

first: Tomas

last: Kloosterman

first: Oscar

last: Kuipers


title: Comparison of RNA expression in paravienal mesophyll (PVM) and palisade parenchyma (PP) cells.

status: Public on Jul 26 2012

city: Pullman

first: Glenn

middle: W

last: Turner

state: WA

address: PO Box 646340, Washington State University

department: Institute of Biological Chemistry

institute: Washington State University

summary:
The paraveinal mesophyll (PVM) of soybean leaves is a layer of laterally expanded cells sandwiched between the palisade and spongy mesophyll chlorenchyma. The vacuoles of PVM cells contain an abundance of a putative vegetative storage protein, VSP (α, β). VSP is is constitutively produced, but is up-regulated during sink limitation experiments involving flower, fruit, or vegetative bud removal.  Soybean vegetative lipoxygenases (Vlx), consisting of 5 isozymes (Vlx, A-D), have been identified as potential storage proteins because they accumulate to high levels with experimental sink limitation and have been co-localized with VSP to the vacuoles of  PVM cells.  We re-investigated the sub-cellular locations of these enzymes with TEM immuno-cytochemistry. We employed laser micro-dissection to compared RNA expression of PVM cells with mesophyll chlorenchyma cells; and we performed a micro-array analysis of soybean leaf samples representing a time-course, sink-limitation, experiment.  We found that none of the Vlx isozymes co-localize with putative storage proteins in PVM vacuoles, and that our sink limitation experiment (typical of those used in the past) induced a strong up-regulation of stress response genes, simultaneous with the up-regulation of the Vlx isozymes.  Our findings do not support a storage function for soybean Vlx.
The microarray results presented here represent our comparison of gene expression within PVM and palisade mesophyll paraenchyma (PP) cells from mature soybean leaves.  For this part of our study both the PVM and palisade parenchyma (PP) cells were isolated from sections of soybean leaves by laser micro-dissection and pressure catapulting (LMPC). Total RNA was isolated from these cells and amplified for microarray analysis.

overall_design: Soybean leaves were fixed with a mixture of  ethanol and acetic acid, embedded in paraffin and sectioned to provide samples for laser micro-dissection with pressure catapulting (LMPC).  Slides were deparaffinized prior to LMPC.  A total of six samples were collected: three biological replicates for PVM cells and three replicates for PP cells. After enough cells were collected for each samples, the cells were pooled for RNA extraction.  RNA was amplified prior to microarray hybridization using the Whole-Transcriptome Ovation Pico RNA Amplification System from NuGEN Technologies, San Carlos, CA, USA.

last: Cuthbertson

first: Sau

last: Voo

first: Matthew

last: Settles

first: Howard

last: Grimes

first: Markus

last: Lange


title: Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud

status: Public on Jul 16 2012

city: New Haven

first: Michael

middle: Jeremy

last: Stulberg

state: CT

address: 219 Prospect St

department: MCDB

institute: Yale University

summary:
We aimed to expand the knowledge of Fgf and Wnt signaling in the zebrafish tailbud. Both pathways are required for proper axis elongation and segmentation and we wished to explore the genes under the control of each pathway during this process.
In addition, we saught to identify crosstalk between the two pathways by determining whether pathway effector expression was being changed after time-resolved modification of each pathway using pharmacological modifiers.

overall_design: Embryos were treated with either 0.3M LiCl, 50uM SU5402, or E2 for 3hours or 7 hours (E2 and SU5402), followed by tailbud dissection and RNA extraction. Conditions were replicated in triplicate.

first: Scott

last: Holley


title: The effects of bud removal on soybean leaf gene expression.

summary:
The paraveinal mesophyll (PVM) of soybean leaves is a layer of laterally expanded cells sandwiched between the palisade and spongy mesophyll chlorenchyma. The vacuoles of PVM cells contain an abundance of a putative vegetative storage protein, VSP (α, β). VSP is is constitutively produced, but is up-regulated during sink limitation experiments involving flower, fruit, or vegetative bud removal.  Soybean vegetative lipoxygenases (Vlx), consisting of 5 isozymes (Vlx, A-D), have been identified as potential storage proteins because they accumulate to high levels with experimental sink limitation and have been co-localized with VSP to the vacuoles of  PVM cells.  We re-investigated the sub-cellular locations of these enzymes with TEM immuno-cytochemistry.  We employed laser micro-dissection to compared RNA expression of PVM cells with mesophyll chlorenchyma cells, and we performed a micro-array analysis of soybean leaf samples representing a time-course, sink-limitation, experiment.  We found that none of the Vlx isozymes co-localize with putative storage proteins in PVM vacuoles, and that our sink limitation experiment (typical of those used in the past) induced a strong up-regulation of stress response genes, simultaneous with the up-regulation of the Vlx isozymes.  Our findings do not support a storage function for soybean Vlx.
The results reported here are from a study designed to evaluate systemic effects of a vegetative bud removal protocol that had been used previously to study accumulation and subsequent mobilization of vegetative storage proteins in soybean.  During these experiments plants were grown for 30 days and then all vegetative buds were removed.  Bud removal was repeated each day for 15 days (designated the "detip" phase) and then new buds were allowed to regrow (designated the "retip" phase). Samples were collected at 5 day intervals.  Total RNA was extracted from selected samples for our microarray experiments.

