title: Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

summary: In order to elucidate the molecular mechanism of gibberellin (GA)-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying GA promotion of maize mesocotyl elongation. These studies showed that the GA receptor GID1, the transcriptional factor MYB, and the genes encoding DELLA protein DWRF8, kinases, Raf, LRR, RLCK, and involved in flavonoid biosynthesis, aminosugars metabolism, cell wall synthesis and modification, might play critical roles in maize mesocotyl elongation.

overall_design: In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of GA3 treatment and UCZ (a GA biosynthesis inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.

first: Zhao

last: Guangwu

first: Fu

last: Junjie

first: Wang

last: Guoying

first: Ma

last: Pan

first: Wu

last: Liwen

last: Jianhua


title: Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

status: Public on Mar 05 2009

city: Madrid

first: Ramon

last: Diaz-Uriarte

state: Madrid

address: Melchor Fernandez Almagro 3

department: Structural Biology and Biocomputing Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Genomic mapping of DNA replication origins (ORIs) in mammals provides a powerful means for understanding the regulatory complexity of our genome. Here we combine a genome-wide approach to identify preferential sites of DNA replication initiation at 0.4% of the mouse genome with detailed molecular analysis at distinct classes of ORIs according to their location relative to the genes. Our study reveals that 85% of the replication initiation sites in mouse embryonic stem (ES) cells are associated with transcriptional units. Nearly half of the identified ORIs map at promoter regions and, interestingly, ORI density strongly correlates with promoter density, reflecting the coordinated organisation of replication and transcription in the mouse genome. Detailed analysis of ORI activity showed that CpG island promoter-ORIs are the most efficient ORIs in ES cells and both ORI specification and firing efficiency are maintained across cell types. Remarkably, the distribution of replication initiation sites at promoter-ORIs exactly parallels that of transcription start sites (TSS) suggesting a co-evolution of the regulatory regions driving replication and transcription. Moreover, we found that promoter-ORIs are significantly enriched in CAGE tags derived from early embryos relative to all promoters. This association implies that transcription initiation early in development sets the probability of ORI activation unveiling a new hallmark in ORI efficiency regulation in mammalian cells.

overall_design: Two biological replicates of lambda-exonuclease treated short nascent strands (100-600 or 300-800 nt in length) were co-hybridised with genomic DNA from the same cells to tiled genomic array covering 10.1 Mb of the mouse genome (Agilent Technologies)

first: Joana

last: Sequeira-Mendes

first: Ramón

last: Díaz-Uriarte

first: Anwyn

last: Apedaile

first: Derek

last: Huntley

first: Neil

last: Brockdorff

first: María

last: Gómez


title: Salmonella enteritidis ciprofloxacin resistance effect on transcription in LB

status: Public on Mar 06 2009

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

summary: comparison of total RNA profiles obtained from ciprofloxacin resistant colonies of two separate Enteritidis isolates with their respective wt parents

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: total RNA of both wt (with reduced cip sensitivity at MIC=0.2 ug/ml) and spontaneous cipR mutants (MIC>32ug/ml) in LB log phase was harvested from Enteritidis strain 104 (from poultry host) and Enteritidis 5408 (from human host), and compared on a PCR product array

first: Steffen

last: Porwollik

first: Seamus

last: Fanning

first: Jonathan

last: Frye


title: Acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation

city: Halifax

first: Yung-Hua

last: Li

state: NS

address: 5981 University Ave. Rm5215

department: Applied Oral Sciences

country: Canada

institute: Dalhousie University

summary:
Global transcriptional analysis of acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation

pH is a major environmental factor that regulates gene expression in many bacteria. Streptococcus mutans in dental biofilms is regularly exposed to cycles of acidic pH during the ingestion of fermentable dietary carbohydrates. The ability of S. mutans to tolerate low pH is crucial for its virulence and the pathogenesis in dental caries. To better understand its acid tolerance mechanisms, we used DNA microarray to perform genome-wide transcriptional analysis of S. mutans in response to acidic pH. The results showed that adaptation of S. mutans to pH 5.5 for 2 hrs induced differential expression of nearly 14% of genes in the genome, including 169 up-regulated genes and 108 down-regulated genes, largely categorized into six groups. Especially, we found that the genes encoding multiple two-component systems, including CiaHR, LevSR, LiaSR, ScnKR, HK/RR07 and ComDE, were up-regulated during acid adaptation. These findings were further confirmed by real time qRT-PCR and phenotypic assays of the gene deletion mutants. The results support that the multiple two-component systems are required for S. mutans to orchestrate its signal transduction networks for optimal adaptation to acidic pH.

overall_design: Total RNAs were isolated from S. mutans UA159 cells (0.6 at OD600) grown in a TYG broth (3% tryptone, 0.3% yeast extract and 20 mM glucose) at either pH 5.5 or pH 7.5. The RNAs were treated with RNase-free DNase 1 and purified by Qiagen RNeasy mini columns. The purified RNAs were used to generate cDNA probes by an indirect labeling method based on the protocol from TIGR. The cDNAs were coupled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen). The labeled cDNA probes from three different cultures of UA159 were hybridized to the S. mutans microarray slides obtained from PFGRC (http://pfgrc.tigr.org). Array hybridization was conducted using a protocol from the PFGRC with minor modification. After hybridization, washes and dried, the array slides were scanned by ScanArray 5000XL Reader (Perkin Elmer, Boston, MA). After the array slides were scanned, the resulting images were loaded into TIGR Spotfinder software (http://www.tigr.org/software/) and overlaid. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, and the intensity values of each spot were determined. Signal intensities of individual channels from an array slide were averaged and normalized using an array data analysis software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis. A t-test was used to determine the consistency of ratios across replicate hybridizations. Only genes whose ratios were ≥ 2-fold changes (either increase or decrease) with 99% confidence interval (P ≤ 0.01) were considered statistically significant.

first: Yongxing

last: Gong

first: Xiao-Lin

last: Tian


title: Breast cancer cells: ER status and fatty acid treatment

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

summary: Estrogen receptor dependent genomic expression profiles in breast cancer cells in response to fatty acids. Estrogen receptor positive cells respond better to omega 3 treatments.

overall_design: two condition experiments: ER positive and negative breast cancer cells exposed to two fatty acids: omega-3 (eicosapentanoic acid) and 6 (arachidonic acid).

first: Marti

last: Jett


title: Transcriptional profiling of MLL5 Knock down vs. control C2C12 myoblasts (S phase enriched)

status: Public on Mar 04 2009

city: Hyderabad

first: Jyotsna

last: Dhawan

state: Andhra pradesh

address: Uppal road

department: Cell Biology

country: India

institute: Centre for cellular and Molecular Biology

summary:
Knockdown of MLL5 led to deregulation of S phase. To understand the molecular basis for this phenotype, we performed microarray analysis of S phase synchronized myoblasts.
Genes differentially regulated by MLL5 knock down were revealed by microarray analysis using NIA15K mouse chips.

overall_design: Control and knock down cells were synchronized at G0 by suspension culture and reactivated to enter S phase by replating for 24hrs in growth medium.

first: Soji

last: Sebastian

first: Prethish

last: Sreenivas

first: Ramkumar

last: Sambasivan

first: Sirisha

last: Cheedipudi

first: Prashanth

last: Kandalla

first: Grace

middle: K

last: Pavlath


title: Gene expression profile prospectively predicts peritoneal relapse after curative surgery of gastric cancer

city: Suita

first: ATSUSHI

last: TAKENO

state: Osaka

address: 2-2, Yamadaoka

department: Surgery

country: Japan

institute: Osaka university

summary:
Purpose: Our study aimed to disclose the specific gene expression profile representing peritoneal relapses inherent in primary gastric cancers and to identify patients at high risk of peritoneal relapse in a prospective study on the basis of the molecular prediction.
Experimental Design: RNA samples from 141 primary gastric cancer tissues after curative surgery were profiled using oligonucleotide microarrays covering 30,000 human probes. Firstly we constructed molecular prediction system and validated the robustness and prognostic validity of the analysis by 500 times multiple random sampling in 56 retrospective set consisting of 38 relapse free and 18 peritoneal relapse patients. Secondly we applied this prediction to 85 prospective set to assess the predictive accuracy and prognostic validity.
Results: In retrospective phase, 500 times multiple random sampling analysis yielded 68% predictive accuracy in average and 22 gene expression profile associated with peritoneal relapse was identified. This prediction could identify significantly poor prognostic patients. In prospective phase, the molecular prediction yielded 76.9% overall accuracy. Kaplan–Meier analysis with peritoneal relapse free survival showed a significant difference between ‘good signature group’ and ‘poor signature group’ (Log-rank p=0.0017). Multivariate analysis by Cox regression hazards model revealed that the molecular prediction was the only independent peritoneal relapse prognostic factor.
Conclusions: Gene expression profile inherent in primary gastric cancer tissues can be useful to predict peritoneal relapse prospectively after curative surgery and individualize postoperative management to improve the prognosis of advanced gastric cancers.

overall_design: Of 141 samples, 56 represented the retrospective phase and 85 represented the prospective phase.


title: Gene expression analysis & Comparative genomic hybridization from Lung cancer Cell lines

status: Public on Mar 03 2009

city: New Haven

first: Pedro

middle: P

last: Medina-Vico

state: CT

address: 266 Whitney Ave, 938 KBT

institute: Yale University

type:
Expression profiling by array
Genome variation profiling by array

summary: Gene expression and Comparative genomic hybridization (CGH) microarrays performed in a set of 8 Lung cancer Cell lines.

