title: Characterization of canine mesenchymal stromal cell lines (MSC)

city: Seattle

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary:
The bone marrow microenvironment is a complex mixture of cells that function in concert to regulate hematopoiesis. Cellular components include fixed nonhematopoietic stromal elements (MSC) as well as monocytes and resident macrophages, which are derived from the hematopoietic stem cells. Clinical studies have shown healing effects, direct or indirect, from the injection of MSC int
Keywords: Cell type comparison

overall_design: Canine bone marrow stromal cells were immortalized by transduction with a replication-defective recombinant retrovirus containing the human papilloma virus E6/E7 genes (pLXSN-16 E6E7), as described for human stromal cell lines in Roecklein and Torok-Storb (Blood 85:997-1005, 1995). Transduced clones were selected with 50 ug/ml G418 and resistant clones were isolated,  grown to confluency and characterized for morphology, cytokine production and cell surface molecule expression. These cells are intended for clinical research in the canine transplantation model, as a complement for existing human stromal cell lines, for mitigation of graft-versus-host disease and radiation effects.

first: Beverly

last: Torok-Storb

first: Marco

last: Mielcarek

first: Aravind

last: Ramakrishnan


title: In vitro dormancy achieved by multiple stresses in Mycobacterium tuberculosis

status: Public on May 01 2008

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

summary:
The human pathogen, Mycobacterium tuberculosis, develops a dormant infection, in which organisms survive within the body. We established a unique in vitro dormancy model based on the characterization of drug-resistance to INH and rifampin. M. tuberculosis cells were maintained in controlled and defined multiple stress conditions with low oxygen (5% dissolved oxygen tension), acid (pH 5.) along with glycerol-deprived medium conditions. To monitor gene expression changes in M. tuberculosis in response to the multiple stresses, we performed microarray analysis at the time point of 1, 2, 3, 6, and 12days after treatment. M. tuberculosis adapting to multiple stresses displayed characteristics associated with persistence in vivo, including entry into a non-replicative state and the repression of genes involved in energy regeneration. Under in vitro multiple-stresses, M. tuberculosis significantly modulated gene expression mainly in response to the starvation stresses. Cells exposed to these multiple stress conditions shows significant drug-resistance. Comparison with other in vivo expression profiles demonstrates induction of several common genes for in vitro dormancy conditions.
Keywords: Stress response in time course.

overall_design: Samples under multiple stress condition were taken at day 1, 2, 3, 6, and 12 for microarray hybridization. More than two technical replicates per biological samples with Cy3/5 dye-swaps.

first: Pappachan

middle: E

last: Kolattukudy

first: Chirajyoti

last: Deb

first: Vinod

last: Dubey

first: Bassam

last: Aboumoelak

first: Jaiyanth

last: Daniel

first: Tatiana

last: Sirakova


title: Fine-Scale Mapping and Sequencing of Structural Variation from Eight Human Genomes

first: Jeffrey

middle: M

last: Kidd

state: WA

address: 1705 NE Pacific St

department: Department of Genome Sciences

country: USA

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary:
Genetic variation amongst individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single-nucleotide changes.  In this manuscript we explore variation on an intermediate scale-particularly insertions, deletions, and inversions affecting from a few thousand to a few million base pairs.  We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number among individuals. Sequencing of a subset of structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence-map of human structural variation-an important standard for genotyping platforms and a prelude to future individual genome sequencing projects.
Keywords: comparitive genomic hybridization, copy number variation, structural variation, fosmid end sequencing

overall_design: CGH analysis targeted against sites identified by fosmid end sequencing.  8 HapMap samples (sources of libraries ABC7-ABC14) are hybed against NA15510 (source of fosmid library G248).

first: Gregory

last: Cooper

first: William

middle: F

last: Donahue

first: Hillary

middle: S

last: Hayden

first: Nick

last: Sampas

first: Tina

last: Graves

first: Nancy

last: Hansen

first: Brian

last: Teague

first: Can

last: Alkan

first: Francesca

last: Antonacci

first: Eric

last: Haugen

first: Troy

last: Zerr

last: Yamada

first: Peter

last: Trang

first: Tera

middle: L

last: Newman

first: Eray

last: Tuzun

first: Ze

last: Cheng

first: Heather

last: Ebling

first: Nadeem

last: Tusneem

first: Robert

last: David

first: Will

last: Gillett

first: Karen

middle: A

last: Phelps

first: Molly

last: Weaver

first: David

last: Saranga

first: Adrianne

last: Brand

first: Wei

last: Tao

first: Erik

last: Gustafson

first: Kevin

last: McKernan

first: Lin

last: Chen

first: Maika

last: Malig

first: Joshua

middle: D

last: Smith

last: Korn

first: Steven

last: McCarroll

last: Altshuler

first: Daniel

last: Peiffer

first: Michael

last: Dorschner

first: John

last: Stamatoyannopoulos

last: Schwarts

first: Deborah


title: Microarray assay of the genetic response of Picea abies to Heterobasidion annosum infection - Loop2

status: Public on May 03 2008

city: Raleigh

first: Chris

state: NC

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

summary:
The hypothesis of the experiment is that infected trees of high resistance express a wider variety of resistance genes than infected trees of low resistance, and that the level of expression of these resistance genes differs between infected and healthy branches. Also, some genes highly expressed in the infected state not expressed in the healthy state may be in response to the wounding rather than the actual infection. By comparing these expressions to that of wounded, uninfected branches, this could also be clarified.
Keywords: stress response

overall_design: Three different Picea abies clones, of increasing resistance to fungal attack, have been infected. For all clones, three rametes have been infected with Heterobasidion of 1 month, by means of cutting the cambium and inoculating a piece of fungus growing in agar in the wound. For the low and medium resistant clone, a fourth ramete has been cut and inoculated with agar not containing any fungal material.

first: Mårten

last: Lind

first: Aleksandra

last: Adomas

first: Guosheng

last: Li

first: Debbie

last: Craig

first: Gunnilla

last: Swedjemark

middle: P

first: Ake

last: Olson

first: Len

last: van Zyl

first: Bo

last: Karlsson

first: Roger

last: Finlay

first: Ron

last: Sederoff

first: Jan

last: Stenlid

first: Frederick

middle: O

last: Asiegbu


title: Microarray assay of the genetic response of Picea abies to Heterobasidion annosum infection - Loop1

last: Smith


title: Pathway analysis of expression QTL data in fat identifies a role for cyclin H in oxidative phosphorylation

city: San Diego

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Genome-wide gene expression profiling has been extensively used to generate biological hypotheses based on differential expression.  Recently, many studies have used microarrays to measure gene expression levels across genetic mapping populations.  These gene expression phenotypes have been used for genome-wide association analyses, an analysis referred to as expression QTL (eQTL) mapping.   Here, eQTL analysis was performed in fat issue from 28 inbred strains of mice.  We focused our analysis on “trans-eQTL bands”, defined as instances in which the expression patterns of many genes were all associated to a common genetic locus.  Genes comprising trans-eQTL bands were screened for enrichments in functional gene sets representing known biological pathways, while genes located at associated trans-eQTL band loci were considered candidate transcriptional modulators.  We demonstrate that these patterns reflect previously characterized relationships between known upstream transcriptional regulators and their downstream target genes.   Moreover, we used this strategy to identify both novel regulators and novel members of known pathways.  Finally, based on putative regulatory relationship identified in our analysis, we validated in vitro a previously uncharacterized role for cyclin H in the regulation of oxidative phosphorylation.
Keywords: strain comparison

overall_design: tissues were taken from different mouse strains under identical baseline conditions

first: Chunlei

last: Wu

first: David

last: Delano

first: Nico

last: Mitro

first: Stephen

middle: V

last: Su

first: Jeff

last: Janes

first: Phillip

last: McClurg

first: Serge

last: Batalov

first: Genevieve

last: Welch

first: Jie

last: Zhang

first: Anthony

last: Orth

first: Richard

middle: J

last: Glynne

last: Cooke

first: Joseph

last: Takahashi

first: Kazu

last: Shimomura

first: Akira

last: Kohsaka

last: Bass

first: Enrique

last: Saez

first: Tim

last: Wiltshire

first: Andrew

middle: I


title: ANTIBIOTICS OVERPRODUCTION IN STREPTOMYCES COELICOLOR A3(2) MEDIATED BY PHOSPHOFRUCTOKINASE A2 DELETION

city: Manchester

first: Giles

last: Velarde

address: MIB

country: United Kingdom

institute: University of Manchester

summary:
Gene expression analysis of S. coelicolor M145 and the delta_pfkA2 mutant. RNA samples were taken in the early exponential phase during growth in fermentors in defined mineral medium.
Keywords: cell type, gene expression, genetic modification

overall_design:
5 Streptomyces ceolicolor Extracts (3 M145 WILD TYPE, 2 M145 Delta_pfkA2 MUTANT) were hybridised with dye swaps on 4 arrays:
- Sco8.26 (M145 RNA No. 1 cy5 + M145 delta_pfkA2 RNA No. 1 cy3)
- Sco8.28 (M145 delta_pfkA2 RNA No. 2 cy5 + M145 RNA No. 3 cy3)
- Sco8.31 (M145 RNA No. 2 cy5 + M145 delta_pfkA2 RNA No. 2 cy3)
- Sco8.37 (M145 delta_pfkA2 RNA No. 1 cy5, M145 RNA No. 2 cy3).