overall_design: Three replicate time course experiments provided RNA samples for our microarray analysis.  Samples were harvested from both bud removal ("detip/retip") plants and untreated controls of the same age that were maintained side-by-side under the same growth conditions. Bud removal plants were designated as "detip" plants during the bud removal phase  and "retip" plants during the regrowth phase.   Bud removal began at time-course day 30 and lasted for 15 days (designated D0 through D15).  Shoot regrowth lasted an additional 15 days (designated R16 through R30). Controls were designate similarly with C0 corresponding to 30 day old plants at the the first day of bud removal and C30 corresponding to day 15 of the regrowth phase.  Samples were collected at 5 day intervals.  Messenger RNA was extracted from selected samples for our microarray experiments. These were from 30 day old plants ( C0, the last day of growth before detipping), 45 day old plants (C15, D15, at day 15 of bud removal), 50 day old plants (C20, R20, day 5 of shoot regeneration), and 60 old plants (C30, R30, day 15 of regrowth).  RNA was extracted from leaf samples using a method developed for tissues containing abundant polysaccharides and polyphenols (Gehrig et al., 2000).  In addition, the extracted RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA).  Each RNA sample examined (C0, C15, C20, C30, D15, R20, R30; each with a minimum of 3 replicates for a total of 22 samples) was converted to cRNA and hybridized to Affymetrix soybean GeneChips (GEO accession # GPL4592) according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).

first: Daniel


title: Transduction of human fibroblasts with Zic3 combined with OCT4, SOX2 and KLF4 induces stable neural progenitor cell lines

status: Public on May 22 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Lineage specific transcription factors (TF) define and reinforce tissue specific cell types. For instance, stable endoderm progenitors were established from human ESC by constitutive expression of SOX7 or SOX17. We hypothesized that combinatorial expression of OCT4, SOX2 and KLF4 together with the neural-lineage TF, Zic3, could directly convert fibroblasts into stable neuronal progenitor cells (NPC). Ensuing colonies predominantly expressed genes present in human NPC, as demonstrated by genome wide transcriptional analysis, and this phenotype could be maintained through many passages.  When injected in immunodeficient mice, Zic3-induced (Zi)NPC form neuroendocrine tumors without evidence of mesoderm or endoderm. In vitro, ZiNPC spontaneously differentiated to neural cells only, and could be differentiated into astrocytes, oligodendrocytes and motor neuron lineages. In conclusion, addition of Zic3 during induced pluripotent stem cell (iPSC) generation, allows for the derivation of stable neural lineage progenitor cells.

overall_design: 3 hESC, 3 hESC-derived neurosphere and 3 ZiNPC samples were analyzed

first: Anujith

last: Kumar

first: Jeroen

last: Declercq

first: Kristel

last: Eggermont

first: Catherine

last: Verfaillie


title: Expression levels of mature miRNAs from Caco2 cell treated with inflammatory cytokines

status: Public on Apr 22 2012

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: We used microarray to determine the miRNA whose expression was changed at 6 hours after inflammatory cytokines (TNFα, IL1α, IL1β, or IL6) treatment.

overall_design: Two-condition experiment; Caco2 control vs Caco2 treated with TNFα, IL1α, IL1β,or IL6 for 6 hours

first: Takeshi

last: Yoshikawa

first: Motoyuki

last: Otsuka


title: Prolactin stimulation of parathyroid adenomas

status: Public on May 01 2012

first: Felix

last: Haglund

address: Karolinska Universitetssjukhuset Solna, CMM L8:01

department: MMK

summary: Primary hyperparathyroidism is a common endocrine disorder frequently affecting postmenopausal women. In this study we have investigated expression of the prolactin receptor (PRLr) in a panel of 37 sporadic parathyroid tumours, as well as functionality in vitro in cultured parathyroid tumour cells. High levels of the prolactin receptor gene (PRLR) transcripts were demonstrated in parathyroid tissues as compared to other reference tissues and breast cancer cells. PRLr products of 60/70 kDa were highly expressed in all parathyroid tumours. In addition varying levels of the 80 kDa PRLr isoform, with known proliferative activity, were demonstrated. In parathyroid tumours PRLr immunoreactivity was observed in cytoplasm in all cases and in addition in the plasma membrane (n = 12) or enlarged lysosomes (n = 4). In normal parathyroid rim PRLr was expressed in cytoplasm and granulae. In in vitro studies of short-term cultured human parathyroid tumour cells prolactin stimulation was associated with transcriptional changes in JAK/STAT, RIG-I like receptor and type II interferon signaling pathways as documented by gene expression profiling. Moreover, PRLR gene expression in parathyroid tumors was significantly inversely correlated with plasma total Ca2+ levels. In conclusion, the prolactin receptor was found highly abundant in human parathyroid gland, parathyroid tumours, correlated with patient Ca2+ levels and functionally responsive to physiological levels of prolactin. These findings suggest a role for the prolactin receptor in human parathyroid adenomas.

overall_design: Expression profiling was done in parathyroid adenomas subjected to prolactin treatment in culture. In addition, corresponding paraffin sections were obtained for verification of PRLr expression by immunohistochemistry. 200 mg/L prolactin (recombinant human prolactin, Cat. No. JM-4687-50, MBL Woburn, MA) was added to 1× 10^6 attached parathyroid tumour cells. Cells were harvested using RNAlater (QIAGEN) and homogenized with QIAshredder for RNA extraction after 3 h and 24 h in culture, respectively. Negative controls were collected in parallel with each case at the same time points. RNA was extracted using QIA Cube, and quality assessed with Bioanalyser and Nanodrop. Expression array profiling and data analysis was done at the KI core facility Bioinformatics and Expression Analysis (BEA, Novum, Huddinge) using the Affymetrix platform and the TITAN ST 1.1 array. A total of 16 samples were analysed including 4 parathyroid adenomas cultured for 3 h or 24 h in the presence of prolactin plus control samples cultured in parallel without prolactin.