overall_design: The search for oncogenes is becoming increasingly important in cancer genetics because they constitute suitable targets for therapeutic intervention. To identify novel oncogenes, activated by gene amplification, we performed high-resolution CGH (Comparative Genome Hybridization) analysis on cDNA microarrays and compared DNA copy number and mRNA expression levels in lung cancer cell lines. We have performed both microarrays (expression and CGH) in a set of 8 human lung cancer cell lines: Calu3, H23, H441, A427, H522, A549, H1299, H2126.

last: Medina

first: Sandra

last: Castillo

first: Montse

last: Sanchez-Cespedes


title: The effect of PLC inhibitor on cold responsive transcriptome.

city: BEAUCOUZE

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary:
Identification of genes induced with the cold via inhibition of the phospholipase C - To answer this question we chose a pharmacological approach. We decided to use molecules that are going to inhibit PLC.
U73343 is an inactive homolog of U73122 (inhibitor of the phospholipase C pathway).
Keywords: treated vs untreated comparison

overall_design: 3 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Eric

last: Ruelland

first: Marie-Laure

middle: L

last: Martin-Magniette


title: DCC binding and function (ChIP-chip: SDC-3, DPY-27, Mock)

status: Public on Mar 01 2009

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

type: Genome binding/occupancy profiling by genome tiling array

summary:
In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X gene products between males (1X) and females (2X).  Here we identify cis-acting regulatory elements that target the C. elegans X chromosome for repression by the DCC.  The DCC binds to discrete, dispersed sites on X of two types.  rex sites recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12 bp consensus motif that is enriched on X.  This motif is critical for DCC binding, is clustered in rex sites, and confers much of X-chromosome specificity.  Motif variants enriched on X by 3.8-fold or more are highly predictive (95%) for rex sites.  In contrast, dox sites lack the X-enriched variants and cannot bind the DCC when detached from X.  dox sites are more prevalent than rex sites and, unlike rex sites, reside preferentially in promoters of some expressed genes.  These findings fulfill predictions for a targeting model in which the DCC binds to recruitment sites on X and disperses to discrete sites lacking autonomous recruitment ability.  To relate DCC binding to function, we identified dosage-compensated and non-compensated genes on X.  Unexpectedly, many genes of both types have bound DCC, but many do not, suggesting the DCC acts over long distances to repress X gene expression.  Remarkably, the DCC binds to autosomes, but at far fewer sites and rarely at consensus motifs.  DCC disruption causes opposite effects on expression of X and autosomal genes.  The DCC thus acts at a distance to impact expression throughout the genome.

Keywords: dosage compensation, condensin, X chromosome, gene expression, epigenetics, C. elegans

overall_design: ChIP-chip experiments included: biological duplicates of SDC-3, a single DPY-27 IP, and a mock IP.

first: Judith

last: Jans

first: John

middle: M

last: Gladden

first: Edward

middle: J

last: Ralston

first: Catherine

middle: S

last: Pickle

first: A

middle: H

last: Michel

first: Rebecca

middle: R

last: Pferdehirt

first: Michael

middle: B

last: Eisen


title: Cellulose-induced regulation of Phanaerochaete chrysosporium genes

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary:
Transcript profiles of Phanerochaete chrysosporium grown on different substrates were analyzed. Array design based on the DoE's Joint Genome Institute's v2.1 annotation. Goal is to define genes involved in cellulose degradation.

Keywords: gene expression under different culture conditions

overall_design: From a data set of 10,004 unique alleles, each Roche NimbleGen (Madison, WI) array featured 12 unique 60mer probes per gene, all in triplicate. (Seven gene models composed mostly of repetitive DNA were represented by only 2 to 11 60mers.) Total RNA was purified from below mentioned media. In short, cultures were harvested by filtering through Miracloth (Calbiochem, EMD Biosciences, Gibbstown, NJ), squeeze dried and snap frozen in liquid nitrogen. Pellets were stored at -80 C until use. Extraction buffer was prepared by combining 10 ml 690 mM para-aminosalicylic acid (sodium salt) (Sigma-Aldrich, St. Louis, MO) with 10 ml 56 mM triisopropylnapthalene sulfonic acid (sodium salt) (Sigma-Aldrich), and placed on ice. To this was added 5 ml 5X RNB (1.0 M Tris, 1.25 M NaCl, 0.25 M EGTA). The pH of the 5X RNB was adjusted to 8.5 with NaOH. The mixture was kept on ice and shaken just before use.  Frozen fungal pellets were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. The ground mycelia were transferred to Falcon 2059 tubes (VWR International, West Chester, PA), and extraction buffer was added to make a thick slurry. The samples were vortexed vigorously and placed on ice until all samples were processed.  One half volume TE-saturated phenol (Sigma-Aldrich) and ¼ volume chloroform (Sigma-Aldrich) were added to each sample and vortexed vigorously.  Samples were spun at 2940 x g in a fixed-angle rotor for 5 minutes.  The aqueous layer was removed to a new tube, and phenol:chloroform extractions were repeated until the interface between the aqueous and organic layers was clear. The final aqueous extractions were placed in clean 2059 tubes, to which was added 0.1 volume 3M sodium acetate, pH 5.2, (DEPC-treated) and 2 volumes absolute ethanol. The tubes were shaken vigorously and stored overnight at -20˚C.  The tubes were spun 1 hour at 2940 x g, the supernatants were decanted, and the pellets were resuspended in 4 ml RNase-free H2O. total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup. RNAs were eluted from the RNeasy spin columns using two spins, for a final volume of 2 ml. The eluted RNAs were ethanol precipitated and stored overnight at -20˚C. The RNAs were spun 1 hour at 2940 x g, washed 1x with 70% ethanol, and resuspended in 50-100ul RNase-free H2O. Three biological replicates per medium were used (15 separate arrays).   RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland). In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 400U of SuperScript II (Invitrogen) for 60 min at 42˚C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07U/ul DNA ligase (Invitrogen), 0.27U/ul DNA polymerase I (Invitrogen), 0.013U/ul RNase H (Invitrogen), at 16˚C for 2 hours.  Immediately following, 10U T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16˚C. Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies) for 10 minutes at 37˚C. Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.  One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D. unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37˚C. Array hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42˚C. Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4. DNASTAR ArrayStar v2.1 (Madison,WI) software was used to quantify and visualize data. Analyses were based on three biological replicates per culture medium. Quantile normalization and robust multi-array averaging (RMA) were applied to the entire dataset.


title: Myc influences embryonic stem cell pluripotency by regulating miRNAs

city: Carlsbad

first: Aimee

last: Jackson

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

summary: Previous studies have demonstrated that the c-Myc transcription factor regulates and cooperates with oncogenic miRNAs to accelerate tumorigenesis. Much recent work has shown that Myc plays an important role in stem cell pluripotency. These findings have prompted us to determine whether Myc regulates embryonic stem cell pluripotency through miRNAs. We have employed both miRNA- and expression- profiling to demonstrate that Myc up- or down-regulates a subset of miRNAs, which in turn influence expression of groups of genes involved in lineage differentiation. Chromatin immunoprecipitation analysis indicates that c-Myc binds proximal to the coding regions of these miRNAs in a dose dependent manner. Moreover, introduction of Myc-targeted miRNAs into murine ES cells significantly retards differentiation upon withdrawal of LIF. Our data suggest that at the ES cell stage, c-Myc acts at least in part through a subset of miRNAs to maintain pluripotency.

overall_design: Synthetic microRNAs were transfected into mouse embryonic stem cells, and expression signatures from these cells were compared to mock-transfected cells (transfection reagent in the absence of microRNA).  Two individual experiments were performed, one containing 12h and 24h timepoints and one containing only a 24h timepoint.  Within each experiment, each individual signature was ratioed to the average of all signatures in the experiment.

first: Chin-Hsing

last: Lin

first: Jie

last: Guo

first: Peter

last: Linsley

first: Robert

middle: N

last: Eisenman


title: DCC binding and function (ChIP-chip: SDC-3, MIX-1, DPY-27, Mock)

overall_design: ChIP-chip experiments included: biological duplicates of SDC-3 and MIX-1 IPs, a single DPY-27 IP, and 3 mock IPs.


title: Babesia Infected/Control LongSAGE libraries for Boophilus microplus ovary tissue

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

state: TX

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

summary:
Babesia infected (and control) ovary tissue was used to construct LongSAGE libraries.   The intent was to find differential gene expression in both libraries.
Details:
The extraction was done using Ambion's ToTALLY RNA kit, and the concatemers where constructed using Invitrogen's I-SAGE Long kit.   The concatmer files (multiple fasta sequence files) were processed using in-house perl scripts to extract the 17bp LongSAGE tags.
**Note: contact person:   Felix D. Guerrero.   email:  felix.guerrero@ars.usda.gov
Keywords: LongSAGE

overall_design:
1 control and 1 treatment library was constructed.  Besides the ovary, gut was also looked at but the data was un-analyzable.