first: Irina

last: Borodina


title: Confirmation of the gene expression pattern in Mxi1-deficient mouse

status: Public on Apr 29 2008

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

institute: Sookmyung Women's University

summary:
For final aim to completes network map between gene that is concerned in cystogenesis, verifies meaning genes connected with cyst formation analyzing gene pattern in Mxi1 KO mouse that have phenotype of polycystic kidney disease. Monitoring meaning genes through microarray analysis, and confirm the function of these genes. Also, find pathway including meaning genes and new pathway related with PKD. Completes network map concerned in cystogenesis through integrates knowing pathway and predicting pathway. Develope diagnostic of cyst disease and cure target through such completed network map, and wish to clear new role of cyst formation connection gene through in vivo model and examine closely control system of cyst formation mechanism.
Keywords: Cystogenesis

overall_design:
Use 1 mouse at each experiment and control.
Indirect labeling of 10g cRNA, using bacterial control mRNA.

first: M

first: K

last: Yoo

first: J

last: Park


title: A secreted isoform of ErbB3 promotes osteomectin expression in bone

city: Houston

first: Nanyue

last: Chen

state: TX

address: 1515 Holcombe Blvd

institute: UT-MD Anderson Cancer Center

summary:
The propensity for prostate cancer to metastasize to bone led us and others to propose that bidirectional interaction between prostate cancer cells and bone are critical for the preferential metastasis of PCa to bone.  We previous identified a secreted isoform of ErbB3 (p45-sErbB3) from the bone marrow supernatants of patients with prostate cancer and bone metastasis. Immunohistochemical analysis of p45-sErbB3 expression in human specimens showed that p45-sErbB3 was highly expressed in metastatic prostate cancer cells in bone. Here we show that p45-sErbB3 stimulates calvarial bone to secrete factors that increase the invasiveness of prostate cancer cells in Boyden chamber invasion assay.  We used gene array analysis to identify p45-sErbB3 regulated osteoblast genes that may enhance the invasiveness of PC-3 cells and found that p45-sErbB3 stimulated the expression of osteonectin, biglycan, and type I collagen in mouse calvaria.  We further showed that recombinant osteonectin increases the invasiveness of PC-3 cells and osteonectin neutralizing antibody blocked p45-sErbB3 mediated invasiveness. These results suggest that p45-sErbB3 enhances the invasiveness of PC-3 cells is due, at least in part, to the stimulation of the secretion of osteonectin from bone.  Thus, p45-sErbB3 mediates the bi-directional interaction between PCa cells and bone through osteonectin.
Keywords: Prostate cancer, bone metastasis, P45-sErbB3, osteonectin

overall_design:
Sample 1: non-treated calvaria RNA, Group 1
Sample 2: sErbB3 (100ng/ml) treated calvaria RNA, Group 2
Array: GE-supper array MM026 (total 96 genes, with 10 housekeeping genes) (service from SuperArray Bioscience Corporation: http://www.superarray.com

first: Xiang-Cang

last: Ye

first: Khoi

last: Chu

first: Nora

last: Navone

last: Sage

first: Li-Yuan

last: Yu-Lee

first: Christopher

last: Logothetis

first: Sue-Hwa

last: Lin


title: H. pylori genotypes and host gene expression profiles

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
H. pylori virulence factors have been suggested to be important in determining the outcome of infection. The H. pylori adhesion protein BabA2 is thought to play an crucial role in bacterial colonization and in induction of a severe gastric inflammation, particularly in combination with expression of CagA and VacA. However, the influence of these virulence factors on the pathogenesis of H. pylori infection, is still poorly understood. To address this question, the inflammatory gene expression profiles from two groups of patients infected with triple-negative strains (lacking expression of CagA, BabA2 and VacAs1, but expressing VacAs2) and triple-positive strains (expressing CagA, VacAs1 and BabA2, but lacking expression of VacAs2) were investigated. The gene expression pattern in the antrum gastric mucosa from patients infected with different H. pylori strains was very similar, and no differentially expressed genes could be identified by pair-wise comparisons. Our data thus suggest a lack of correlation between the host inflammatory responses in the gastric mucosa and expression of the BabA2, CagA and VacAs1 genes.
Keywords: diseases analysis

overall_design: Two groups of patients who infected with double-positive strains (type I strains, expressing CagA and VacAs1 genes) and triple-negative strains (lacking the CagA, BabA2 and VacAs1, but expressing VacAs2) were investigated in this study.

first: Sicheng

last: Wen


title: Gene expression in Histone H1 null mutant cells

city: Atlanta

first: Hideharu

last: Hashimoto

state: GA

address: 1510 Clifton

department: Biochemistry

institute: Emory University

summary:
In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804]) but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities (Hashimoto et al., DNA repair (2007) [17613284]), so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Next we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analysis those gene expression pattern in wild-type, K11, and K11-5 cells (Hashimoto et al., NAR (2010), PMID:20156997)
Keywords: gene expression array-based, count

overall_design: Apoptosis is induced in H1 null cells, so we inhibit apoptosis with pan-caspase inhibitor, Z-VAD-FMK and extract RNAs.

first: Yasunari

last: Takami

first: Tatsuo

last: Nakayama

first: Yoichi

last: Shinkai


city: Santa Clara

first: Nick

last: Sampas

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

summary:
Genetic variation amongst individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single-nucleotide changes.  In this manuscript we explore variation on an intermediate scale-particularly insertions, deletions, and inversions affecting from a few thousand to a few million base pairs.  We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number among individuals. Sequencing of a subset of structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence-map of human structural variation-an important standard for genotyping platforms and a prelude to future individual genome sequencing projects.
Keywords: comparative genomic hybridization

overall_design: The DNA samples are a panel of 8 Hapmap samples, described by E. Eichler et al. (2007, Nature 447, 161-165).  This set of 7 female, and one male samples are from from the Coriell Cell Repository, and is comprised of samples from four populations: four Yoruban, two CEPH, one Chinese, and one Japanese.  The reference sample, NA15510, is female and also from the Corriel Cell Repository.  This sample has been extensively characterized, (for example in Tuzan et al. 2005, Nature Genetics 10, p1038) and has been recommended for use in CNV detection programs to allow meaningful comparison of data between studies (discussed in Scherer, et al. 2007, Nature Genetics Supplement 39: S7-S15). Each of these samples was hybridized in pairs with the reversed labeling polarities.  Additionally, 3 self-self control hybridizations were carried out for the reference sample, NA15510, one on each hybridization date.

first: Jeffrey

last: Kidd

first: Gregory

last: Cooper

first: William

last: Donahue

first: Hillary

last: Hayden

first: Tina

last: Graves

first: Nancy

last: Hansen

first: Brian

last: Teague

first: Can

last: Alkan

first: Francesca

last: Antonacci

first: Eric

last: Haugen

first: Troy

last: Zerr

last: Yamada

first: Peter

last: Tsang

first: Tera

last: Newman

first: Eray

last: Tüzün

first: Ze

last: Cheng

first: Heather

last: Ebling

first: Nadeem

last: Tusneem

first: Robert

last: David

first: Will

last: Gillett

first: Karen

last: Phelps

first: Molly

last: Weaver

first: David

last: Saranga

first: Adrianne

last: Brand

first: Wei

last: Tao

first: Erik

last: Gustafson

first: Kevin

last: McKernan

first: Lin

first: Maika

last: Malig

first: Joshua

last: Smith

last: Korn

first: Steven

last: McCarroll

last: Altshuler

first: Daniel

last: Peiffer

first: Michael

last: Dorschner

first: John

last: Stamatoyannopoulos

last: Schwartz

first: Deborah

last: Nickerson

first: James

middle: C


title: PPARγ activation promotes infiltration of alternatively activated macrophages into adipose tissue.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Background: Obesity is associated with infiltration of macrophages into adipose tissue. Adipose macrophages may contribute to an elevated inflammatory status by secreting a variety of pro-inflammatory mediators, including TNFalpha and IL-6. Recent data suggest that during diet-induced obesity the phenotype of adipose-resident macrophages changes from alternatively activated macrophages towards a more classical and pro-inflammatory phenotype. Here, we explore the effect of PPARγ-activation on obesity-induced inflammation in 129SV mice fed a high fat diet for 20 weeks. High fat feeding increased bodyweight gain, adipose tissue mass and liver triglycerides. Rosiglitazone treatment further increased adipose mass, reduced liver triglycerides and changed adipose tissue morphology towards smaller adipocytes. Surprisingly, rosiglitazone markedly increased the number of macrophages in adipose tissue, as shown by immunohistochemical analysis and quantification of macrophage marker genes CD68 and F4/80+. In adipose tissue, markers for classically activated macrophages including IL-18 were down regulated whereas markers characteristic for alternatively activated macrophages (Arginase 1, IL-10) were up regulated by rosiglitazone. Importantly, conditioned media from rosiglitazone-treated alternatively activated macrophages neutralized the inhibitory effect of macrophages on 3T3-L1 adipocyte differentiation, suggesting that alternatively activated macrophages may be involved in mediating the effects of rosiglitazone on adipose tissue morphology and mass. Our results suggest that short term rosiglitazone treatment increases infiltration of alternatively activated macrophages in adipose tissue. The alternatively activated macrophages might play a role in PPARγ-dependent expansion and remodeling of adipose tissue.
Keywords: metabolic state analysis