first: Ming

last: Lu


title: Molecular pathology of the ARF induced by choline deficiency and of the protection afforded by fish oil

status: Public on Dec 06 2011

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

summary: Male weanling Wistar rats from the Animal Facility at the Center for Experimental and Applied Pathology were divided into 4 groups and fed the following diets: 1) choline-deficient diet with VO [corn and hydrogenated oils) as lipids (CDVO); 2) choline-supplemented diet with VO as lipids (CSVO); 3) choline-deficient diet with MO as lipid (CDMO); and 4) choline-supplemented diet with MO as lipid (CSMO). Authors have adhered to appropriate NIH Guide for the Care and Use of Laboratory Animals. It is known that female rats are more resistant than male rats to AKI. Animals were sacrificed after receiving the experimental diets for 6 days. The left kidney was fixed in formaldehyde-buffer and stained with hematoxiline-eosin for histopathological analysis. The right kidney was cryopreserved for microarray analysis. Cryopreserved kidney was wrapped with aluminum foil and broken with a hammer previously wrapped with tape paper on a counter covered in aluminum. The pieces of the kidney were located in a mortar with liquid nitrogen to keep cryopreservation and were pulverized with a pestle. Nitrogen was added as it evaporated. The tissue was broken up to be completely pulverized. Powder was placed with a spatula in a cryotube supported on a dry ice with a layer of aluminum above. Before proceeding with another sample and to avoid contamination, the mortar, the pestle and the spatula were washed with tap water, distilled water and then alcohol. The tape of the hammer, the aluminum on the counter and the latex gloves were also replaced by new ones. Total RNA was purified from 30 milligrams of frozen rat kidney pools, using RNeasy Mini Kit [Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions. The biological concentration, integrity and quality of the RNA obtained were performing using NanoDrop 2000c (Thermo Fisher Scientific, Delaware, USA) and RIN (RNA Integrity Number). Five hundred nanograms of total RNA were processed and hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array (Affymetrix Inc, Singapore, Singapore), according to Ambion WT Expression Kit instructions (Ambion Inc, Texas, USA). Total RNA obtained during the tissue extraction was processed to obtain a double strand cDNA. After that we performed a in-vitro transcripition to generate antisence cRNA (aRNA). This aRNA was used to generate a single-stranded DNA (ss-DNA) using random primers and the dUTP +dNTP mix. The resulting single-stranded DNA (ss-DNA) containing the unnatural uracilbase is then treated with Uracil DNA Glycosylase, which specifically removes the uracilresidue from the ss-DNA molecules. In the same reaction, the APE 1 enzyme then cleaves the phosphodiester backbone where the base is missing, leaving a 3’-hydroxyland a 5’-deoxyribose phosphate terminus. Before this prosses, shorts ss-DNA fragments were labeled by terminal deoxynucleotidyl transferase (TdT) that covalently linked the 3’-hydrosyl phosphate terminus whit Biotin Allonamide Triphosphate. The GeneChip® Rat Gene 1.0 ST Array enables whole-genome, gene-level expression studies for well-characterized genes. It is a single GeneChip®-brand array comprised of more than 722 254 unique 25-mer oligonucleotide features accounting for more than 27 342 gene-level probe sets. Results were scanned with GeneChip® Scanner 3000 7G (Affymetrix Inc, Tokyo, Japan), and normalized by RMA algorithm using Affymetrix Expression Console Software. In addition, call values were retrieved by MAS5 algorithm, and only genes with a “p” (present) call value were used in the analysis. Differentially expressed genes were identified using limma (www.bioconductor.org) and “p” adjusted values and absolute log fold change greater than 1.5 were used for gene selection.

overall_design: For each condition, CDVO, CSVO, CDMO and CSMO, 2 pools of 3 animals each were carried out with the powder obtained. Each sample represents a pool of 3 animals, sample subpooling is a strategy that can be used to reduce the variance but still allow studies to encompass biological variation. Once all samples were pooled, cryotubes were preserved in nitrogen until RNA extraction. phosphate terminus whit Biotin Allonamide Triphosphate.

first: Valeria

last: Denninghoff

first: Georgina

last: Ossani

first: Ana

last: Uceda

first: Matias

last: Rugnone

first: Elmer

last: Fernandez

first: Cristobal

last: Fresno

first: Alejandra

last: Avagnina

first: Boris

last: Elsner

first: Alberto

last: Monserrat


title: Gene expression profiles of dental neural crest progenitor cells (dNC-PCs) and stem cells of exfoliated descidious teeth (SHED)

status: Public on Apr 12 2012

city: Regensburg

first: Christian

last: Morsczeck

address: Franz-Josef Strauss Allee 11

institute: University of Regensburg

summary: We analysed gene expression profiles in dental stem cells before and after osteogenic differentiation day 7.