**************  Analysis Results  **********

Ovary Infected:
	Project tags: 				8750
	Project files(concatemers/sequences): 	703
	Project Duplicate Dimers(ditags):	1612
	Unique tags				5315
	Total tags inc. ditags			11974
	% of tags in duplicate ditags		36%

Ovary Control:
	Project tags: 				6764
	Project files(concatemers/sequences): 	368
	Project Duplicate Dimers(ditags):	846
	Unique tags				3937
	Total tags inc. ditags			8456
	% of tags in duplicate ditags		25%

first: Felix

middle: D

last: Guerrero

first: Glen

middle: A

last: Scoles

first: Kylie

middle: G

last: Bendele


title: The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

city: Mol

first: Jef

last: Hooyberghs

address: Boeretang 200

country: Belgium

institute: VITO nv

summary:
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning.  Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution.  The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.

Keywords: experiment to assess technical aspects of hybridization in microarrays

overall_design: The study consists of four experiments. Each experiments consists of one slide with eight identical microarrays which were hybridized with an identical solution but at a different concentration. Per experiment a single target sequence in solution was used for hybridization: target1 to target4 (Table 1 main manuscript or description of samples below). Each target oligo was bought in duplicate,  referred to as oligos a and b. In experiment 1 and 2 a fragmentation step (f) was applied. More details can be found in the main manuscript especially Table 3.

first: Paul

last: Van Hummelen

first: Enrico

last: Carlon


title: Expression data from malting barley seeds

city: Fort Collins

first: Nora

last: Lapitan

state: CO

address: Plant Science Bldg

department: Soil and Crop Sciences

institute: Colorado State University

summary:
Malting is seed germination under strictly controlled environmental conditions. Malting quality is a complex phenotype that combines a large number of interrelated components, each of which shows complex inheritance. Currently, only a few genes involved in determining malting quality have been characterized. This study combined transcript profiling with phenotypic correlations to identify candidate genes for malting quality.
We used the Barley1 GeneChip® array to identify differentially expressed genes in four malting stages relative to dry seed in the barley variety Morex, and to identify differentially expressed genes among four barley varieties.
Keywords: time course and genotype differences

overall_design: Four malting barley cultivars were micromalted: Morex and Legacy (6-row), Merit and Harrington (2-row). Two to three batches of micromalting (biological replications) were performed. For each micromalting experiment, 20 g samples were collected for Morex at four stages: steeping, 24 h germination (day 1), 93 h germination (day 4), and finished malt after kilning was completed. Ungerminated, dry seed of Morex was used as reference sample. In another experiment, seeds of Legacy, Harrington, and Merit were micromalted and 20 g samples were collected for each variety during day 1 and day 4 germination stages. Expression profiles were compared among the four cultivars separately for day 1 and day 4.

first: Ann

last: Hess

first: Anna

last: Botha

first: Blake

last: Cooper

first: Timothy

last: Close

first: Christopher

last: Lawrence

first: Jolanata

last: Menert

first: Deborah

last: Badillo


title: Identification of novel transcriptional regulators involved in differentiation and function of monocyte and macropahge

status: Public on Feb 27 2009

city: Berlin

first: Agnes

last: Baek

address: Ihnestrasse 63-73

department: Dept. of Vetebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Maturation of blood monocytes into tissue macrophages and subsequent inflammatory response was mimicked in U937 cells of human histocytic lymphoma origin. Whole genome array analysis was employed to evaluate gene expression profile to identify underlying transcriptional networks implicated during the processes of differentiation and inflammation. In addition to already known transcription factors (i.e. MAFB, EGR, IRF, BCL6, NFkB, AP1, Nur77), gene expression analysis further revealed novel genes (i.e. MEF2, BRI, HLX, HDAC5, H2AV, TCF7L2, NFIL3) previously uncharacterized to be involved  in the differentiation process. A total of 58 selected genes representing cytokines, chemokines, surface antigens, signaling molecules and transcription factors were validated by real time PCR and compared to primary monocyte-derived macrophages. Beside the verification of several new genes, the comparison reveals individual heterogeneity of blood donors.

overall_design: U937 cells were differentiated into monocytes by VitD3 (24 hrs) or into marophages by PMA (6 hrs, 12 hrs, 24 hrs and 32 hrs). Cells differentiated for 24 hrs by PMA are further stimulated by LPS for 2 hrs. Total RNA from 6 case samples were subjected to differential gene expression in comparison to undifferentiated U937 cells.

first: Scholastica

first: Stefan

last: Haas

first: Holger

last: Hackstein

first: Gregor

last: Bein

first: Maria

last: Hernandez-Santana

first: Sascha

last: Sauer

first: Hans

last: Lehrach

first: Harald

last: Seitz


title: Effects of overexpression of EhMyb-dr on transcription in Entamoeba histolytica

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

summary: A myb domain containing protein of the SHAQKY family, EhMyb-dr, was overexpressed in E. histolytica trophozoites, and effects on transcription were measured.

overall_design: Two arrays of trophozoites expressing Myc tagged EhMyb-dr were compared to two arrays performed on wild type trophozoites. The effects of transfection and drug were controlled for by including data from trophozoites expressing irrelevant plasmids, and grown in the same level of G418. All parasites were of strain HM-1:IMSS

first: Jason

last: Hackney

first: Upinder

last: Singh


title: Cell cycle-regulated gene expression in tobacco cells

status: Public on Feb 28 2009

city: Nagoya

first: Masaki

last: Ito

address: Chikusa

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary:
Tobacco BY-2 cells can be highly synchronized by treatment with an inhibitor of DNA synthesis, aphidicolin. For comprehensive understanding of cell cycle-regulated gene expression in tobacco, microarray analysis was conducted in synchronized cultures of BY-2 cells. Cells were treated with aphidicolin for 24 hours to block the entry into and progression through the S phase. After release from the aphidicolin block, cells were sampled every 2 h from 0–16 h. cDNA probes prepared from these samples were hybridised to a custom-made16K microarray. We performed this procedure twice independently to identify transcripts that reproducibly showed similar cell cycle-regulated expression. A total of 883 putative cell cycle-regulated transcripts were identified from 16,896 duplicated spots on the microarrays. These transcripts could be categorised into 10 classes on the basis of transcript expression patterns in the cell cycle.

Keywords: time course

overall_design: Synchronization experiments were repeated twice (experiments A and B). In each experiment, cells were sampled every 2 h during the culture periods (0-16 h), and used for microarray analysis.

first: Kiichi

last: Kato

first: Ivan

last: Gális

first: Shiori

last: Suzuki

first: Satoshi

last: Araki

first: Taku

last: Demura

first: Marie-Claire

last: Criqui

first: Thomas

last: Potuschak

first: Pascal

last: Genschik

first: Hiroo

last: Fukuda

first: Ken

last: Matsuoka


title: DCC binding and function (ChIP-chip: SDC-2)

first: Barbara

last: Meyer

overall_design: ChIP-chip experiments included: biological duplicates of SDC-2.

first: Judith

last: Jans

first: John

last: Gladden

first: Edward

last: Ralston

first: Catherine

last: Pickle

first: A

last: Michel

first: Rebecca

last: Pferdehirt

first: Michael

last: Eisen


title: Nickel and binary metal mixtures in Daphnia magna after 96h

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

institute: University of Antwerp

summary: The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses.  In this study, gene expression and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction.  Furthermore, genes involved in oxygen transport and heme metabolism (hemoglobin, δ-aminolevilunate synthase) were down-regulated. Applying a Partial Least Squares regression on nickel fingerprints and biochemical (sub)organismal parameters revealed a set of co-varying genes (hemoglobin, RNA terminal phosphate cyclase, a ribosomal protein and an “unknown” gene fragment). An inverse relationship was seen between the mRNA expression levels of different cuticula proteins and available energy reserves. In addition to the nickel exposure, daphnids were exposed to binary mixtures of nickel and cadmium or nickel and lead. Using multivariate analysis techniques, the mixture gene expression fingerprints (Ni2++Cd2+, Ni2++Pb2+) were compared to those of the single metal treatments (Ni2+, Cd2+, Pb2+).  It was hypothesized that the molecular fingerprints of the mixtures would be additive combinations of the gene expression profiles of the individual compounds present in the mixture. However, our results clearly showed additionally affected pathways after mixture treatment (e.g. additional affected genes involved in carbohydrate catabolic processes and proteolysis), indicating interactive molecular responses which are not merely the additive sum of the individual metals. These findings, although indicative of the complex nature of mixture toxicity evaluation, underline the potential of a toxicogenomics approach in gaining more mechanistic information on the effects of single compounds and mixtures.

overall_design: In general, a universal reference design was used. The following analysis (normalization and statistical analysis) was performed. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments). Subsequently, a MIAME compliant platform, the BioArray Software Environment Database (BASE 1.2.12, http://www.islab.ua.ac.be/base/) was used for storage, further evaluation and succeeding statistical analysis of the microarray datasets. After a local background correction, spots with a foreground larger than the mean local background +2 standard deviations for one or both colours were selected for further analysis. The Log2 transformed Cy3/Cy5 ratio data were normalized by implementation of a Locally Weighed Scatterplot Smoothing (Lowess) (Yang et al., 2002) step, which is an intensity-based method. Significant vertical cut-off values of log -0.85 and 0.85 were determined through multiple self-self hybridizations. These were performed by labelling the same biological material with both Cy3 and Cy5 dyes and hybridizing them simultaneously on a microarray slide. To statistically evaluate the microarray results, Significance Analysis of Microarrays (SAM) described by Tusher et al. (2001) was applied on the Lowess normalized datasets. With this SAM approach a false discovery rate (FDR) below 5% was applied. As a result genes with log2 ratios outside the confidence interval of -0.85 and 0.85 were considered as differentially expressed gene fragments when FDR was below 5%.