overall_design: Pure bred wild-type (129S1/SvImJ) male mice received a low fat diet or high fat diet for 21 weeks, providing 10 or 45% energy percent in the form of triglycerides (D12450B or D12451, Research Diets, New Brunswick, USA). The lard component in these diets was replaced by palm oil.  In the last week of diet intervention, half of the mice receiving the HFD were switched to HFD supplemented with Rosiglitazone (0.01 % wt/wt). Animals were sacrificed in the fed state. Epididymal adipose tissue was excised and frozen in liquid nitrogen. Pooled RNA samples from 5 mice per experimental group were used for microarray analysis. Samples were hybridized on Affymetrix GeneChip Mouse Genome 430-2.0 plus arrays. Five microgram total RNA was labelled according to the Affymetrix One-cycle Target Labeling Assay, fragmented and hybridized according to Affymetrix's protocols.

first: Rinke

last: Stienstra

first: Caroline

last: Duval

first: Shohreh

last: Keshtkar

first: Jeroen

last: van der Laak

first: Sander

last: Kersten

last: Müller


title: Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes

status: Public on Apr 24 2008

first: Fan

last: Shen

address: 3420 Central Expressway

institute: Affymetrix, Inc

summary:
Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes

Background
DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. We have previously reported a comprehensive view of CNVs in the HapMap DNA collection using high density 500K EA (Early Access) SNP genotyping arrays which revealed greater than 1,000 CNVs ranging in size from 1kb to over 3Mb. Although the arrays used most commonly for GWAS predominantly interrogate SNPs, CNV identification and detection does not necessarily require the use of DNA probes centered on polymorphic nucleotides and may even be hindered by the dependence on a successful SNP genotyping assay.
Results
In this study, we have designed and evaluated a high density array predicated on the use of non-polymorphic oligonucleotide probes for CNV detection. This approach effectively uncouples copy number detection from SNP genotyping and thus has the potential to significantly improve probe coverage for genome-wide CNV identification. This array, in conjunction with PCR-based, complexity-reduced DNA target, queries over 1.3M independent NspI restriction enzyme fragments in the 200bp to 1100bp size range, which is a several fold increase in marker density as compared to the 500K EA array. In addition, a novel algorithm was developed and validated to extract CNV regions and boundaries.
Conclusions
Using a well-characterized pair of DNA samples, close to 200 CNVs were identified, of which nearly 50% appear novel yet were independently validated using quantitative PCR. The results indicate that non-polymorphic probes provide a robust approach for CNV identification, and the increasing precision of CNV boundary delineation should allow a more complete analysis of their genomic organization.
Keywords: Copy number variation (CNV) detection

overall_design: A set of five genomic DNA samples containing different numbers of X chromosomes (1X to 5X sample set, including NA15510 and NA10851) were hybridized to Nsp copy number (CN) arrays in triplicate to evaluate detection of copy number variation using high density, non-polymorphic oligonucleotide probes.  6 Hapmap samples were hybridized to Nsp CN arrays to evaluate Mendelian inheritance of CNVs.


title: HtrA1-dependent proteolysis of TGF-β controls both neuronal maturation and developmental survival

status: Public on Apr 16 2008

city: Caen

first: Benoit

middle: Denis

last: Roussel

address: Bd Becquerel

department: GIP Cyceron

country: France

institute: INSERM

summary:
Transforming growth factor-β (TGF-β) signalling controls a number of cerebral functions and dysfunctions including synaptogenesis, amyloid-β accumulation, apoptosis and excitotoxicity. Using cultured cortical neurons prepared from either wild type or transgenic mice over-expressing a TGF-β responsive luciferase reporter gene (SBE-Luc), we demonstrated a progressive loss of TGF-β signalling during neuronal maturation and survival. Moreover, we showed that neurons exhibit increasing amounts of the serine protease HtrA1 (high temperature responsive antigen 1) and corresponding cleavage products during both in vitro neuronal maturation and brain development. In parallel of its ability to promote degradation of TGF-β1, we demonstrated that blockage of the proteolytic activity of HtrA1 leads to a restoration of TGF-β signalling, subsequent overexpression of the serpin type -1 plasminogen activator inhibitor (PAI-1) and neuronal death. Altogether, we propose that the balance between HtrA1 and TGF-β could be one of the critical events controlling both neuronal maturation and developmental survival.
Keywords: HtrA1 / neuronal survival / PAI-1 / TGF-β signalling / tPA

overall_design:
Total RNA were extracted from 3 cultures of 2 DIV Human neurons. For each stage, equal amounts of each RNA were pooled and 5µg were reverse-transcribed, labelled and hybridized on pangenomic microarrays.
Each pool was hybridized in duplicate dye-swap independent experiments.

first: Severine

last: Launay

first: Eric

last: Maubert

first: Nathalie

last: Lebeurrier

first: Annette

last: Tennstaedt

first: Mara

last: Campioni

first: Fabian

last: Docagne

first: cecilia

last: Gabriel

first: Luce

last: Dauphinot

first: Marie-Claude

last: Potier

last: Ehrmann

first: Alfonso

last: Baldi

first: Denis

last: Vivien


title: Gene differential expression between attachment and detachment of zebra mussel

status: Public on Apr 19 2008

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

summary:
A zebra mussel byssus cDNA microarray was used to identify the differentially expressed genes between attachment and detachment.
Keywords: Gene differential expression

overall_design: The zebra mussels were divided in to two groups: AT and DT. In group AT all the zebra mussels were kept in the water attached for 48 hours while in group DT, the individuals were kept detached underwater for 48 hours. The feet of the zebra mussels were taken from each group. Four replicates, including four individual feet each replicate, were taken from each group for total RNA extraction. Four microarray hybridization performed between AT and DE. In each group, two cDNA replicates were labeled with Alexa 555 while the other two were labeled with Alexa 647. Every hybridization happened between two cDNA samples from different group with different labels.

first: Mohamed

last: Faisal


title: Transcriptomic analysis of responses to infectious salmon anemia virus infection in macrophage-like cells

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary:
The aquatic orthomyxovirus infectious salmon anemia virus (ISAV) is an important pathogen for salmonid aquaculture, however little is known about protective and pathological host responses to infection. We have investigated intracellular responses during cytopathic ISAV infection in the macrophage-like Atlantic salmon kidney (ASK) cell line by microarray analysis (1.8K SFA2.0 immunochip) and a functional assay for glutathione. Gene transcription changed rapidly and consistently with time and with minor differences between two virus isolates. While several pro-inflammatory and antiviral immune genes were induced, genes involved in cell signaling and integrity were down-regulated, suggesting isolation of infected cells from cell-to-cell interaction and responses to external signals. Differential expression of genes regulating cell cycle and apoptosis implied opposite cues from host cell and virus. This was in pace with massive down-regulation of genes involved in biosynthesis and processing of nucleotides and nucleic acids. Significant down-regulation of several genes involved in metabolism of reactive oxygen species suggested increased oxidative stress, which was confirmed by a functional assay showing reduced levels of glutathione during infection. Testing of expression data against a microarray database containing diverse experiments revealed candidate marker genes for ISAV infection. Our findings provide novel insight into cellular host responses and determinants for acute cytopathic ISAV infection.
Keywords: Infectious salmon anemia virus (ISAV); Host response; Molecular pathology; Microarray; Macrophage; Oxidative stress

overall_design: ASK cells infected with ISAV isolate 2 and 4 and mock-infected were cultured in triplicates and total RNA pooled from each at the following time-points post-infection; 1, 3 and 5 days. For microarray analysis, single-slide hybridisation was applied between infected RNA (Cy5 labelled) and control RNA (Cy3 labelled) for each time-point. Results were verified by real-time qPCR.