overall_design: Total RNAs were isolated from dental stem cells at day 0 (before differentiation) and after 7 days of differentiation

first: Oliver

last: Felthaus

first: Werner

last: Götz

first: Gottfried

last: Schmalz

first: Martin

last: Gosau

first: Tobias

last: Ettl

first: Jürgen

last: Siemonsmeier

first: Andreas

last: Jäger

first: Torsten

middle: E

last: Reichert


title: KRAS-genotype dependent gene expression pattern in colorectal cancer

status: Public on May 18 2012

city: Kiel

first: Christoph

last: Röcken

address: Arnold-Heller-Str. 3/14

department: Pathology

institute: Christian-Albrechts-University Kiel

summary:
Colorectal cancer (CRC) is still one of the most common causes of cancer-related death worldwide (World Health Organization, Fact sheet N°297, October 2011). Though, therapeutic options improved over the past years, the prognosis of metastatic colorectal cancer (mCRC) remains poor with a median survival of 18-21 months.
Monoclonal antibodies targeting the epidermal growth factor receptor (EGFR) are used for the palliative treatment of metastatic colorectal cancer (mCRC) carrying a KRAS-wildtype. Among the tumors with a KRAS-wildtype, only 35% respond, and alterations of other signaling molecules and pathways modulate therapeutic response. In this study we analyzed the effect of KRAS-mutations on intracellular signaling cascades to find new therapeutic approaches for patients with mCRC. Reverse-phase protein array and gene array technology was applied to sixteen adenocarcinomas of the sigmoid colon carrying either wildtype (n=8) or mutant (n=8) KRAS. Differential expression was validated on 49 sigmoid cancers by RT-PCR, Western blot and immunohistochemistry. In a screening for members of signaling pathways known to have a high impact on tumor development in colon cancer, we found 14 proteins downregulated in tumors with mutated KRAS. Subsequently, we compared the data of the protein arrays with the results of gene expression arrays performed with the same samples. We confirmed the differential expression of eight genes as a function of the KRAS genotype of the tumor. To further validate the differential expression of these candidates, we performed quantitative expression analysis and immunohistochemical staining of an independent validation series comprising 49 CRC patient samples. It was clearly demonstrated that the expression of EGFR is decreased in colorectal carcinomas with a mutant KRAS genotype.

overall_design: mRNA was obtained from 16 patients with colorectal cancer (8 with and 8 without KRAS-mutation). mRNA was extracted from neoplastic and non-neoplastic colon mucosa and analyzed separately by Affymetrix Human Gene 1.1 ST GeneChips finally generating 32 separate data sets.

first: Ann-Kathrin

last: Wenke

first: Holger

last: Armbruster

first: Katharina

last: Balschun

first: Julia

last: Starmann

last: Sültmann


title: Transcript profiling of soybean msh1 RNAi transgenic lines

status: Public on Nov 29 2011

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

summary: The soybean msh1 RNAi transgenic line show various growth phenotype. We use microarray analysis to characterize gene expression pattern for two of the phenotypes - variegation and stunted growth.

overall_design: Wild type and msh1 RNAi variegated and stunted tissues were collected for RNA extration and hybridization on Affymetrix.

first: Sally

last: Mackenzie


title: Danio rerio: wilde-type control vs. tbx5 morpholino

city: keelung

first: jenn-kan

last: Lu

address: 2 Pei-Ning Road,Keelung

department: Aquaculture

summary: Using an oligonucleotide-based microarray analysis to study the expression of special genes in tbx5 morphants, we demonstrated that GH and some GH-related genes were markedly downregulated.

overall_design: Two condition experiments, tbx5 morpholino vs. wilde-type control Danio rerio embryo.

first: Jenher

first: Jenkann

first: Tzu-Chun

last: Tsai

first: Hsinyu

last: Lee

first: Shuyu

last: Yeh

first: Renbing

last: Tang

first: Anhang

last: Yang

first: SieLin

last: Choo


title: Molecular characterization of the incompatible and compatible interaction of soybean rust disease in Rpp3-containing PI462312 line

status: Public on Nov 28 2011

city: Ames

first: PLEXdb Curator

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: Experimental design:  1 genotype: PI- (resistant USDA Plant Introduction (PI462312) line containing SBR Rpp3 resistance gene)  3 treatments: Virulent soybean rust (Phakopsora pachyrhizi Tw80-2) challenge, avirulent soybean rust challenge (Hw94-1) & mock infection  3 replications  6 time points: 12, 24, 72, 144, 216 and 288 hours after inoculation  TOTAL: 54 Affymetrix GeneChip(R) Soybean Genome Arrays    Mock treatment: 0.01% Tween 20  Hawaii 94 treatment: 500,000 spores per ml in 0.01% Tween 20  Taiwan 80-2 treatment: 500,000 spores per ml in 0.01% Tween 20   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Martijn van de Mortel (for Steve Whitham).  The equivalent experiment is GM36 at PLEXdb.]

overall_design: pathogen isolates: Mock - time: 12 hai(3-replications);  pathogen isolates: Mock - time: 24 hai(3-replications);  pathogen isolates: Mock - time: 72 hai(3-replications);  pathogen isolates: Mock - time: 144 hai(3-replications);  pathogen isolates: Mock - time: 216 hai(3-replications);  pathogen isolates: Mock - time: 288 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai(3-replications);  pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai(3-replications);  pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai(3-replications)

first: Martin

last: van de Mortel


title: PDGF-BB modulates hematopoiesis and tumor angiogenesis by inducing erythropoietin production in stromal cells.