first: Anneleen

last: Soetaert

first: Wim

last: De Coen


title: Transcriptional Profiling of Neisseria gonorrhoeae biofilm

city: Iowa City

first: Megan

middle: L.

last: Falsetta

state: IA

address: 51 Newton Road

department: Microbiology

institute: University of Iowa

summary: Neisseria gonorrhoeae, the etiologic agent of gonorrhea, is frequently asymptomatic in women, often leading to chronic infections.  One factor contributing to this may be biofilm formation.  N. gonorrhoeae can form biofilms over glass and plastic surfaces.  There is also evidence that biofilm formation may occur during natural cervical infection.  To further study the mechanism of this biofilm formation, transcriptional profiles of N. gonorrhoeae biofilm were compared to planktonic profiles.  Biofilm RNA was extracted from N. gonorrhoeae 1291 grown for 48 hours in continuous flow chambers over glass.  Planktonic RNA was extracted from the biofilm runoff.   When biofilm was compared to planktonic growth, 3.8 % of the genome was differentially regulated.  Genes highly up-regulated in biofilm included aniA, norB, and ccp, which play critical roles in anaerobic metabolism and oxidative stress tolerance.  Down-regulated genes included the nuo gene cluster (NADH dehydrogenase) and the cytochrome bcI complex, which are involved in aerobic respiration and are thought to contribute to endogenous oxidative stress.  Furthermore, we determined that aniA, ccp, and norB insertional mutants are attenuated for biofilm formation over glass and transformed human cervical epithelial cells (THCEC).  This data suggests that biofilm formation could minimize oxidative stress during cervical infection and allow N. gonorrhoeae to maintain a nitric oxide steady state that may be anti-inflammatory.

overall_design: Six biofilm flow chambers were inoculated with N. gonorrhoeae strain 1291 wildype.  Flow chambers were inoculated with approximately 1 ml of a cell suspension (in biofilm media) from an overnight plate that was suspended to an OD600 of 0.3.   Two flow cells each were supplied by a single reservoir of media and the runoff from these two flow cells was passed through a sterile glass wool filter for the removal of detached biofilm flocs, and collected in a sterile waste flask and cultured to assess culture purity.  At this time, the waste flask was replaced with a second sterile flask containing 10 ml of RNAlater® (Qiagen Corporation, Valencia, CA) and 100 µl of 10% sodium azide.  For the final 24 hours of biofilm growth, the filtered planktonic effluent was collected in this solution to preserve the RNA and prevent transcriptional changes from occurring.  Planktonic RNA was extracted from the collected effluent of the two flow cells, while each biofilm RNA was extracted directly from these two flow cells.  RNA purity was assessed on an Agilent 2100 Bioanalyzer (Quantum Analytics, Foster City, CA), and only samples with RNA integrity numbers of 7.5 or greater were used for hybridization to microarrays.  All six samples had RNA integrity numbers of 7.5 or greater.  Therefore, we elected to hybridize the two samples with the highest integrity numbers.

last: Bair

first: Shan

middle: C

last: Ku

first: Rachel

last: vaden Hoven

first: Christopher

middle: T

last: Steichen

first: Alastair

last: McEwan

last: Jennings

last: Apicella


title: Role of Manganese Efflux for Signaling and Pathogenesis in Streptococcus pneumonia

city: Memphis

first: Jason

middle: W

last: Rosch

state: TN

address: 262 Danny Thomas Place

department: Infectious Disease

institute: St Jude Children's Hospital

summary: Microarray analysis of Streptococcus pneumoniae TIGR4 transcriptome in response to manganese as the transcriptome changes in response to intracellular manganese accumulation via a mutation in sp1552/mntE a manganese efflux protein.

overall_design: Investigating role of manganese efflux and accumulation in S. pneumoniae: 3 TIGR4 in ThyB vs. TIGR4 in Mn  and 3 TIGR4 in Mn vs mntE1 in Mn replicate 3

first: Yong-Dong

last: Wang

first: Granger

last: Ridout

first: Elaine

last: Tuomanen


title: Gene expression in striatums of Foxp2-hum, Foxp2-ko and wild-type mice

status: Public on Mar 02 2009

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary: It has been proposed that two amino acid substitutions in the transcription factor FOXP2 have been positively selected during human evolution due to effects on aspects of speech and language. Here, we introduce these substitutions into the endogenous Foxp2 gene.of mice. Although these mice are generally healthy, they have qualitatively different ultrasonic vocalizations, decreased exploratory behavior and decreased dopamine concentrations in the brain suggesting an effect of the humanized Foxp2 allele on basal ganglia. In the striatum, a part of the basal ganglia that is affected in humans with a speech deficit due to one non-functional FOXP2 allele, we find that medium spiny neurons have increased dendrite lengths and increased synaptic plasticity. Since mice carrying one non-functional Foxp2 allele show opposite effects, this suggests that alterations in cortico-basal ganglia circuits might have been important for the evolution of speech and language in humans. In this particular experiment, we investigate the effects of human Foxp2 (Foxp2hum) and the non-functional Foxp2 allele on striatal gene expression in embryonic, young and adult mice.

overall_design: We determined genome-wide gene expression patterns in striatal biopsies from Foxp2hum/hum, Foxp2wt/ko and Foxp2wt/wt mice using high-density oligonucleotide arrays. The animals were derived from two independent FoxP2 knock-in strains and one knock-out strain. In total 71 animals were used, 29 males and 42 females. The mice ages were E16.5, P15, P18,  P21 and P95 when sacrificed. The microarrays were processed in totally six batches.

first: Wolfgang

last: Enard

first: Sabine

last: Gehre

first: Kurt

last: Hammerschmidt

last: Hölter

first: Torsten

last: Blass

first: Martina

middle: K

last: Brückner

first: Christiane

last: Schreiweis

first: Christine

last: Winter

first: Reinhard

last: Sohr

first: Lore

last: Becker

first: Victor

last: Wiebe

first: Birgit

last: Nickel

first: Thomas

last: Giger

first: Uwe

last: Müller

first: Svante

last: Pääbo


title: Transcriptional Profiling Analysis of Host response to Clostridium perfringens Infection in Broilers

city: college station

first: Huaijun

last: Zhou

address: 101 Kleberg Center

department: Poultry Science

institute: Texas A&M University

summary: Necrotic enteritis is a disease caused by Clostridium perfringens, which threatens poultry production in the absence of dietary antibiotics. A total number of 144 Ross broilers were reared in 12 pens with each hosting 12 birds.  Each 6 pens of birds were fed medicated (bacitracin at 55 ppm) or non-medicated starter diets (Nutreco Canada Agresearch) immediately after the chicks were placed. At day 18, birds were challenged with C. perfringens (107 cfu per ml mixed with feed). Spleens were collected from 12 birds of each group at day 18 (before infection), 19, 20, and 22. A low-density chicken immune microarray was used to study gene expression profiling of host response to C. perfringens infection. Six biological replicates (2 birds per biological replicate) for each treatment group were labeled with either Cy5 or Cy3 with dye swap. A total of 24 arrays were used for this study. Gene signal intensity was globally normalized by LOWESS and expressed as log2 ratios. A mixed model including treatment, time, array, subgrid (random effect), dye, and all interactions among treatment and time was used to identify differentially expressed genes between post-infection vs. pre-infection, among post-infections, and between medication treatments, at the 5% significance level. The results indicated subtle medication effects on gene expression of these immune-related genes compared to bacterial infection effect. Our findings strongly suggest that both cell-mediated and antibody-mediated immune responses via MHC class I and II systems were actively involved in the host defense against C. perfringens infection in broilers. The unique cytokine signaling pathway and apoptosis cascade found in the study provide a new insight of molecular regulation of host immune response. Collectively, the findings of the present study will shed light on the molecular mechanisms underlying C. perfringens infection in broilers.

overall_design: There were two groups: medicated and non-medicated. Spleen were collected to isolate total RNA for gene expression profiling.For the microarray study, two birds from each pen were pooled within each group. To account for any bias inherent to the fluorescent dyes, three of the six medicated replicates were labeled with Cy3 and the other three were labeled with Cy5 at each time point. The same design was applied for the non-medicated group. There were six hybridizations between medicated and non-medicated replicates at each time point. Twenty-three out of 24 arrays were used (data from one array were discarded due to poor quality).

first: Joshua

last: Gong

first: Jennifer

last: Brisbin

first: Hai

last: Yu

first: Aimie

last: Sarson

first: Weiduo

last: Si

first: Shayan

last: Sharif

first: Yanming

last: Han


title: Gender-specific gene response to exercise

status: Public on Feb 25 2009

city: Tübingen

first: Stephan

last: Symons

address: Sand 14

department: Department for Information and Cognitive Sciences

institute: Center for Bioinformatics Tuebingen

summary:
The immunological reaction to exercise has been investigated with increasing intensity in the last 10-20 years, with most human studies performed in male subjects. Recently, gender-specific aspects have received growing attention, but studies carefully monitoring the influence of gender, including the menstrual cycle, are rare. Here, we report gene expression patterns in response to a run at 93% of the individual anaerobic threshold of 9 women with regular menstrual cycles and no use of oral contraceptives who ran both at day 10 (follicular phase, F) and at day 25 (luteal phase, L) of their cycle. 12 male subjects (M) served as controls. The mRNA was pooled group wise and processed on a gene expression microarray encompassing 789 genes, including major genes of the inflammatory and anti-inflammatory reaction. The differences of gene expression between time points t0 (before run) and t1 (after run) were analyzed. Females in L showed a higher extent of regulation than females in F or men. Among those genes which were up-regulated above 1.5 fold change (log2), pro-inflammatory genes were significantly enriched (p=0.033, after Bonferroni correction) in L, while this was not the case in F or M. Conversely, women in L showed a strong trend towards down-regulation of anti-inflammatory genes. Some prominent genes like interleukin (IL)-6 and IL1RN (coding for IL-1 receptor antagonist, also used as IL1RA) were clearly regulated in opposite directions in L as opposed to F and M. In conclusion, women in L showed a distinctly different pattern of gene regulation in response to exercise, compared with women in F or M. The overall direction of gene expression changes of women in L is clearly pro-inflammatory. This finding accentuates a need for careful consideration of the female cyclic phase when investigating women in exercise immunology studies. Our results may also have implications relevant to other forms of stress in females.