first: Sven

last: Jørgensen

first: Berit

last: Lyng Schiøtz

first: Caird

last: Rexroad

first: Tor

last: Gjøen


title: Circulating Cells in Coronary Collateral Artery Growth

status: Public on Apr 17 2008

city: Amsterdam

first: Stephan

middle: Henrik

last: Schirmer

address: Meibergdreef 9

department: Cardiology

institute: Academic Medical Center

summary:
Background: Collateral artery growth, also termed arteriogenesis, occurs upon narrowing or occlusion of a major artery. To date, attempts to stimulate arteriogenesis in patients for therapeutic purposes have not been successful. Experimental models showed that circulating cells orchestrate arteriogenesis. In humans, a large heterogeneity exists in the arteriogenic response. We hypothesized that good arteriogenic responders (GARs) and bad arteriogenic responders (BARs) differ in gene expression profiles of circulating cells, thereby disclosing potential new therapeutic strategies for the stimulation of arteriogenesis.  Methods: A total of 45 patients scheduled for percutaneous coronary intervention (PCI) for single-vessel coronary artery disease underwent intracoronary measurements of collateral flow index (CFI) to distinguish between GARs (CFI>0.21) and BARs (CFI≤0.21). Monocytes and CD34+ stem cells were collected from peripheral blood. A fraction of monocytes was further processed to obtain stimulated monocytes and macrophages. Whole genome transcriptome analysis was performed on all four cell types.
Results: LPS-stimulated monocytes showed 244 genes differentially expressed (false discovery rate < 0.05) between GARs and BARs. Macrophage gene expression correlated with stimulated monocytes, while resting monocytes and stem cells revealed no differential gene expression. Stimulated monocytes from GARs showed a strongly attenuated response in several interferon- and apoptosis-related genes, which was corroborated at the protein level.  Conclusions Circulating cells from GARs and BARs distinctively differ in their gene expression profiles upon stimulation. The reduced expression of interferon and apoptosis genes in GARs may lead to novel therapeutic approaches for the stimulation of collateral artery growth.
Keywords: disease state analysis, stress response analysis, natural defense mechanism analysis

overall_design: in total 189 arrays analyzed, of which 47 technical replicates (142 biological samples). CD34+ stem cells, resting CD14+ monocytes, stimulated monocytes and macrophages were analyzed, all from two patient groups of different coronary collateral support.

middle: H

first: Joost

last: Fledderus

first: Anton

last: Horrevoets

first: N

last: van Royen


title: Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

status: Public on Apr 15 2008

first: Amy

last: VanFossen

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

institute: NC State Unversity

summary:
Caldicellulosiruptor saccharolyticus is an extremely thermophilic, Gram-positive anaerobe, which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2 and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to co-utilize glucose and xylose, make this bacterium an attractive candidate for microbial bioenergy production.  Glycolytic pathways and an ABC-type sugar transporter were significantly up-regulated during growth on glucose and xylose, indicating that C. saccharolyticus co-ferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks represents a highly desirable feature of a lignocellulose-utilizing, biofuel-producing bacterium.
Keywords: substrate response

overall_design: C. saccharolyticus was subcultured (overnight) 3 times on the substrate of interest in modified DSMZ 640 medium before inoculating a pH-controlled (pH = 7) 1-liter fermentor containing 4 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (~OD660 = 0.3-0.4) and harvested by centrifugation and rapid cooling to 4 °C and stored at -80 °C.  To elucidate the central carbon metabolic pathways and their regulation, transcriptome analysis was performed after growth on glucose, xylose and a 1:1 mixture of both substrates. L-Rhamnose, which was likely to follow another pathway, was used as a reference substrate.

first: Harmen

last: van de Werken

first: Marcel

last: Verhaart


title: Gene expression profiling of Bruguiera gymnorhiza under salt stress

city: Hachioji

first: Yuichi

last: Tada

state: Tokyo

address: 1404-1 Katakura

country: Japan

institute: Tokyo University of Technology

summary:
To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment.
Keywords: time course, stress response, root type comparison

overall_design: Samples were collected from each set of three trees at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment, that is 27 trees were used in total. RNA was extracted from mixture of the samples from 3 trees to average genotypes of 3 trees.

first: Takuya

last: Yamanaka


title: Detection of Human Viruses from wastewater sewage extracts

status: Public on Apr 18 2008

city: East Lansing

first: Mark

last: Wong

state: MI

address: 3 Natural Resources

department: Crops and Soil Sciences

summary:
Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses.
Keywords: Detection of pathogens within environmental sample (Viruses)

overall_design: Environmental viruses were concentrated using organic flocculation with Beef Extract supplemented with glycine. Viruses were concentrated using 2 successive rounds of centrifugation and resuspended in Sodium Phosphate buffer. Viral nucleic acid was extracted, labeled and hybridized unto the microarray to determine the presence of target viruses within the sample.

first: Joan

last: Rose


title: The gene expression profiles in response to fungal infection in hemocytes.

first: Young-Joon

last: Kim

address: Yonsei Univ 134 Sinchon-dong Seodaemun-gu

institute: Yonsei University

summary:
The object of the microarray data is to find several genes effected by fungal infection.
Keywords: stress response

overall_design:
In order to establish the gene expressino levels in response to fungal infection in hemocytes, B.bassiana were injected into the posterior end of third instar larvae using a tungsten needle and incubated for 1h at 25 celcius degree.
To compare with non-infected hemocytes, total RNA from infected hemocytes were labeled by Cy5, total RNA from non-infected hemocytes were labeled by Cy3, and hybridized to chip.

first: Li-Hua

last: Jin


title: Gene expression profiling on mouse models of dilated cardiomyopathy

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary:
Cardiomyopathies are heart muscle disorders characterised by chamber dilation often accompanied by wall thinning, severe systolic and diastolic dysfunction and frequently heart failure. Although several genes were found to be differentially expressed the cellular and molecular basis of the disease still remains poorly understood. We performed expression profiling on cardiac samples from six different mouse disease models: muscle LIM protein- (MLP), ErbB2-, ErbB4- and plakoglobin-deficient mice, doxorubicin treated mice and doxorubicin treated ErbB4 deficient mice. We aimed at the identification of general cardiomyopathy expression patterns as well as mouse model specific ones.
Keywords: expression profiling, mouse models for cardiomyopathy

overall_design: For each mouse model investigated RNA of 4-8 individuals was pooled and targets were hybridised in four technical replicates on agilent cDNA microarrays. In a two color approach two dye swaps were performed with the cardiomyopathy samples and their wildtype/healty controls.

first: Cecilia

last: Hertig

first: Elisabeth

last: Ehler

first: Alistair

last: Garratt

first: Patricia

last: Ruiz Noppinger


title: Gene expression profiling of hepatitis development and hepatocarcinogenesis initiation in LEC rats.

status: Public on Apr 25 2008

city: Toulouse

first: Françoise

last: Guéraud

address: 180, Chemin de Tounefeuille BP3, Cedex 9

department: UMR1089 INRA-ENVT

institute: Institut National de la Recherche Agronomique (INRA)

summary:
LEC rats are considered as interesting model for studying hepatitis and development of hepatocarcinogenesis related to copper accumulation and oxidative stress. LEC rats have a mutation in a gene related to liver copper excretion, the Atp7b gene. As a consequence, this rat strain shows an abnormal copper accumulation in the liver. This is believed to be the origin of the acute hepatitis and the subsequent  hepatocellular carcinoma that spontaneously develop in these rats. Here, we present the gene expression profiles of LEC rats at different disease stages. LEC rats were classified as normal 6 weeks old (6w), normal 9 weeks old (9w), slight jaundice and jaundice according to age and disease state. D-penicillamine, a copper chelator agent, blocks both hepatitis and tumor development. D-penicillamine-trated LEC rats were used as control rats for gene expression comparison as they showed neither hepatitis development nor tumor marker expression. Gene expression differences in protein metabolism and tumor marker proteins add to the known oxidative stress and inflammation characterization of the hepatitis process, leading to new insights concerning hepatitis and hepatocarcinogenesis development.
Keywords: disease state analysis

overall_design: 6 weeks old LEC rats, 6 rats per group, were sacrified at different hepatitis stages. Biochemical and histological analyses were performed in order to classify the rats into normal, slight jaundice or jaundice groups. D-penicillamine-treated LEC rats (100 mg/kg/day p.o.) were used as control rats since they behave as normal rats. Microarray analysis was performed on liver samples, one replicate per rat, using dyes swap.

first: Adriana

last: Marquez

first: Balbine

last: Roussel

first: Veronique

last: Le Berre

first: Serguei

last: Sokol

first: Jean-Marie

last: François

first: Saul

last: Villa-Treviño

first: Alain

last: Paris

last: Gueraud


title: CIITA locus binding of H3ac, H4ac, STAT1, IRF1 antibodies in IFNg treated and untreated HeLa cells using nimblegen array

city: Toronto

first: Zhaodong

last: Xu

state: Ontario

address: Mc6-424, 399 Bathurst Street

department: Genetics & Development Division

country: Canada

institute: TWRI, UHN

type: Genome binding/occupancy profiling by genome tiling array

summary:
Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 122kb CIITA locus(HG17)
Keywords: ChIP-chip

overall_design: three replicates for each marker at each state.