status: Public on Dec 04 2011

first: Ola

last: Larsson

department: Department of oncology-pathology

summary: The platelet-derived growth factor (PDGF) signaling system contributes to tumor angiogenesis and vascular remodeling. Here, we show PDGF-BB markedly induces erythropoietin (EPO) mRNA and protein expression by targeting the PDGFR-beta+ stromal and perivascular compartments. In mouse tumor models, PDGF-BB-induced EPO promotes tumor growth via two mechanisms: 1) paracrine stimulation of tumor angiogenesis by directly inducing endothelial cell proliferation, migration, sprouting and tube formation; and 2) endocrine stimulation of extramedullary hematopoiesis leading to increased oxygen perfusion and protection against tumor-associated anemia. Similarly, delivery of an adenovirus-PDGF-BB to tumor-free mice markedly increases EPO production and hematopoietic parameters. An EPO blockade specifically attenuates PDGF-BB-induced tumor growth, angiogenesis and hematopoiesis. At the molecular level, we show that the PDGF-BB-PDGFR-beta signaling system activates EPO promoter via in part transcriptional regulation of ATF3 by possible association with c-Jun and SP1. These findings uncover a novel mechanism of PDGF-BB-induced tumor growth, angiogenesis and hematopoiesis.

overall_design: Comparison of S17 stromal cells treated with PDGF-BB for 72h to control

first: Yihai

last: Cao


title: Soy LGI Protein NILs, seed fill

status: Public on Nov 22 2011

summary: Evaluation of transcripts from soybean seed tissue during seed fill for a pair of near-isogenic lines contrasting in seed protein and oil and carrying an introgression at the linkage group I protein QTL region.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Yung-Tsi Bolon.  The equivalent experiment is GM11 at PLEXdb.]

overall_design: genotype: LoProt - time: 25-50(3-replications);  genotype: LoProt - time: >50-100(3-replications);  genotype: LoProt - time: >100-200(3-replications);  genotype: LoProt - time: >200-300(3-replications);  genotype: HiProt - time: 25-50(3-replications);  genotype: HiProt - time: >50-100(3-replications);  genotype: HiProt - time: >100-200(3-replications);  genotype: HiProt - time: >200-300(3-replications)

first: Yung-Tsi

last: Bolon

first: Carroll

last: Vance


title: Calorie restriction-like effects of 30 days of resveratrol supplementation on energy metabolism and metabolic profile in obese humans

status: Public on Nov 08 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Resveratrol is a naturally occurring compound that profoundly affects energy metabolism and mitochondrial function and serves as a calorie restriction mimetic, at least in animal models of obesity. Here we treated 10 healthy, obese men with placebo and 150 mg/day resveratrol in a randomized double-blind cross-over study for 30 days. Resveratrol supplementation significantly reduced sleeping- and resting metabolic rate. In muscle, resveratrol activated AMPK, increased SIRT1 and PGC-1alpha protein levels, increased citrate synthase activity, and improved muscle mitochondrial respiration on a fatty acid-derived substrate. Furthermore, resveratrol elevated intramyocellular lipid levels, and decreased intrahepatic lipid content, circulating glucose, triglycerides, alanine-aminotransferase, and inflammation markers. Systolic blood pressure dropped and HOMA index improved after resveratrol. In the postprandial state, adipose tissue lipolysis and plasma fatty acid and glycerol decreased. In conclusion, we demonstrate that 30 days of resveratrol supplementation induces profound metabolic changes in obese subjects, mimicking the effects of calorie restriction.

overall_design: double-blind randomized cross-over study, Expression profiling by microarray

first: Silvie

last: Timmers

first: Ellen

last: Konings

first: Lena

last: Bilet

first: Riekelt

middle: H

last: Houtkooper

first: Tineke

last: van de Weijer

first: Joris

last: Hoeks

first: Sophie

last: van der Krieken

first: Dongryeol

last: Ryu

first: Sander

last: Kersten

first: Esther

last: Moonen-Kornips

first: Gijs

last: Goossens

first: Matthijs

middle: K

last: Hesselink

first: Iris

last: Kunz

first: Vera

middle: B

last: Schrauwen-Hinderling

last: Blaak

first: Johan

last: Auwerx

first: Patrick

last: Schrauwen


title: Soybean transcriptome response to aluminum stress in roots of Al-tolerant genotype (PI 416937): time course

status: Public on Oct 05 2011

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary:
Gene expression profiling in soybean under aluminum stress:  Transcriptome response to Al stress in roots of Al-tolerant genotype (PI 416937).
Aluminum (Al) toxicity is a major constraint of crop production on acid soils. Many commercial soybean cultivars and advanced breeding lines have been evaluated for Al tolerance. Aluminum tolerance is quantitatively inherited trait in soybean making it difficult for genetic improvement. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient and effective programs aimed at improving Al tolerance trait   The molecular mechanisms of Al tolerance is poorly understood in soybean. The objective of the research was to identify candidate  aluminum tolerance genes in soybean  Al-tolerant soybean genotype PI 416937 seedlings were exposed to zero or 10 µM Al in growth chamber under hydroponic conditions for four time span of 2, 12, 48 and 72 hrs in a randomized complete block design with three replications. Microarray analysis was made on mRNA isolated from 1 cm log tap root tips using Affymetrix soybean array with over 68,000 probe sets Glycine max L and wild soybean combined. Both novel and known genes were discovered in response to Al treatment. They include Al tolerance relevant proteins, families of transcription factors, zinc finger, bZIP, WRKY, MYB, ADR6, and NAC domain proteins were induced likely regulating Al tolerance downstream genes. Stress related proteins, cytochrome P450, glutathione-s transferase, glutaredoxin family and ascorbic acid biosynthesis protein were induced as signatures of cellular detoxification mechanisms. An ABC type multidrug resistance protein that could act as citrate transporter or Al exporter was up-regulated, a key Al tolerance mechanisms in several species. A cell wall loosening enzyme endoxylglucan hydrolases were also up-regulated probably reversing the wall rigidification caused by Al and promoting root growth under Al stress. Phytosulfokines growth factor involved in cell division and proliferation was up-regulated likely as a direct counter action to Al toxicity which inhibits root growth by limiting cell division and elongation. In conclusion, the Al tolerance candidate genes identified herein are potential targets for future genetic engineering and molecular breeding work on Al tolerance trait in soybean which in turn would contribute to gain in soybean productivity on acid soils.