Keywords: time course, stress response

overall_design:
Time course transcription profiling of stress-related genes in 9 females in follicular (d10) and luteal (d25) phase and 12 male probands before and after 1 hour running at 93% VIAT.
Indirect reference design. 3 groups: Male, Females in luteal phase, Females in follicular phase. 2 time points. RNA pooled for each group, timepoint. 1 replicate per array, total 6 arrays.

first: Northoff

last: Hinnak

first: Derek

last: Zieker

first: Eva

middle: V

last: Schaible

first: Katharina

last: Schäfer

first: Stefanie

last: Thoma

first: Markus

last: Löffler

first: Asghar

last: Abbasi

first: Simon

last: Perikles

first: Andreas

middle: M

last: Niess

first: Elvira

last: Fehrenbach


title: Investigation of colominic acid effects on immortalized Schwann cells

city: Hannover

first: Cornelia

last: Repenning

address: Callinstr 5

institute: Institut fuer Technische Chemie

summary:
The purpose of the present study is to influence of CA coating on immortalized Schwann cells in vitro in comparison to standard culture conditions as well as to laminin as a positive standard. CA is a homopolymer of polysialic acid (PSA), which has – attached to the neuronal cell adhesion molecule (NCAM) – emerged as particulate attractive candidate for promoting morphological plasticity of axonal processes during axonal path finding and activity-dependent remodelling.

For this purpose self-spotted microarrays with 352 neurospecific genes were hybridized with mRNA from immortalized Schwann cells cultivated on different coating conditions: In order to enable a comprehensive comparison to the established coating material laminin as well as to standard coating conditions (cultivation on the cell culture surface) a loop-design has been chosen, which is based on the dye-swap design and facilitates a direct comparison of the different states.

overall_design: Results from 3 microarrays are summarized in this study. The samples originate from different coatings. Microarrays were hybridized in a loop design with one common reference using a dye swap approach.

first: Frank

last: Stahl

first: Thomas

last: Scheper


title: Studies on the production of fungal polyketides in Aspergillus nidulans using systems biology tools

city: Kgs. Lyngby

first: Mikael

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary: Using genetic engineering tools available for the model organism Aspergillus nidulans, we constructed two recombinant strains; one expressing the model polyketide Penicillium griseofulvum 6-methylsalicylic acid (6-MSA) polyketide synthase gene, and one expressing the 6-MSA gene and overexpressing the native phosphoketolase (phk) for increasing the pool of polyketide precursor levels. The physiology of the recombinant strains and a reference wild type were characterized on glucose, xylose, glycerol and ethanol medium in controlled bioreactors. Glucose was found to be the preferable carbon source for 6-MSA production and 6-MSA titers up to 455 mg/L were achieved. Our findings indicate that overexpression of phk does not directly improve 6-MSA production on glucose but if the lower glycolysis is lowered, it is possible to obtain quite high conversion yields of sugar to 6-MSA. Systems biology tools were employed for in-depth analysis of the metabolic processes. Transcriptome analysis of 6-MSA producing strains on glucose and xylose in the presence and absence of phk overexpression combined with flux and physiology data enabled us to propose a model of phk/6msas interaction describing two different responses influencing 6-MSA production.

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Four strains on two carbon sources

first: Gianni

last: Panagiotou

last: Grotkjaer

first: Torsten

last: Regueira

first: Jens

last: Nielsen

first: Lisbeth

last: Olsson


title: Sex-differences in the control of gluconeogenesis and hepatic glucose output in rats

status: Public on Feb 26 2009

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

summary:
In the present study we tested the hypothesis that male and female rat livers respond differently to a change in nutrient availability or to insulin treatment. Healthy normal rats were used to determine the effects of mild starvation or insulin injections on hepatic lipid and carbohydrate turnover as well as gene expression.
Keywords: Hepatic glucose output, gluconeogenesis, gene expression, respons to insulin treatment and mild starvation

overall_design: Two-condition experiment. Biological replicates: male rat livers +/- mild starvation (n=8), female rat livers +/- mild starvation (n=8), Treated with saline or insulin (i.p.) for 40 minutes. One replicate per array.

middle: E

first: Louisa

last: Cheung

first: Kamal

last: Yassin

first: Moira

last: Lewitt

first: Roxana

last: Merino

first: Faheem

last: Tahir

first: Kerstin

last: Brismar

first: Claes-Göran

last: Östenson

first: Gunnar

last: Norstedt

first: Petra

last: Tollet-Egnell


city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary:
Role of PPARalpha in the effects of DEHP on the hepatic expression of a selection of mouse genes related to nuclear receptor signaling.

Di-(2-ethylhexyl)-phthalate (DEHP), a widely used plasticizer, is detected in consumer’s body fluids. Contamination occurs through environmental and food chain sources. In mouse liver, DEHP activates the peroxisome proliferator-activated receptor alpha (PPARalpha) and regulates the expression of its target genes. Several in vitro investigations support the simultaneous recruitment of additional nuclear receptor pathways.  We investigated, in vivo, the hepatic impact of low doses of DEHP on PPARalpha activation, and the putative activation of additional signalling pathways. Wild-type and PPARalpha-deficient mice were exposed to different doses of DEHP. Gene expression profiling delineated the role of PPARalpha and revealed a PPARalpha-independent regulation of several prototypic Constitutive Androstane Receptor (CAR) target genes.   This finding demonstrates that CAR also represents a transcriptional regulator sensitive to phthalates. CAR-mediated effects of DEHP provide a new rationale for most endpoints of phthalates toxicity described previously, including endocrine disruption, hepatocarcinogenesis and the metabolic syndrome.

Keywords: Treatment effect

overall_design: One-color macroarrays, 6 experimental conditions: Wild type (WT) and PPARalpha-deficient mice (PPAR) were treated with vehicle (Ctrl) or with di-(2-ethylhexyl)-phthalate (DEHP) at 20 mg/kg/day (D20) or 200 mg/kg/day (D200) for 21 days, Biological replicates: 10 for each group, One replicate per array

first: Alexandre

last: Eveillard

first: Frederic

last: Lasserre


title: Overexpression of NtmybA2 in tobacco BY-2 cells

first: Masaki

last: Ito

summary:
Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2∆C) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media).

Keywords: Genetic modification

overall_design: 1.  pPZP-35S vector control, 2. NtmybA2 overexpressor, 3. C-truncated NtmybA2 (NtmyA2∆C) overexpressor

first: Kiichi

last: Kato

first: Ivan

last: Gális

first: Shiori

last: Suzuki

first: Satoshi

last: Araki

first: Taku

last: Demura

first: Marie-Claire

last: Criqui

first: Thomas

last: Potuschak

last: Genschik

first: Hiroo

last: Fukuda

first: Ken

last: Matsuoka


title: Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene

city: Ames

first: PLEXdb Curator

middle: Sudhansu

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip.    Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4.       Experiment Design:    C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil.  Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai).  Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2).  Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates.  Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen.  The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications).    Treatment Description:    The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1).      For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil.  Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai).  Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2].  This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus.  This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected.  Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate.  Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen.       ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Roger P Wise.  The equivalent experiment is BB46 at PLEXdb.]

overall_design: genotype: Mla6 - pathogen isolates: 5874 - time: 0(3-replications);  genotype: Mla6 - pathogen isolates: 5874 - time: 8(3-replications);  genotype: Mla6 - pathogen isolates: 5874 - time: 16(3-replications);  genotype: Mla6 - pathogen isolates: 5874 - time: 20(3-replications);  genotype: Mla6 - pathogen isolates: 5874 - time: 24(3-replications);  genotype: Mla6 - pathogen isolates: 5874 - time: 32(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 0(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 8(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 16(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 20(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 24(3-replications);  genotype: Mla6 - pathogen isolates: K1 - time: 32(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 0(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 8(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 16(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 20(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 24(3-replications);  genotype: 11542  - pathogen isolates: 5874 - time: 32(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 0(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 8(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 16(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 20(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 24(3-replications);  genotype: 11542  - pathogen isolates: K1 - time: 32(3-replications)

first: Roger

middle: P

last: Wise


title: IgM Abs to Apoptosis-associated Determinants recruit C1q and enhance dendritic cell phagocytosis of apoptotic cells

status: Public on Feb 23 2009

city: La Jolla

first: Gregg

last: Silverman

address: 9500 Gilman Dr

department: Medicine

institute: UC San Diego School of Medicine

summary:
Natural antibodies, which arise without known immune exposure, have been described that specifically recognize cells dying from apoptosis but their role in innate immunity remains poorly understood. Herein, we show that the immune response to neo-antigenic determinants on apoptotic thymocytes is dominated by antibodies to oxidation-associated antigens, phosphorylcholine (PC), a head group that becomes exposed during programmed-cell death, and malondialdehyde (MDA), a reactive aldehyde degradation product of polyunsaturated lipids produced following exposure to reactive-oxidation species. While natural antibodies to apoptotic cells in naïve adult mice were dominated by PC and MDA specificities, the amounts of these antibodies were substantially boosted by treatment of mice with apoptotic cells. Moreover, the relative amounts of PC and MDA antibodies was affected by VH gene inheritance. Antibody interactions with apoptotic-cells also mediated the recruitment of C1q, which alone can promote apoptotic-cell phagocytosis by immature dendritic cells. Significantly, IgM-antibodies to both PC and MDA were primary factors in determining the efficiency of serum-dependent apoptotic-cell phagocytosis. Hence, we demonstrate a mechanism by which certain natural antibodies that recognize neo-antigens on apoptotic cells, in naïve mice and those induced by immune exposure to apoptotic-cells, can enhance the functional capabilities of immature dendritic cells for phagocytic engulfment of apoptotic cells.