first: Rod

last: Bremner

first: Tao

last: Yu


title: CGH analysis of Campylobacter jejuni isolates previously analyzed by Multi-Locus Sequence Typing

status: Public on Apr 21 2008

city: Lethbridge

first: Eduardo

middle: N

last: Taboada

state: Alberta

address: PO Box 640, TWP Rd. 9-1

institute: Public Health Agency of Canada

summary:
In this experiment, we hava analyzed a set of 45 C. jejuni strains by CGH and MLST in order to investigate whether the strain relationships inferred from the analysis of a small number of loci (MLST) reflect whole-genome gene conservation patterns observed by CGH.
Keywords: individual hybridizations, comparative genomic hybridization

overall_design: We performed microarray CGH on 45 strains previously characterized by MLST. Genomic DNA from each experimental strain was compared in a CGH experiment against the reference strain NCTC 11168. We measured signal intensity for each tester strain versus the control strain NCTC 11168. Values represent mean of replicate spots. Replicate arrays are not included.

first: Joanne

last: MacKinnon

first: Christian

last: Luebbert

first: Victor

last: Gannon

first: John

last: Nash

first: Kris

last: Rhan


title: SWCoV1 series; viral detection in Beluga whale liver

city: St. Louis

first: David

last: Wang

state: MO

address: 660 South Euclid Avenue

department: Molecular Microbiology

institute: Washington University School of Medicine

summary:
This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver.
Keywords: viral detection

overall_design: The series includes 2 control whale livers and 1 whale liver containing SWCoV1.

first: Kathie

last: Mihindukulasuriya

first: Guang

last: Wu

first: Judy

last: St. Leger

first: Robert

last: Nordhausen


title: Microarray analysis to identify novel genes regulated by Cholera toxin in bone marrow-derived dendritic cells (BMDCs)

status: Public on Apr 14 2008

city: Pittsburgh

first: Prabir

last: Ray

state: PA

address: 3459 Fifth Avenue

department: Medicine/Pulmonary

institute: University of Pittsburgh

summary:
The mechanisms by which dendritic cells (DCs) induce differentiation of naïve CD4+ T cells  along the Th2 lineage is not well understood given that DCs themselves do not produce IL-4. In the present study, we undertook a microarray approach to identify genes involved in the induction of Th2 differentiation by DCs treated with a Th2-skewing adjuvant cholera toxin (CT). In the microarray analysis, murine bone marrow derived immature DCs were treated with CT. Of particular interest was tthe significant upregulation of the expression of c-kit. The upregulation of c-kit on DCs is critical for the induction of a Th2 response.
Keywords: cholera toxin, bone marrow derived dendritic cells, gene expression array-based (RNA / spotted DNA/cDNA)

overall_design: Murine bone marrow cells were cultured in the presence of GM-CSF (10 ng/ml)  for 6 days . On day 6 the cells were harvested and purified  using magnetically labeled anti mouse CD11c+ beads .  The DCs were stimulated with CT (1 ug/ml)  for 24 hours and the RNA was isolated.

first: Anuradha


title: Radiation-induced gene translation profiles reveal tumor type and cancer specific components

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
The goal of this study was to compare the radiation-induced gene translation profiles generated from human tumor cell lines that are treated with radiation.
Keywords: stimulus or stress design

overall_design: A panel of cell lines included 5 gliomas, 4 pancreatic carcinomas, 3 breast carcinomas and 2 non-small cell lung carcinomas. In addition, radiation-induced gene translation profiles were generated for 4 normal human cell lines: a skin fibroblast (BJ), 2 lung fibroblasts (MRC5, MRC9) and mammary epithelial (MEC). Specifically, cell lines were exposed to 2 Gy or sham irradiated, polysome-bound RNA was isolated 6h later and subjected to microarray analyses. Each cell line was evaluated in biological replicates.

first: Sandhya

last: Kumaraswamy

first: Prakash

last: Chinnaiyan

first: Xing

last: Lu

first: Kevin

last: Camphausen

first: Philip

last: Tofilon


status: Public on Apr 10 2008

city: Sendai

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

summary:
Background: Chromatin remodeling complexes facilitate the access of enzymes that mediate transcription, replication or repair of DNA by modulating nucleosome position and/or composition. Ino80 is the DNA-dependent Snf2-like ATPase subunit of a complex whose nucleosome remodeling activity requires actin-related proteins, Arp4, Arp5 and Arp8, as well as two RuvB-like DNA helicase subunits. Budding yeast mutants deficient for Ino80 function are not only hypersensitive to reagents that induce DNA double strand breaks, but also to those that impair replication fork progression.
Results: To understand why ino80 mutants are sensitive to agents that perturb DNA replication, we used chromatin immunoprecipitation to map the binding sites of the Ino80 chromatin remodeling complex on four budding yeast chromosomes. We found that Ino80 and Arp5 binding sites coincide with origins of DNA replication and tRNA genes. In addition, Ino80 was bound at 67% of the promoters of genes that are sensitive to ino80 mutation. When replication forks were arrested near origins in the presence of hydroxyurea (HU), the presence of the Ino80 complex at stalled forks and at unfired origins increased dramatically. Importantly, the resumption of DNA replication after release from a HU block was impaired in the absence of Ino80 activity. Mutant cells accumulated double-strand breaks as they attempted to restart replication. Consistently, ino80-deficient cells, although proficient for checkpoint activation, delay recovery from the checkpoint response.
Conclusions: The Ino80 chromatin remodeling complex is enriched at stalled replication forks where it promotes the resumption of replication upon recovery from fork arrest.
Keywords: ChIP-chip

overall_design:
• The goal of the experiment
Genome-wide localization of Ino80 on chromosome in Saccharomyces cerevisiae
• Keywords
DNA replication, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI)
• Experimental factor
Distribution of Ino80 in random culture
Distribution of Ino80 in G1 phase
Distribution of Ino80 in early S phase
• Experimental design
ChIP analyses: W303 background cells expressing Myc-tagged Ino80 were used for the ChIP using anti-Myc monoclonal antibody (9E11).
ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI) was used.
• Quality control steps taken
Confirmation of several loci by quantitative real time PCR.

first: Kenji

last: Shimada

first: Thomas

last: Schleker

first: Kazuto

last: Kugou

first: Kunihiro

last: Ohta

first: Masahiko

last: Harata

first: Susan

middle: M

last: Gasser


status: Public on Apr 11 2008

first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary:
CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion followed by bioprime random labeling, and hybridization to AtTILE1 forward array.
Study on constitutive and ploymorphic CG methylation between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of CG methylation in reciprocal hybrids.
Keywords: genomic hybridization

overall_design: Each genotype by enzyme combination has four replicates, Single chanel. Total four genotypes (Col, Van, Col female x Van male, Van female x Col male). Two enzyme treatments (HpaII, MspI). Total 32 samples.

first: Xu

last: Zhang

first: Shinhan

last: Shiu


title: Carbon nutrition of pathogenic and commensal E. coli

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

summary:
Transcriptome profiling of E. coli MG1655, E. coli EDL933, E. coli ECOR26, and E. coli Nissle 1917 grown on mouse cecal mucus as carbon source
The carbon sources that support growth of pathogenic E. coli O157:H7 in the mammalian intestine have not previously been investigated.  In vivo, pathogenic E. coli EDL933 primarily grows as dispersed single cells within the mucus layer that overlies the mouse cecal epithelium.  We therefore compared the pathogen and commensal E. coli MG1655 for their mode of metabolism in vitro on a mixture of the sugars known to be present in cecal mucus and found that the two strains used the thirteen sugars in a similar order and co-metabolized as many as nine sugars at a time.  We conducted a systematic mutational analysis of E. coli EDL933 and E. coli MG1655 with lesions in the pathways used for catabolism of thirteen mucus-derived sugars and five other compounds for which the corresponding gene system was induced in the transcriptome of cells grown on cecal mucus.  Each of 18 catabolic mutants in both genetic backgrounds was fed to streptomycin-treated mice together with the respective wildtype parent strain and their colonization was monitored in fecal plate counts.  None of the mutations corresponding to the five compounds not found in mucosal polysaccharides resulted in colonization defects.  Based on the mutations that caused colonization defects, we determined that both E. coli EDL933 and E. coli MG1655 used arabinose, fucose, and N-acetylglucosamine in the intestine.  In addition, E. coli EDL933 used galactose, hexuronates, mannose and ribose, whereas E. coli MG1655 used gluconate and N-acetylneuraminic acid.  The colonization defects of six catabolic lesions were found to be additive in E. coli EDL933, but not E. coli MG1655.  The data indicate that pathogenic E. coli EDL933 uses sugars that are not used by commensal E. coli MG1655 to colonize the mouse intestine.  The results suggest a strategy whereby invading pathogens gain advantage by simultaneously consuming several sugars that may be available because they are not consumed by the commensal intestinal microbiota.
Keywords: growth condition: carbon source was mouse cecal mucus

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli strains were grown on MOPS minimal medium containing 10 mg/ml of mucus or 0.2% glucose in 10 ml standing culture in testtubes and harvested at OD600 = 0.4.