overall_design: One genotype PI 416937 (p); four time points: (2, 12, 48, and 72 hrs), with replicates (2 or 3)

first: K

last: Soliman

first: D

last: Duressa


title: Comprehensive molecular characterization of the soybean rust disease [Embrapa-Soja - Iowa State Univ; 2005]

first: PLEXdb Curator

summary: Experimental design:  2 genotypes: PI230970 (resistant USDA Plant Introduction (PI) line containing SBR Rpp2 resistance gene) & Embrapa-48 (susceptible Brazilian cultivar)  2 treatments: Soybean rust challenge & mock infection   3 replications  10 time points: 6, 12, 18, 24, 36, 48, 72, 96, 120, 168hai  TOTAL: 120 Affymetrix GeneChip(R) Soybean Genome Arrays   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Martijn van de Mortel.  The equivalent experiment is GM2 at PLEXdb.]

overall_design: genotype: PI230970 - time: 006 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 006 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 012 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 012 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 018 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 018 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 024 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 024 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 036 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 036 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 048 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 048 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 072 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 072 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 096 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 096 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 120 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 120 - Treated or untreated: Mock(3-replications);  genotype: PI230970 - time: 168 - Treated or untreated: SBR(3-replications);  genotype: PI230970 - time: 168 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 006 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 006 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 012 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 012 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 018 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 018 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 024 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 024 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 036 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 036 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 048 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 048 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 072 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 072 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 096 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 096 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 120 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 120 - Treated or untreated: Mock(3-replications);  genotype: Embrapa48 - time: 168 - Treated or untreated: SBR(3-replications);  genotype: Embrapa48 - time: 168 - Treated or untreated: Mock(3-replications)

first: Martijn

last: van de Mortel

first: Baum

last: Whitham


title: Gene expression profiling in Al-tolerant and Al-sensitive soybean under aluminum stress

status: Public on Oct 07 2011

summary:
Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes.
Aluminum toxicity is the most important constraint of crop production on acid soils. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient breeding programs to improve Al tolerance. This research was undertaken to identify candidate Al-tolerance genes in soybean. Two soybean genotypes PI 416937 (Al-tolerant) and Young (Al-sensitive) seedlings were exposed to zero or 10 µM Al in a growth chamber under hydroponic conditions for four time spans of 2, 12, 48 or 72 hrs. Microarray analysis was made on mRNA isolated from 1 cm long tap root tips using an Affymetrix soybean genome array. Both novel and previously reported aluminum-responsive genes were identified. The differentially expressed genes were enriched for metabolism, stress response and transporters. Multiple putative Al-tolerance genes uniquely induced in the tolerant genotype includes the up-regulation of previously identified transcription factors auxin down regulated-like protein (ADR6-like) and basic leucine zipper (bZIP 94), sulfur transmembrane transport protein and lipid transfer protein (Sec 14 ) and novel genes that include rare cold inducible protein (RCI2B ), GPI-transamidase, malonyl-COA: Isoflavone 7-O-glucoside-6˝-O-malontransferase, a cell proliferation protein (WPP2), Oleosin protein, pectinestrease inhibitor, and impaired sucrose induction1. The genes identified in this study will be utilized as important genetic resources for future improvement of Al tolerance in soybean.
Key words: Soybean, Al tolerance, gene expression, microarray

overall_design: Two genotypes: PI 416937 (p) and Young (y); two treatments: aluminum or untreated; four time points: 2, 12, 48, and 72 hrs; 2 or 3 replicates.


title: Genome-wide mRNA analysis substantiates high-grade central osteosarcoma cell lines and xenografts as representative for their originating primary tumor type

status: Public on Sep 21 2011

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

summary: Conventional high-grade osteosarcoma is a primary malignant bone tumor, which is most prevalent in adolescence. Survival rates of osteosarcoma patients have not improved significantly in the last 25 years. Aiming to increase this survival rate, a variety of model systems are used to study osteosarcomagenesis and to test new therapeutic agents. Such model systems are typically generated from an osteosarcoma primary tumor, but undergo many changes due to culturing or interactions with a different host species, which may result into differences in gene expression between primary tumor cells, and tumor cells from the model system. We aimed to investigate whether gene expression profiles of osteosarcoma cell lines and xenografts are still comparable to those of the primary tumor. Osteosarcoma can be subdivided into several histological subtypes, of which osteoblastic, chondroblastic, and fibroblastic osteosarcoma are the most frequent ones. Using nearest shrunken centroids classification, we have generated an expression profile that can predict these histological subtypes in both osteosarcoma biopsies (n=66), as well as in two osteosarcoma model systems, i.e. osteosarcoma cell lines (n=13) and xenografts (n=18). Based on the preservation of mRNA expression profiles that are characteristic for the histological subtype we propose that these model systems are representative to the primary tumor from which they are derived.

overall_design:
Genome-wide expression profiling was performed on pre-treatment diagnostic biopsies of 76 resectable high-grade osteosarcoma patients from the EuroBoNet consortium (www.eurobonet.eu). Samples with a main histological subtype (n=66) were selected for subsequent subtype analyses. Out of the EuroBoNeT panel of 19 cell lines, 13 cell lines were recorded to belong to a main histological subtype. This set of 13 cell lines contained 4 cell lines derived from fibroblastic, and 9 cell lines derived from osteoblastic osteosarcomas. The 13 osteosarcoma cell lines IOR/MOS, IOR/OS10, IOR/OS14, IOR/OS15, IOR/OS18, IOR/OS9, IOR/SARG, KPD, MG-63, MHM, OHS, OSA, and ZK-58 were maintained in RPMI 1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin (Invitrogen) as previously described (PMID: 19787792). The osteosarcoma xenograft model is described in Kresse et al. (PMID: 21713766) In short, human tumors were implanted directly from patient samples and successively passaged subcutaneously in nude mice. Eighteen different xenografts were used, of which 3 were derived from chondroblastic, and 15 from osteoblastic osteosarcomas.