Keywords: Natural antibodies, Inflammation, Complement, Apoptosis

sample_organism:
Mus musculus
unidentified

platform_organism:
Homo sapiens
Mus musculus

overall_design: In the study presented here, a total of 11 custom-spotted protein slides were hybridized with a T15 IgM monoclonal antibody at three different concentrations, an isotype control IgM, 2 slides were hybridized with serum from naїve mice, 2 slides incubated with serum from mice immunized with apoptotic cells, 2 slides were incubated with serum from mice immunized with saline, and a negative control slide with no antibody hybridized

first: Yifang

last: Chen

first: Yong-beom

last: Park

first: Ekta

last: Patel

middle: J


title: Comparison of relative transcript and protein abundance in Plasmodium falciparum schizont stage parasites

city: Singapore

first: Bernardo

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

summary:
Background: Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, the quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic developmental cycle is accompanied by a continuous cascade of gene expression. Although such analyses have proven immensely useful, the precise correlations between transcript and protein abundance remain under-scrutinized.
Results: Here, we present a quantitative time-course analysis of relative protein abundance for schizont-stage parasites (34-46 hours post-invasion) based on 2D-gel electrophoresis of protein samples labeled with DIGE fluorescent dyes. For this purpose we analyzed parasite samples taken at four-hour intervals from a tightly synchronized culture and established more than 500 individual protein abundance profiles with high temporal resolution and quantitative reproducibility. Approximately half of all profiles exhibit a significant change in abundance and 12% display an expression peak during the observed 12-hour time interval. Intriguingly, identification of 54 protein spots by mass spectrometry revealed that 58% of the corresponding proteins including actin-I, enolase, eIF4A, eIF5A, and several heat shock proteins are represented by more than one isoform, presumably due to post-translational modifications, with the various isoforms of a given protein frequently showing different expression patterns. Furthermore, comparisons with transcriptome data generated from the same parasite samples reveal significant post-transcriptional gene expression regulation.
Conclusions: Together, our data indicate that both post-transcriptional and post-translational events are widespread and of presumably great biological significance during the intra-erythrocytic development of P. falciparum.

Additional comment: In essence, the microarray data generated in this study is a repeat of the transcriptome analysis described in Bozdech et al., PLoS Biol 2003, 1(1):E5. Differences include (1) an improved set of oligonucleotides [see Hu et al., BMC Bioinformatics 2007, 8:350] used in the study associated with this GEO entry, and (2) the sampling at only four timepoints during the intra-erythrocytic development cycle (schizont stage) to match and complement the samples processed in the concomitant proteomics analysis.

overall_design: Four timepoint samples were harvested from a tightly synchronized 6 liter biofermenter culture of P. falciparum during schizont stage (at 34, 38, 42, and 46 hours post-invasion) and compared against a 3D7 RNA reference pool.

first: Neng

last: Zhang

first: Sachel

last: Mok

first: Peter

middle: R

last: Preiser

first: Zbynek

last: Bozdech


title: Analysis of genome-wide binding of the insulator factors CTCF and CP190

status: Public on Feb 21 2009

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary:
We identified about 3000 CTCF sites in the genome. In addition to binding to CTCF sites we found CP190 to bind to transcriptional start sites of actively transcribed genes where it inversely correlates with nucleosome occupancy.

Keywords: ChIP-chip

overall_design: CTCF and CP190 ChIP. 2 biological replicates per experiment. dye-swaps as indicated in sample description.

first: Bartkuhn

last: Marek

first: Tobias

last: Straub

middle: B

last: Becker

first: Renkawitz

last: Rainer


title: Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth

status: Public on Feb 24 2009

city: London

first: Helen

middle: Alison

last: Fletcher

address: Keppel Street

department: IID

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

summary:
Transcpripts upregulated by both BCG and PPD were identified in 5 infants and pathway analysis and gene ontology were performed using differentially expressed genes

Keywords: response to antigen stimulation

overall_design: In this study the frozen PBMC of 5 infants were thawed and stimulated for 12 hours with either BCG or PPD or rested in media alone for 12 hours.  The transcripts from the unstimulated PBMC were compared to the PPD and BCG induced transcripts

middle: A

first: Willem

last: Hanekom


title: dyrk1a

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

summary:
Transcription profiling of transgenic down syndrome mouse model to show the role of DYRK1A gene. The molecular mechanisms that lead to the cognitive defects characteristic of Down syndrome (DS), the most frequent cause of mental retardation, have remained elusive. Here we use a transgenic DS mouse model to show that DYRK1A gene dosage imbalance deregulates chromosomal clusters of genes located near neuron-restrictive silencer factor (REST/NRSF) binding sites. We
found that DYRK1A binds the SWI/SNF-complex known to interact with
REST/NRSF. Mutation of a REST/NRSF binding site in the promoter of the
REST/NRSF target gene L1cam modifies the transcriptional effect of Dyrk1Adosage imbalance on L1cam. DyrkA dosage imbalance perturbs Rest/Nrsf levels with decreased Rest/Nrsf expression in embryonic neurons and increased expression in adult neurons. We identified a coordinated deregulation of multiple genes that are responsible for the cellular phenotypic traits present in DS such as dendritic growth impairment and microcephaly during prenatal cortex development. Dyrk1a overexpression in primary mouse cortical neurons reduced the neuritic complexity. In the postnatal hippocampus, DYRK1A overexpression suppresses a form of synaptic plasticity that may be sufficient to cause DS cognitive defects. We propose that DYRK1A overexpression-related neuronal gene deregulation generates the
brain phenotypic changes that characterize DS, with an accessory role for the gene dosage imbalance of other chromosome 21 genes.

overall_design:
Transgenic embrionic brain regions versus wild type mice were analysed. The log2 values represent Cy5/Cy3 ratio (transgenic Cy5/wild type Cy3).
Each array was scanned under a green laser (543 nm for Cy3 labeling) or a red laser (633 nm for Cy5 labeling) using a ScanArray Lite scanning confocal fuorescent scanner with 10 u resolution (laser power: 85% for Cy5 and 90% for Cy3, gain: 75% for Cy5 and 70% for Cy3). Scanned output files were analyzed using the GenePix Pro 3.0 software. Each spot was defined by automatic positioning of a grid of circles over the image. The average and median pixel intensity ratios calculated from both channels and the local background of each spot were determined. Local background corrected intensity ratios was determined for each spot. The background-corrected expression data were filtered for flagged spots and weak signal. Normalization was performed by the global Lowess method. Student’s t-test was applied to determine the p value.

first: Aude-Marie

last: Lepagnol-Bestel

first: Gilles

last: Maussion

first: Frédérique

last: Quignon

first: Bedel

last: Ngimbous

first: Nicolas

last: Ramoz

first: Sandrine

last: Imbeaud

first: Yann

last: Loe-Mie

first: Karim

last: Benihoud

last: Agier

first: Paul

last: Salin

first: Ana

last: Cardona

first: Suonavy

last: Khung-Savatovsky

first: Pekka

last: Kallunki

first: Jean-Maurice

last: Delabar

first: Laszlo

middle: G

last: Puskas

first: Hervé

last: Delacroix

first: Lawrence

last: Aggerbeck

first: Anne-Lise

last: Delezoide

first: Olivier

last: Delattre

first: Philip

last: Gorwood

first: Jean-Marie

last: Moalic

first: Michel

last: Simonneau


title: Fetal liver development

city: Tokyo

first: Chen

last: Yenrong

address: yayoi 1-1-1, bunkyo_ku

institute: the university of Tokyo

summary:
Hepatoblasts emerging at E8.5 from the foregut endoderm proliferate vigorously and differentiate to hepatocytes and biliary epithelial cells. To find genes important for hepatocyte differentiation during development, we compared gene expression profiles of hepatoblasts/immature hepatocytes at E12.5 and E17.5.  As Dlk, also known as Pref-1, is expressed in hepatoblasts/immature hepatocytes, we performed a microarray analysis of the Dlk+ cells isolated from livers at E12.5 and E17.5.