first: Joe

last: Grissom


title: Molecular Classification and Prediction of Survival in Non-Small-Cell Lung Cancer

city: Basel

first: Wolfgang

middle: Ernst Gustav

last: Budach

address: Klybeckstrasse

department: BMD/NV&D

country: Switzerland

institute: Novartis Pharma AG

summary:
BACKGROUND: Global gene expression analysis provides a comprehensive molecular characterization of non-small cell lung cancer. The aim of this study was to evaluate the feasibility of integrating expression profiling into routine clinical work-up by including minute bronchoscopic biopsies and develop a robust prognostic gene expression signature
METHODS: Tissue samples from a series of 41 chemotherapy-naïve non-small cell lung cancer patients and 15 control patients with inflammatory lung diseases were obtained during routine clinical work-up and gene expression profiles were gained using a highly sensitive oligonucleotide array platform (Novachip ; 34'207 transcripts). Gene expression signatures were analyzed by correlation with histological and clinical parameters and validated on independent published datasets and immunohistochemistry.
RESULTS: Tumor tissue classification based on the gene expression results was strongly dependent on the proportion of tumor cells present in the biopsies and showed an overall sensitivity of 80% and specificity of 89%. For prognostication we developed a metagene consisting of 13 genes, which was validated on 4 independent published datasets. The robustness of this metagene has been demonstrated by a virtual independence from tumor cells present in the biopsies. Furthermore, vascular endothelial growth factor-beta, one of the key prognostic genes was validated by immunohistochemistry on 508 independent tumor samples.
CONCLUSIONS: The proposed strategy of integrating functional genomics into routine clinical work-up allows molecular tumor classification and prediction of survival in patients with non-small cell lung cancer of all stages and is suitable for an integration in the daily clinical practice.
Keywords: Gene expression profiling for disease state analysis in lung cancer patients

overall_design: 56 lung biopsies, 4 different Phenotypes: NSCLC-squa., NSCLC-NOS, NSCLC-Adeno, Ctr.-Infl.

first: Florent

last: Baty

first: Michaël

last: Facompré

first: Sergio

last: Kaiser

first: Martin

last: Schumacher

first: Miklos

last: Pless

first: Lukas

last: Bubendorf

first: Spasenija

last: Savic

first: Estelle

last: Marrer

last: Buess

first: Jeanne

last: Kehren

first: Michael

last: Tamm

last: Brutsche


title: cis sequence effects on gene expression

city: Rockville

first: Andrew

middle: W

last: Bergen

address: 6120 Executive Blvd

department: Cancer Epidemiology & Genetics

institute: NCI/NIH

summary:
Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation provides insight into biological mechanisms that underlie gene regulation and function. We investigated the role of sequence variation in cis on gene expression (cis sequence effects) in a group of genes frequently studied in cancer research. We assessed the
proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects, and compared our results to the literature.

Keywords: genetical genomics

overall_design:
Thirty lymphoblastoid cell lines drawn from the SNP500Cancer resource were cultured in triplicate. The intersection of gene expression profiling data at N=697 candidate genes and genomic sequencing data at N=552 candidate genes from these cell lines yielded data at thirty candidate genes with strong and variable gene expression suitable for the
investigation of cis sequence effects. We used regression on SNP genotype in an additive model, the single-point additive model of Mander, and the haplotype phylogeny scanning approach of Templeton to evaluate associations between individual SNPs, all SNPs at a
gene, and diplotypes, with log-transformed and rank-invariant normalized mean gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p<0.05) association with gene expression using one or more methods. Data were available for fourteen candidate genes common to the literature and our analysis,
five of which exhibited significant cis effects in this study. Using the literature results as a “gold standard”, and after excluding two genes that exhibited discordant literature results, our study concordantly identified 4 of 5 genes, and 6 of 7 genes as exhibiting and not exhibiting significant cis sequence effects, respectively.

first: Andrea

last: Baccarelli

first: Timothy

middle: K

last: McDaniel

first: Kenneth

last: Kuth

first: Ruth

last: Pfeiffer

first: Jerry

last: Kakol

first: Patrick

last: Bender

first: Kevin

last: Jacobs

first: Bernice

last: Packer

first: Stephen

last: Chanock

first: Meredith

last: Yeager


title: mRNAs associated with Ago2: Ago2, Ago2+miR-1, Ago2+miR-124, mock transfected

status: Public on Apr 08 2008

city: Stanford

first: Daniel

last: Hogan

address: 279 Campus Dr B439

institute: Stanford University

summary:
As a core RISC component, Ago2 associates with miRNAs and target mRNAs. To identify these mRNAs, we ran lysate from HEK293T cells over a FLAG resin from 2 conditions: +FLAG-Ago2, +mock transfection.  To identify mRNAs associated with specific miRNAs, we ran lysate from HEK293T cells over a FLAG resin from 2 conditions: +FLAG-Ago2 & miR-1, and +FLAG-Ago2 & miR-124.
Set of arrays that are part of repeated experiments
Compound Based Treatment: mock transfected
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed


title: Expression data  HEK293T cells transfected with either Ago2, Ago2 + miR-1, Ago2 + miR-124,  mock

summary:
HEK293T cell expression data from four conditions: mock transfection, Ago2 transfection, Ago2 & miR-1 transfection, and Ago2 & miR-124 transfection. RNA was isolated directly from 10cm dishes using Trizol reagent and amplified.
Set of arrays that are part of repeated experiments
Compound Based Treatment: FLAG-Ago2 transfection
Keywords: Biological Replicate

overall_design:
Biological Replicate
Using regression correlation


title: NaCl: Plant Small RNAs

status: Public on Apr 07 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
au07-08_nacl - nacl - Small RNAs induced under salt stress. - Arabidopsis seedlings have been treated with 150 mM NaCl in orden to determine small RNAs specifically induced by this stress.
Keywords: treated vs untreated comparison

overall_design: 3 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Miguel

last: A. botella

first: Marie-Laure

middle: L

last: Martin-Magniette


title: miRNA arrays: Ago2 transfected vs. Mock, Ago2 IP vs. total RNA

summary:
miRNAs were enriched from HEK293T cells using the ambion FLASHPAGE fractionater after mock transfection, Ago2 transfection, and FLAG-Ago2 IP. miRNAs were labeled and hybridized: Ago2 transfected vs. mock transfection and Ago2 transfected vs. Ago2 IPs.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate


first: Yukako

last: Oma

overall_design:
• The goal of the experiment
Genome-wide localization of Ino80 and Arp5 on chromosome in Saccharomyces cerevisiae
• Keywords
DNA replication, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI)
• Experimental factor
Distribution of Ino80 and Arp5 in wild type in random culture
Distribution of Ino80 in G1 cells
Distribution of Ino80 in early S phase cells
• Experimental design
ChIP analyses: W303 background cells expressing Myc tagged Ino80 were used for the ChIP using anti-Myc monoclonal antibody (9E11).
ChIP analyses: W303 background cells expressing Myc tagged Ino80 were used for the ChIP using anti-Arp5 polyclonal antibody.
ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI) was used.
• Quality control steps taken
Confirmation of several loci by quantitative real time PCR.

first: Kenji

last: Shimada

first: Thomas

last: Schleker

first: Kazuto

last: Kugou

first: Kunihiro

last: Ohta

first: Masahiko

last: Harata

first: Susan

last: Gasser


title: Gene Expression Profiles in Intracranial Arteries and Abdominal Aortae

status: Public on Apr 04 2008

city: Detroit

first: Gerard

last: Tromp

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary:
Gene expression profiles were used to identify pathways common to arteries from different vascular beds.
We used the Illumina Sentrix-6 whole-genome microarray platform to identify genes that are expressed in common between abdominal aorta and intracranial arteries of the circle of Willis.
Keywords: Characterization of expression in normal arteries from different vascular beds: intracranial arteries and abdominal aorta.

overall_design: Intracranial vessels and abdominal aortae were obtained from cadavers and preserved in RNAlater. RNA was isolated from single artery samples.

first: Helena

last: Kuivaniemi

first: Shantel

last: Weinsheimer

first: Guy

last: Lenk


title: Genome-wide transcriptional profiling of Lactobacillus acidophilus' response to bile

status: Public on Apr 05 2008

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary:
Lactobacillus acidophilus NCFM is an industrially important strain used extensively as a probiotic culture. Tolerance of the presence of bile is an attribute important to microbial survival in the intestinal tract. A whole-genome microarray was employed to examine the effects of bile on the global transcriptional profile of this strain, with the intention of elucidating genes contributing to bile tolerance. Genes involved in carbohydrate metabolism were generally induced, while genes involved in other aspects of cellular growth were mostly repressed. A 7-kb eight-gene operon encoding a two-component regulatory system (2CRS), a transporter, an oxidoreductase, and four hypothetical proteins was significantly upregulated in the presence of bile. Deletion mutations were constructed in six genes of the operon. Transcriptional analysis of the 2CRS mutants showed that mutation of the histidine protein kinase (HPK) had no effect on the induction of the operon, whereas the mutated response regulator (RR) showed enhanced induction when the cells were exposed to bile. These results indicate that the 2CRS plays a role in bile tolerance and that the operon it resides in is negatively controlled by the RR. Mutations in the transporter, the HPK, the RR, and a hypothetical protein each resulted in loss of tolerance of bile. Mutations in genes encoding another hypothetical protein and a putative oxidoreductase resulted in significant increases in bile tolerance. This functional analysis showed that the operon encoded proteins involved in both bile tolerance and bile sensitivity.
Keywords: stress response

overall_design: We used a Reference Sample design, where each sample was compared using a dye swap to a common reference sample (early log-phase L. acidophilus cultures resuspended in fresh MRS [pH ~6.8]).