Osteosarcoma and xenograft tissue was handled as previously described in Buddingh, Kuijjer et al. (PMID: 21372215) Osteosarcoma cell lines were prepared as in Ottaviano et al. (PMID: 19787792) RNA isolation, synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips were performed as described in Buddingh, Kuijjer, et al. (PMID: 21372215) Microarray data processing and quality control were performed using the statistical language R as described in Buddingh, Kuijjer, et al. (PMID: 21372215) We performed a factorial LIMMA analysis comparing 50 osteoblastic, 9 chondroblastic, and 7 fibroblastic osteosarcomas pre-chemotherapy biopsies. Probes with Benjamini and Hochberg False discovery rate-adjusted P-values < 0.05 were considered to be significantly differentially expressed. The gene expression profile was generated on the dataset of biopsies using Bioconductor package PAMR. Internal cross-validation was performed 50 times. A threshold was selected where the error rate of the prediction profile was minimal. The minimum error rate was representative of 50 independent simulations. In order to minimize optimization bias, we validated the profile on an independent dataset of osteosarcoma biopsies (n=5), containing 1 chondroblastic osteosarcoma and 4 osteoblastic osteosarcomas. We subsequently applied the validated prediction profile to two independent datasets, the first consisting of gene expression data of osteosarcoma cell lines, the second of xenografts. Expression of the probes that composed the prediction profile was verified using a factorial LIMMA analysis, comparing chondroblastic, fibroblastic, and osteoblastic osteosarcoma biopsy samples.

middle: L

first: Heidi

last: Namløs

middle: I

last: Hauben

first: Isidro

last: Machado

first: Stine

last: Kresse

first: Massimo

last: Serra

first: Antonio

last: Llombart-Bosch

first: Pancras

last: Hogendoorn

first: Leonardo

middle: A

last: Meza-Zepeda

first: Ola

last: Myklebost

first: Anne-Marie

last: Cleton-Jansen


title: Expression data from the seed coats of black (iRT) and brown (irT) soybean variant for alleles of the R locus

status: Public on Aug 23 2011

city: Ottawa

first: Nikola

last: Kovinich

state: Ontario

address: 960 Carling

department: Bioprocesses

country: Canada

institute: Agriculture and Agri-Food Canada

summary:
The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 – 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development.
We used microarrays to determine global gene expression differences between black (iRT) and brown (irT) soybean seed coats at the transition stage of seed development (300 – 400 mg  fresh seed weight).

overall_design: To identify the complete set of gene transcripts that are differentially expressed between the seed coats of black (iRT) and brown (irT) Clark isolines, seed coats were dissected at the transition stage of seed development (300 – 400 mg fresh seed weight) for microarray analysis using the Affymetrix Soybean GeneChip. To ensure seed coats were of the same stage of development, the days post anthesis, pod length, pod color, embryo morphology, and transcript levels of the developmental marker gene Gm-r1083-1191, a putative cutin biosynthesis gene, and DFR1 were ensured to be equivalent between black (iRT) and brown (irT) isolines.

first: Nik

first: Brian

last: Miki


title: Gene expression profiles of DFCs and SHED 48 hours after in vitro transfection with a TP53 plasmid, a SP1 plasmid, or an empty vector.

status: Public on Aug 25 2011

first: Christian

last: Morsczeck

summary: Dental follicle is a loose connective tissue that surrounds the developing tooth. Dental follicle cells (DFCs) have a promising potential for tissue engineering applications including periodontal and bone regeneration. However, little is known about the molecular mechanisms underlying osteogenic differentiation. In a previous study we detected that more than 35 % of genes that are regulated during osteogenic differentiation of DFCs have promoter binding sites for the transcription factors TP53 and SP1. However, the role of these transcription factors in dental stem cells is still unknown. We hypothesize that both factors influence the processes of cell proliferation and differentiation in dental stem cells. Therefore, we transiently transfected DFCs and dental pulp stem cells (SHED; Stem cells from human exfoliated decidiuous teeth) with expression vectors for these transcription factors. After overexpression of SP1 and TP53, SP1 influenced cell proliferation and TP53 osteogenic differentiation in both dental cell types. The effects on cell proliferation and differentiation were less pronounced after siRNA mediated silencing of TP53 and SP1. This indicates that the effects we observed after TP53 and SP1 overexpression are indirect and subject of complex regulation. Interestingly, upregulated biological processes in DFCs after TP53-overexpression resemble the downregulated biological processes in SHED after SP1-overexpression. Here, regulated processes are involved in cell motility, wound healing and programmed cell death. In conclusion, our study demonstrates that SP1 and TP53 influence cell proliferation and differentiation and similar biological processes in both SHED and DFCs.

overall_design: Total RNAs were isolated from dental follicle cells after 48 hours of transfection with a TP53 expressions plasmid, a SP1 expressions plasmid and for control with an empty vector.