Keywords: fetal liver cells comparing

overall_design: Mouse hepatoblasts were isolated from E12.5 and E17.5 fetal liver using anti-mouse Dlk monoclonal antibody (mAb) according to a previous report and dissolved in Trizol reagent. The cDNA samples synthesized from total RNA were used for a microarray analysis with the mouse GEM2 microarray. One array, no replicates.

first: Koji

last: Nakamura

first: Hiroyuki

last: Yanai


title: Wild dolphin PBL analysis

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

summary:
To determine what can the transcriptome tell us about populations of free-ranging bottlenose dolphins, Tursiops truncatus.
Keywords: health assessment

overall_design: A total of 151 individuals were sampled from 4 different geographic location in U.S. waters between June of 2003 and June of 2006. Of the 151 dolphins, 59 were from Charleston, 35 from Indian River Lagoon, FL, 32 from Sarasota Bay, FL and 25 from St. Josephs Bay FL. Total RNA extracted from blood leukocytes of wild dolphins was analyzed and different sets of genes were used as classifiers in a machine learning approach, Artificial Neural Networks (ANN).

first: Annalaura

last: Mancia


title: Time course study of Mediterranean mussel (M. galloprovincialis, Lmk, 1819) digestive gland treated with okadaic acid

status: Public on Feb 19 2009

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

summary:
Mytilus galloprovincialis (Lmk, 1819) is economically relevant bivalve specie. In Adriatic Sea, periodical temperatures increases define optimal growth conditions for Dinoflagellate spp which can reach high concentrations also in filter-feeding mussels, thus causing potential human health problems. The most commonly used methods for the detection of Diarrhoeic Shellfish Poisoning  biotoxins have either a low sensitivity or are too expensive to be used for routine tests. Genomic tools, such as microarray platforms, provide a reliable and alternative solution to overcome these problems.
In this study we used a mussel cDNA microarray for studying gene expression changes in mussels exposed to Okadaic acid. Mussels collected in the Gulf of Trieste, located in Northern Adriatic Sea, were fed with Okadaic acid-spiked invertebrates for five weeks. In a time course experiment we were able to describe an early acute response just from the first 4th day time point. Among the differentially expressed genes we found a general up-regulation of stress proteins and proteins involved in cellular synthesis. Overall, we identified 34 transcripts candidate as useful markers to monitor OA-induced stress in mussels. This study contributes to the characterization of many potential genetic markers that could be used in future environmental monitoring, and could lead to explore new mechanisms of stress tolerance in marine mollusc species.

Keywords: Time course, stress response

overall_design: Loop Design experiment including 5 time points (T0 = control samples, T1 = 3 days post treatment, T2 = 1 week post treatment, T4 = 3 weeks post treatment, T6 = 5 weeks post treatment). 3 biological replicates were done for a total number of 15 samples

first: Chiara

last: Manfrin

first: Rene'

first: Silvia

last: Battistella

first: Paola

last: Venier

first: Alberto

last: Pallavicini


title: Sanguinarine, putative anticancer therapeutic, interacts,modulates and transcripts in the context of chromatin

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

institute: Jawaharlal Nehru Centre for Advanced scientific Research

summary: DNA binding anticancer agents cause alteration in chromatin structure and dynamics. Here, we report the dynamic interaction of the DNA intercalator and potential anticancer, plant alkaloid, Sanguinarine (SGR) with chromatin. Association of SGR with different levels of chromatin structure was found to be enthalpydriven. Apart from DNA it binds with comparable affinity to histones and induces chromatin aggregation. The dual binding property of SGR leads to inhibition of core histone modifications. Although, it potently inhibits H3K9 methylation by G9a in vitro, H3K4 and H3R17 methylation are more profoundly inhibited in cells. SGR inhibits histone acetylation both in vitro and in vivo. It does not affect the in vitro transcription from DNA template but significantly represses acetylation dependent chromatin transcription.  SGR mediated repression of epigenetic marks and the alteration of chromatin geography, also result in modulation of global gene expression. These data conclusively, show the anticancer DNA binding intercalator as a modulator of chromatin modifications and transcription in the chromatin context.

overall_design: The total RNA was isolated from control and treated cells using TRIZOL (Invitrogen) method. The Micromax direct labeling kit, MPS502 (PerkinElmer) was used to synthesize the labeled cDNA from 70 ug of total RNA and further process the hybridized cDNA on the array. All the steps were carried out according to manufacturer’s instructions (www.perkinelmer.com/lifesciences). The array slides were scanned immediately by PerkinElmer Scan array Gx Microarray scanner. The Scan array software (PerkinElmer) was used for grid wise normalization of array images. Two arrays were used with at least one biological treatment of cells and dye swap experiment were included in the final analysis. . The data was analysed by GeneSpring GX and Biointerpreter software from Genotypic Technology, Bangalore. The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were reproducible from both replicates.

first: Selvi

last: BR


title: DCC binding and function (ChIP-chip: DPY-27)

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary:
In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X gene products between males (1X) and females (2X).  Here we identify cis-acting regulatory elements that target the C. elegans X chromosome for repression by the DCC.  The DCC binds to discrete, dispersed sites on X of two types.  rex sites recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12 bp consensus motif that is enriched on X.  This motif is critical for DCC binding, is clustered in rex sites, and confers much of X-chromosome specificity.  Motif variants enriched on X by 3.8-fold or more are highly predictive (95%) for rex sites.  In contrast, dox sites lack the X-enriched variants and cannot bind the DCC when detached from X.  dox sites are more prevalent than rex sites and, unlike rex sites, reside preferentially in promoters of some expressed genes.  These findings fulfill predictions for a targeting model in which the DCC binds to recruitment sites on X and disperses to discrete sites lacking autonomous recruitment ability.  To relate DCC binding to function, we identified dosage-compensated and non-compensated genes on X.  Unexpectedly, many genes of both types have bound DCC, but many do not, suggesting the DCC acts over long distances to repress X gene expression.  Remarkably, the DCC binds to autosomes, but at far fewer sites and rarely at consensus motifs.  DCC disruption causes opposite effects on expression of X and autosomal genes.  The DCC thus acts at a distance to impact expression throughout the genome.

Keywords: dosage compensation, condensin, X chromosome, gene expression, epigenetics, C. elegans

overall_design: ChIP-chip with DPY-27

first: Judith

last: Jans

first: John

last: Gladden

first: Edward

last: Ralston

first: Catherine

middle: S

last: Pickle

first: A

middle: H

last: Michel

first: Rebecca

last: Pferdehirt

first: Michael

last: Eisen


title: Gene expression analysis of Drosophila melanogaster S2 cells after RNAi-mediated depletion of the insulator factor CP190

first: Marek

last: Bartkuhn

summary: We analyzed transcriptional effects after depletion of Drosophila melanogaster S2 cells from CP190 via specific dsRNA treatment in comparison to cells treated with control dsRNA.

overall_design: Drosohila melanogaster S2 cells were treated with either CP190-specific dsRNA or control dsRNA corresponding to the firefly luciferase gene. Four independent replicates were performed.

first: Rainer

last: Renkawitz


title: Gene expression analysis of Drosophila melanogaster S2 cells after RNAi-mediated depletion of the insulator factor CTCF

summary: We analyzed transcriptional effects after depletion of Drosophila melanogaster S2 cells from CTCF via specific dsRNA treatment in comparison to cells treated with control dsRNA.

overall_design: Drosohila melanogaster S2 cells were treated with either CTCF-specific dsRNA or control dsRNA corresponding to the firefly luciferase gene. Four independent replicates were performed.


title: FFPE study using MIP copy number platform - breast cancer II

status: Public on Feb 18 2009

city: Santa Clara

first: Yuker

last: Wang

address: 3380 Central Expressway

institute: Affymetrix

summary:
A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali
 ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.

overall_design: Various collections of FFPE samples have been assayed by MIP

first: Victoria

last: Carlton

first: Malek

last: Faham


title: Effects of single oral exposure of adult Sprague-Dawley rats to p-tert-octylphenol on uterine gene expression

status: Public on Feb 20 2009

city: Laval

first: Patrick

last: Devine

state: QC

address: 531 boulevard des Prairies

department: INRS-Institut Armand-Frappier

institute: Institut national de la recherche scientifique

summary:
Contamination of the environment with endocrine disrupting chemicals (EDCs) has raised concerns about potential health hazards for humans and wildlife. P-tert-octylphenol (OP) is one such ubiquitous chemical reported to bind to the estrogen receptor (ER) and alter expression of estrogen-responsive genes. Human and wildlife exposure to OP are likely, due to its persistence in the environment and its presence in food, water and items of daily use. Detrimental effects of OP exposures on the reproductive system have been observed in some, but not all, in vivo experiments. This study compared estrogenic effects of OP in vitro with those in vivo in adult female rats, attempting to better mimic real-life exposures in adults. In vitro, OP bound to human ER weakly and accelerated proliferation of MCF-7 cells.  Adult Sprague-Dawley rats were given OP by gavage either once (125 mg/kg OP) or daily for 35 days (25, 50, 125 mg/kg).  Body and organ weights and ovarian follicle populations were unaltered in OP-exposed adult rats after either time point, despite detectable levels of OP in reproductive organs. Toxicity of OP was demonstrated by a slightly reduced growth rate and slightly altered estrous cycle, but there were no significant estrogen-like changes in histomorphology or microarray analyses of gene expression of uterine tissue.  Prepubertal rats exposed by gavage to 125 or 250 mg/kg OP for three days failed to show any uterotrophic effects, although E2 caused a 3-fold increase in uterine weight. These results do not support a dose-dependent, estrogenic mode of action for OP.