first: Maria

middle: A

last: Azcarate-Peril


title: Wind-responsive changes in poplar leaves of different developmental stages

status: Public on Apr 03 2008

city: Seibersdorf

first: Silvia

last: Fluch

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

country: Austria

institute: Austrian Research Centers GmbH

summary:
A developmental series of wind-treated Populus leaf tissue was subjected to array analyses in order to address the issue of age-dependent responsiveness to environmental changes. The following developmental stages were defined for the experiment: Y – “youngest leaf” including the shoot tip = smallest fully enrolled leaf; E – “expanded leaf” = oldest leaf that had not reached full leaf thickness; M – “mature leaf” = 5th leaf below E = has reached full leaf expansion and full leaf thickness; O – “old leaf” = 5th leaf below E.
Keywords: transcription profiling

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design: Two-condition experiment, control (K) vs. Wind-treated (W) leaves. Biological replicates: 3 control (1-3), wind-exposed (1-3), independently grown and harvested. One swap replicate per array.

first: S

first: C

last: Olmo

last: Tauber

first: M

last: Sierschneider

first: D

last: Kopecky

first: T

last: Reichenauer

first: I

last: Matusikova


title: Detection of virulence and antibiotic resistance gene families

status: Public on Apr 02 2008

city: Livermore

first: Crystal

last: Jaing

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

summary:
Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known and novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.
Keywords: detection, pathogen, virulence mechanism

sample_organism: Staphylococcus aureus subsp. aureus Mu50

overall_design: In this report, we describe the process used to design our first generation functional array for highly sensitive detection of virulence and antibiotic resistance gene families. We discuss the probe design algorithms, including virulence gene sequence selection, and our protocols for sample preparation, amplification, labeling, hybridization, and data analysis. We present the results from experiments designed to assess whether the array can detect virulence gene orthologs from organisms without perfect match probes on the array, using both targeted mismatch probes and hybridizations to DNA from other organisms. Also, we report the results from limit of detection studies, using known amounts of bacterial DNA spiked into aerosol samples to measure the minimal concentration required for detection of virulence elements against a complex background.

first: Shea

last: Gardner

first: Kevin

last: McLoughlin

first: Nisha

last: Mulakken

first: Peter

last: Williams

first: Tom

last: Slezak


title: Herpes simplex host shutoff attenuates antiviral state

first: Seth

middle: Daniel

last: Crosby

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
Herpes simplex virus mutants lacking the vhs gene are severely attenuated in animal models of pathogenesis and exhibit reduced growth in primary cell culture. As a result of these properties vhs-deleted virus have been proposed as live-attenuated viruses. Despite these findings and their implications for vacccines, the mechanisms by which vhs promotes infection in cell culture and in vivo are not understood. In this study we demonstrate that vhs-deficent viruses replicate to reduced levels in interferon(IFN)- primed cells. Furthermore, vhs-defective viruses induce increased levels of IFNβ and IFNβ-stimulated genes, and increased levels of eIF2α phosphorylation in infected cells. In addition, we demonstrate a generalized over-expression of viral RNAs following infection with a vhs-deficient virus. This suggests increased expression of IFN pathway inducing double stranded RNA, a potent pathogen-associated molecular pattern (PAMP). Together these data show that vhs likely functions to reduce innate immune responses and thereby acts as critical determinant of viral pathogenesis.
Keywords: time course, genetic modification

overall_design: Time course (1,3,6,9 & 12h) of HSV infected mouse embryo fibroblasts.  Wild type (KOS) virus is co-hybridized with vhs null virus (NHB).  Each time-point is hybridized in quadruplicate.

middle: D

first: TracyJo

last: Pasieka

first: Diane

middle: E

last: Alexander

first: David

last: Leib


title: DNA methylation by HELP for Integrative epigenomic study in leukemia samples

status: Public on Apr 01 2008

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

summary:
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation is a hallmark of cancer and plays a central role in determining tumor phenotype.  We predicted that integration of different genome-wide epigenetic regulatory marks along with gene expression levels would provide greater power in capturing biological differences between leukemia subtypes. Gene expression, cytosine methylation and histone H3 lysine 9 (H3K9) acetylation were measured using high-density oligonucleotide microarrays in primary human acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) specimens. We found that DNA methylation and H3K9 acetylation distinguished these leukemias of distinct cell lineage, as expected, but that an integrative analysis combining the information from each platform revealed hundreds of additional differentially expressed genes that were missed by gene expression arrays alone. This integrated analysis also enhanced the detection and statistical significance of biological pathways dysregulated in AML and ALL. Integrative epigenomic studies are thus feasible using clinical samples and provide superior detection of aberrant transcriptional programming than single-platform microarray studies.
Keywords: DNA methylation by HELP

overall_design: 5 acute leukemia samples (2 ALL and 3 AML) in triplicate. Replicate #3 from sample ALL2 was discarded due to bad hybridization quality. No dye swap was performed.


title: Tumor biopsies from 71 untreated patients with mantle cell lymphoma

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

summary:
The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma
Keywords: lymphochip; MCL; untreated

first: Thomas

last: Dandekar

first: Julia

last: Engelmann

first: Andreas

last: Rosenwald


title: Pharmacogenomics of IFNb therapy

city: Amsterdam

first: Cornelis

last: Verweij

department: Dept. of Pathology

institute: VU Medical Center

summary:
This experiment set is used for the manuscript entitled: Pharmacogenomics of Interferon-b therapy in multiple sclerosis: Baseline IFN signature determines pharmacological differences between patients. In this study we generated and analyzed pre- and post- IFNb treatment gene expression patterns of RRMS patients with the aim of identifying pre-existing and/or drug-induced signatures that will allow us to make predictions on the expected pharmacological effects of IFNb treatment. We show that the expression level of IFN response genes prior to treatment, determines the pharmacological differences between patients with MS at the molecular level. A group of 16 Dutch patients (10 females and 6 males) with clinically definite relapsing-remitting MS was recruited from the outpatient clinic of the MS Centre Amsterdam. Mean age at start of IFNb therapy is 40.6 +/- 7.7, mean EDSS is 2.3 +/- 1.3 (range 1-6). Blood samples were obtained just before treatment and 1 month after start of the therapy. Patients received Avonex, Betaferon, Rebif 22 or Rebif 44.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Compound Based Treatment: Before and 1 month after IFNb therapy
Keywords: compound_treatment_design

overall_design: Complex


title: Global chromatin domain organization of the Drosophila genome

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by array

summary:
In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 34% of the fly genome is organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and share biological functions. Furthermore, fewer chromosomal rearrangements occur inside chromatin domains than outside domains during evolution. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution.
Keywords: DamID

overall_design: DamID experiments for multiple chromatin proteins was performed in Drosophila cell cultures. Samples were hybridized to spotted cDNA arrays. Every experiment was repeated at least 2 times, with one sample in the reverse dye orientation. When hybridization was performed 4 times, two samples were hybridized in the reverse dye orientation.

first: Elzo

last: de Wit

first: Ulrich

last: Braunschweig

first: Frauke

last: Greil

first: Harmen

middle: J

last: Bussemaker


title: Expression profiles of E. coli groESL(-) cells expressing human Hsp60(wt)/Hsp10 or Hsp60-(p.Val98Ile)/Hsp10 operons

city: Århus

first: Peter

last: Bross

address: Brendstrupgaardsvej 100

department: Institute for Clinical Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

summary:
To identify regulatory responses that could give clues as to the cause(s) of the growth arrest observed in E. coli cells expressing mutant Hsp60-(p.Val98Ile) and Hsp10 versus cells expressing wild type Hsp60 and Hsp10, we performed microarray analyses. We reasoned that the decreased chaperonin activity of the Hsp60-(p.Val98Ile) protein would greatly impair or abolish folding of E. coli proteins that depend on chaperonin assistance. The resulting decreased levels of various activities may cause compensatory up-regulation or deregulation of genes. The transcriptomes of cells shifted to expression of the arabinose-inducible chaperonin operon with either the Hsp60-(p.Val98Ile) mutant or the wild type Hsp60 from the second plasmid were compared. RNA samples from three independent cultures expressing the mutant or two independent cultures expressing wild type Hsp60 were pooled, respectively.
Keywords: Comparison of cells expressing two different variants of Hsp60

overall_design:
B178 (groELS)-deleted cells double-transformed with two plasmids harboring an IPTG-inducible operon with wild type human Hsp60 and Hsp10 and a second plasmid harboring an arabinose inducible operon with either Hsp60-(p.Val98Ile) and Hsp10 (mutant cells) or wild type Hsp60 and Hsp10 (wild type cells) were grown in dYT medium (21) supplemented with kanamycin (10 mg/L), ampicillin (100 mg/L) and IPTG (0.1mM) at 30°C in a shaking water bath. At OD536 ≈ 0.1 bacteria were harvested by centrifugation at ambient temperature, resuspended in fresh medium, and 0.2% arabinose was added. Growth was continued at 30°C. After 10 hours 3ml samples were withdrawn and RNA was isolated.
Two independent transformant clones of the wild type cells and three of the mutant cells were grown in this way. The RNA preps from the 2 wild type and the three mutant cells, respectively, were pooled, cDNA was synthesized, labelled and subjected to Affymetrix arrays.