first: Oliver

last: Felthaus

first: Sandra

last: Viale-Bouroncle

last: Driemel

first: Torsten

last: Reichert

first: Gottfried

last: Schmalz


title: Impact of celR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Cellobiose

status: Public on Jul 25 2011

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔcelR to D39 wild-type grown M17 medium + 0.5 % (w/v) Cellobiose (CM17).

overall_design: One condition design comparision of two strains including a dye swap.

first: Tomas

middle: G

last: Kloosterman

first: Oscar

last: Kuipers


title: GmMPK4 is a negative regulator of SA-mediated defense response

status: Public on Jun 02 2011

first: PLEXdb Curator

middle: Sudhansu

summary: GmMPK4 silencing was performed in Glycine max (Williams 82) using virus-induced gene silencing (VIGS) mediated by Bean pod mottle virus (BPMV). Microarray analysis was performed to compare the transcriptional profile of GmMPK4-silenced plants vs vector control plants.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jianzhong Liu.  The equivalent experiment is GM25 at PLEXdb.]

overall_design:
genotype: Williams 82(4-replications)
genotype: GmMPK4-silenced Williams 82(4-replications)

first: Jianzhong

last: Liu


title: Impact of copY delation on the transcriptome of Streptococcus pneumoniae D39

status: Public on Jul 10 2011

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 copY-stop mutant to D39 wild-type grown in CDM without added copper.

middle: P


title: The cop operon is required for copper homeostasis and contributes to virulence in Streptococcus pneumoniae

summary:
High levels of copper are toxic and therefore bacteria must limit free intracellular levels to prevent cellular damage. In this study, we show that a number of pneumococcal genes are differentially regulated by copper, including an operon encoding a CopY regulator, a protein of unknown function (CupA) and a P1-type ATPase, CopA, which is conserved in all sequenced Streptococcus pneumoniae strains. Transcriptional analysis demonstrated that the cop operon is induced by copper in vitro, repressed by the addition of zinc and is autoregulated by the copper-responsive CopY repressor protein. We also demonstrate that the CopA ATPase is a major pneumococcal copper resistance mechanism and provide the first evidence that the CupA protein plays a role in copper resistance. Our results also show that copper homeostasis is important for pneumococcal virulence as the expression of the cop operon is induced in the lungs and nasopharynx of intranasally infected mice, and a copA(-) mutant strain, which had decreased growth in high levels of copper in vitro, showed reduced virulence in a mouse model of pneumococcal pneumonia. Furthermore, using the copA(-) mutant we observed for the first time in any bacteria that copper homeostasis also appears to be required for survival in the nasopharynx.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome analysis of the zebrafish embryonic host response to Edwardsiella tarda infection

status: Public on Oct 01 2011

city: Amsterdam

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

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


title: Transcriptional response of Streptococcus pneumoniae to copper

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0mM to 0.05 mM copper.

overall_design: Two condition design comparision of one strain including a dye swap.


title: Genotyping in Neuroblastoma Primary tumors

status: Public on Sep 15 2011

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

type: Genome variation profiling by genome tiling array

summary: We performed genotyping  of Neuroblastoma Primary tumors  using Illumina HumanHap 550 - v1,v3,v3duo and 610 Quad genotyping beadchips.

first: Edward

last: Attiyeh


title: Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors

status: Public on Oct 13 2010

city: Harbin

first: Yanming

last: Zhu

state: Heilongjiang

address: Wood Street 59

department: Life sciences

institute: Northeast Agriculture University

summary: Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO(3) stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO(3) highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (P < 0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response.

overall_design: Young leaves of three-week-old Glycine soja were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, leaves from three plants originating from the same experiment, condition and cultivar was pooled.

first: Ying

last: Ge

first: Yong

last: Li

first: De-Kang

last: Lv

first: Yan-Ming


title: PHK Cells: control vs. cyclosporine vs. 11R-VIVIT

status: Public on Nov 08 2010

city: Okayama city

first: Atsushi

last: Fujimura

institute: Okayama university

summary:
Calcineurin/NFAT signaling pathway has been shown to play important roles in various tissues such as the immune system, cardiac muscle and neuron. Although recent studies have shown that the pathway is involved in the regulation of hair growth, the precise mechanism is still unclear. In this study, we examine the molecular mechanism which is regulated by calcineurin/NFAT pathway, using two specific inhibitors for the pathway.
Transcriptional profiling of human keratinocyte cell line, PHK cells, comparing control untreated PHK cells with cyclosporin A (CsA)-treated or 11R-VIVIT-treated PHK cells. Goal was to identify the effects of NFAT inhibitors on PHK cell proliferation.
Cyclosporine A is a chemical compound, which strongly inhibits calcineurin phosphatase activity cooperating with cyclophilin, resulting in inhibition of NFAT signaling pathway.  11R-VIVIT is a cell-permeable peptide, which specifically interacts with NFAT and inhibits its binding to calcineurin, resulting in competitive inhibition of NFAT signaling pathway.

overall_design:
Three-condition experiment; untreated PHK cells, CsA-treated PHK cells and 11R-VIVIT-treated PHK cells.
Supplementary files: Significantly up-regulated genes across 4 different comparisons.

first: Kazuhito

last: Tomizawa


title: Transcriptional response of Streptococcus pneumoniae D39 to Zinc

status: Public on May 13 2011

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM Plus 0mM Zn2+ to grown in CDM plus 0.2 mM Zn2+.

overall_design: Two condition design comparison of Wild-type strain including a dye swap