Keywords: treatment-control

overall_design: Individual uterine RNA samples from 4 female ~35-day old rats per treatment (4 OP and 4 vehicle) sacrificed on the second day of diestrus after a single dose of OP (125 mg/kg/day in propylene glycol) or solvent (propylene glycol, PG) by gavage on the first day of diestrus were compared with liver RNA pooled from all 8 rats (as reference, combined OP and solvent treatment groups). Comparisons were made between treatments.  Liver cDNA was always marked with Cy5 and uterine cDNA was always marked with Cy3.

first: Sukhdeep

middle: K

last: Sahambi


title: FFPE study using MIP copy number platform - breast cancer I

summary:
A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali
 ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA

overall_design: Various collections of FFPE samples have been assayed by MIP.

last: faham


title: Pathogenic Natural Antibodies Recognizing Annexin IV Are Required to Develop Intestinal Ischemia-Reperfusion Injury

first: Gregg

last: Silverman

summary:
Intestinal ischemia-reperfusion (IR) injury is initiated when natural IgM antibodies recognize neo-epitopes that are revealed on ischemic cells. The target molecules and mechanisms whereby these neo-epitopes become accessible to recognition are not well understood. Proposing that isolated intestinal epithelial cells (IEC) may carry IR-related neo-epitopes, we used in vitro IEC binding assays to screen hybridomas created from B cells of unmanipulated wild type C57BL/6 mice. We identified a novel IgM monoclonal antibody (mAb B4) that reacted with the surface of IEC by flow cytometric analysis and was alone capable of causing complement activation, neutrophil recruitment and intestinal injury in otherwise IR-resistant Rag1-/- mice. Monoclonal Ab B4 was found to specifically recognize mouse annexin IV. Pre-injection of recombinant annexin IV blocked IR injury in wild type C57BL/6 mice, demonstrating the requirement for recognition of this protein in order to develop IR injury in the context of a complex natural antibody repertoire. Humans were also found to exhibit IgM natural antibodies that recognize annexin IV. These data in toto identify annexin IV as a key ischemia-related target antigen that is recognized by natural Abs in a pathologic process required in vivo to develop intestinal IR injury.

Keywords: Natural antibodies, Annexin, Ischemia Reperfusion, Inflammation, Complement

overall_design: In the study presented here, a total of 4 custom spotted antigen slides were hybridized with  known  antibodies.

first: Liudmilla

last: Kulik

first: Sherry

middle: D

last: Fleming

first: Chantal

last: Moratz

first: Jason

middle: W

last: Reuter

first: Aleksey

last: Novikov

first: Kuan

last: Chen

first: Kathy

last: Andrews

first: Adam

last: Markaryan

first: Richard

last: Quigg

first: George

middle: C

last: Tsokos

first: V

last: Holers


title: FFPE study using MIP copy number platform - bladder/colorectal/kidney/liver

first: Yuker

last: Wang

last: Carlton


title: FFPE study using MIP copy number platform - colorectal

first: Victoria

last: Faham


title: A mesodermal gene regulatory network directed by zebrafish No tail

city: Cambridge

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

summary:
Using chromatin immunoprecipitation combined with microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies. We show floating head (flh) is a direct transcriptional target of Ntl in the notochord and that TBS in the flh  upstream region are required for Ntl directed expression. Using this genome-scale data we have assembled a Gene Regulatory Network that describes mesoderm formation and patterning in the early zebrafish embryo and which predicts a role for Ntl in somite segmentation.

Keywords: ChIP-chip

overall_design: Genomic array design.  Microarrays were designed as described below and manufactured by Agilent Technologies (www.agilent.com). We have previously described the ChIP-chip technique in zebrafish and the design of promoter microarrays which cover a 2kb region around the transcription start sites (TSSs) of 11,512 zebrafish genes based on Zv4 (Wardle et al, 2006. Genome Biology 7:R71). In order to capture additional regulatory information further from the basal promoter region we also designed an expanded set of 60mer probes that cover 9kb upstream and 3kb downstream of the TSS of these genes using the same parameters as for the 2kb microarrays.  We also incorporated several sets of control probes, both positive and negative. On each array there are 753 negative probes designed against zebrafish gene desert regions and Arabidopsis thaliana genes. In addition we included duplicates of promoter probes for several genes that we anticipated may be bound by factors of interest for this and other studies  (wnt11, flh, vent, msgn1, myod, fgf8, pcdh8) and these probes are arrayed on both slides slide.  We also included in this design 502 intensity control probes. Finally there are 2,256 controls added by Agilent. The final design contained 378,002 probes, including 365,537 experimental probes divided between nine microarray slides: slides 1-8 contained 40,616 experimental probes and slide 9 contained 40, 609. Further information on design and manufacture of the microarrays can be found on the Agilent Technologies website (www.agilent.com).

first: Rosalind

last: Morley

first: Kim

last: Lachani

first: Damian

last: Keefe

first: Michael

last: Gilchrist

first: Paul

last: Flicek

first: James

last: Smith


title: High-resolution mapping of HP1 redistribution in a position-effect variegation model

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Position-effect variegation (PEV) is the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin. white-mottled X-chromosomal inversions in Drosophila are classic PEV models that show variegation of the eye color gene white due to its relocation next to pericentric heterochromatin. To obtain insight into the mechanism of PEV, we constructed detailed binding maps of Heterochromatin Protein 1 (HP1), a major component of heterochromatin, on white-mottled chromosomes. We find that HP1 invades euchromatin across the inversion breakpoints over ~175kb and ~30kb, causing de novo association of HP1 with 20 genes. However, HP1 binding levels in these regions show substantial local variation; white is most strongly bound by HP1 and is one of only two genes that are substantially repressed by heterochromatin. HP1 binding to the invaded region is exceptionally sensitive to the dosage of the histone methyltransferase Su(var)3-9, indicating that the de novo formed heterochromatin is relatively unstable. Our molecular maps demonstrate that heterochromatin can invade a normally euchromatic region, yet the strength of HP1 binding and effects on gene expression are highly dependent on local context.

Keywords: DamID, gene expression, genetic modification.

overall_design: The study comprises of two DamID experiments and two gene expression experiments.   DamID:  The first DamID experiment establishes HP1 binding profile in male heads of three fly lines; wild-type Oregon-R-S and two fly lines with white-mottled-4 chromosomal inversions; w[m4e] and w[m51b]. Each binding profile has 4 biological replicates, each dye orientation is hybridized twice.   The second DamID experiment profiles HP1 in a Su(var)3-9 mutant (w[m4]) and a sibling control fly line (Contr) which has wild type Su(var)3-9.  Expression profiling:  The first experiment contains three sets of expression profiles that measure gene expression in male heads of wild-type (Oregon-R-S), w[m4e] or w[m51b] flies.  The second experiment measures gene expression in male heads of flies that had w[m4] and hemizygous of Su(var)3-9, sibling control flies had w[m4] and wildtype Su(var)3-9. This experiment was done to establish the effect of a Su(var)3-9 mutation on the expression of white on w[m4]. The second experiment was done twice, using two different control fly lines as suppliers of the not affected wild-type chromosomes in the crosses (A=OregonRS and B=w[1118]).

first: Maartje

last: Vogel

first: Ludo

last: Pagie

first: Marja

last: Nieuwland

first: Ron

middle: M

last: Kerkhoven


title: Mismatch oligonucleotides in yeast

city: New Haven, BASS 437

last: Seringhaus

address: 266 Whitney Ave

department: Molecular Biophysics & Biochemistry

institute: Yale University

type: Genome variation profiling by genome tiling array

summary:
Tiled 10kb region centered around ACT1 gene (YFL039C, CHROMOSOME 6 @ coords 48760-59195), double-stranded, 36mers at 1bp spacing, with mismatches and deletions; also tiled 6 genes of interest (YBL092W, YGR155W, YOL040C, YOR312C, YMR242C, YLR229C), coding strand only, 36mers at 1bp spacing, with some mismatches and deletions

Keywords: Mismatch hybridization experiment

overall_design: Tiled perfect match and various designs of mismatch oligonucleotide for several yeast genes. Goal was to observe the influence of various MM types on hybridization behavior in yeast and compare it to human (see related slide).

first: Joel

last: Rozowsky

first: Thomas

last: Royce

first: Ugrappa

last: Nagalakshmi

first: Justin

last: Jee

last: Snyder

first: Mark

last: Gerstein


title: Changes in gene expression in MKK2 and MKKKC5 mutants: wt vs mutant comparison

status: Public on Feb 15 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary:
The mkkkC5 mutant, a knockout line of MAPKKKC5, shows changes in growth and development, as well as an altered Alternaria sensitivity. It was shown by Brader and Djamei et al.(2007) that Alternaria brassicicola sensitivity is also influenced by MKK2-activity. Aim of this experiment is to access the transcriptional changes in the mkkkc5plants as well as in plants overexpressing a constitutively active MKK2-version (MKK2EE). The second part of the experiment addresses transcriptional changes in these plants after Alternaria brassicicola infection. -
au07-09_alternaria - mkk2ee and mkkkc5 mutants
Keywords: wt vs mutant comparison

overall_design:
Comparison between the over-expressed mutant of the MKK2 gene and the KO mutant for the MKKKC5 gene versus the wild type.
4 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Heribert

last: Hirt

first: Sarah-

last: Himbert

first: Marie-Laure

middle: L

last: Martin-Magniette


title: FFPE study using MIP copy number platform - kidney

first: Yuker

last: Wang

summary: A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.

first: Victoria

last: Carlton

first: Malek

last: Faham