first: Søren

last: Naundrup

first: Jakob

last: Hansen

first: Marit

last: Nielsen

first: Jane

last: Christensen

first: Mogens

last: Kruhøffer

first: Johan

last: Palmfeldt

last: Corydon

first: Debbie

last: Ang

first: Costa

last: Georgopoulos

first: Niels

last: Gregersen

first: Kåre


title: wounded vs unwounded hemocyte deficient embryos

city: Bristol

first: Mark

middle: Owen

last: Winfield

address: Woodland Road

department: Biological Sciences

institute: Bristol University

summary:
Wounded versus unwounded embryos lacking the hemocyte lineage were compared.
Keywords: wounded vs unwounded srp mutant embryos

overall_design: Serpent mutant embryos were wounded by laser ablation and compared to unwounded.


title: hemocyte minus versus hemocyte plus drosophila embryos

summary:
Drosophila embryos that were lacking the hemocyte lineage were compared to wild-type embryos.
Keywords: genetic modification

overall_design: Wild-type drosophila embryos were compared to serpent mutant embryos.


title: wounded versus nonwounded drosophila embryos

summary:
Elucidation of the wound response genes in Drosophila embryos
Keywords: response to wounding

overall_design: wild-type drosophila embryos were wounded by laser ablation and compared to unwounded embryos.


title: Mapping translocation breakpoints by next-generation sequencing

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary:
Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterisation of breakpoints in disease-associated BCRs has been instrumental in the molecular elucidation of a wide variety of genetic disorders. However, mapping chromosome breakpoints using traditional methods, such as in situ hybridization with fluorescent dye-labeled bacterial artificial chromosome clones (BAC-FISH), is rather laborious and time consuming. In addition, the resolution of BAC-FISH is often insufficient to unequivocally identify the disrupted gene. To overcome these limitations, we have performed shotgun sequencing of flow-sorted derivative chromosomes using ‘next generation’ (Solexa/Illumina) multiplex sequencing-by-synthesis technology. As shown here for three different disease-associated BCRs, the coverage attained by this platform is sufficient to bridge the breakpoints by PCR amplification, and this procedure allows to determine their exact nucleotide positions within few weeks. Its implementation will greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations.
Keywords: Array CGH

overall_design: Array CGH was performed in three carriers of balanced translocations to exclude DNA copy number changes.


title: Analysis of colorectal tissue from APC- and MYH-associated polyposis patients

city: Lisbon

first: Joana

last: Cardoso

address: Av. Prof Egaz Moniz

country: Portugal

institute: Faculty of Medicine

summary:
Expression profiling is a well established tool for the genome-wide analysis of the transcriptional activity of human neoplasia. However, the high sensitivity of this approach combined with the well-known cellular and molecular heterogeneity of cancer often result in extremely complex and extended expression signatures of difficult functional interpretation. The majority of sporadic colorectal cancer cases are triggered by mutations in the APC tumor suppressor gene leading to constitutive activation of the Wnt/b-catenin signaling pathway and adenoma formation. Notwithstanding this common genetic basis, colorectal cancers are very heterogeneous in their degree of differentiation, growth rate and malignant potential. Here, we applied cross-species comparison of expression profiles of intestinal polyps derived from hereditary colorectal cancer patients carrying APC germline mutations, and from a mouse model carrying a targeted inactivating mutation in the mouse homologue Apc. This comparative approach resulted in the establishment of a conserved signature encompassing 166 genes differentially expressed between adenomas and normal intestinal mucosa in both species. Functional analysis of the conserved genes revealed a general increase in cell proliferation and the activation of the Wnt/b-catenin signal transduction pathway, as expected from the selection of APC/Apc-mutant intestinal adenomas. Moreover, the conserved signature is able to resolve expression profiles from hereditary polyposis patients carrying APC germline mutations from those with bi-allelic incativation of the MYH gene.
Keywords: normal versus tumor comparison; compare expression profiles from microdissected samples with distinct germline mutations (FAP vs. MAP).

overall_design: Here, we report the expression profiles from normal and intestinal adenomatous tissue from FAP (familial adenomatous polyposis) and MAP (MUTY-associated polyposis) patients with established APC and MUTY germline mutations. Total RNA samples were obtianed by laser capture microdissection.

first: Claudia

last: Gaspar

first: Patrick

last: Franken

first: Lia

last: Molenaar

first: Hans

last: Morreau

first: Gabriela

last: Möslein

first: Julian

last: Sampson

first: Judith

last: Boer

first: Renee

middle: X

last: de Menezes

first: Riccardo

last: Fodde


title: MaPTOL on MmREST

city: San Diego

first: Olivier

last: Harismendy

address: 10550 North Torrey PInes Road

department: Neurobiology

institute: The Scripps Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Genome Wide location of MmREST binding sites in a developping embryo
Keywords: Transcription factor binding sites analysis; ChIP-seq

overall_design: One ChIP with anti-REST antibody on E12.5 embryos extract

first: Jason

last: Iacovoni

first: Robyn

last: Meech


title: Influence of Water Chemistry on Toxicogenomics of Chronic Lead Toxicity to the Fathead Minnow (Pimephales promelas)

first: Edward

last: Mager

address: 4600 Rickenbacker Cswy.

department: MBF

institute: University of Miami, RSMAS

summary:
Despite major successes in reducing the risks of lead (Pb) exposure over the past few decades, two issues of considerable importance remain unresolved:  (1) how differences in water chemistry influence acute and chronic Pb toxicity, and (2) the elucidation of specific toxic mechanisms and modes of action (MOA). To more clearly define the water chemistry parameters mediating Pb toxicity we evaluated the effects of hardness (as CaSO4) and DOC (as humic acid (HA)) during chronic (150d) exposures to the fathead minnow (Pimephales promelas).  Traditional toxicological endpoints were examined alongside gene expression analyses to help clarify the underlying mechanisms and MOA of Pb toxicity and to identify robust molecular markers of exposure and effect.
Keywords: time course, chronic lead (Pb) exposure

overall_design: To analyze the gene expression responses to low-level Pb exposures fish were exposed +/- Pb in low ionic strength base water and fish collected at 2d, 4d, 10d, and 30d for microarray analysis.  Equal amounts of RNA from all no lead controls were pooled (18 fish total for 2d & 4d exposures; 12 fish total for 10d & 30d exposures) as reference samples for hybridization with each of 3 separate biological replicate pools (6 fish total for 2d & 4d exposures; 4 fish total for 10d & 30d exposures) of RNA from age-matched, lead-exposed fish.  Each pair of hybridizations was repeated with dye-swaps.  Additional repeats were performed for various arrays to ensure quality of data obtained from initial hybridization.

first: Henri

last: Wintz

first: Chris

last: Vulpe

first: Kevin

middle: V

last: Brix

first: Martin

last: Grosell


title: Heparan sulfate in skin wounds

city: Tromsoe

first: Svetlana

last: Zykova

address: Breivika

department: Medical Faculty

institute: University of Tromsoe

summary:
Standardized skin wounds were established surgically on mice and allowed to heal during a 15-day period. Expression of genes related to heparan sulfate biosynthesis was studied in wound bed and edges during the healing process.
Keywords: Time course

overall_design: Total RNA was isolated from wound edge (regenerating skin) and wound bed at 2, 6 and 15 days post wounding, as well as from intact control skin. Three animals were used for each time point.

middle: N

first: Xingbin

last: Ai

first: Per

last: Lindahl

first: Dorothe

last: Spillmann

first: Stefan

last: Scheidl

first: Erik

last: Larsson

first: Dmitri

last: Svistounov

first: Marion

last: Kusche-Gullberg

first: Trond

middle: G

last: Jenssen

first: Charles

middle: P

last: Emerson

first: Ulf


title: cDNA expression profiles of wild-type and fl-mutant upland cotton ovules during fiber initiation peroid

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

summary:
We constructed cDNA library from 0-10 day post anthesis cotton fibers when fiber cells begin to initiate and elongate throughout this peroid. We randomly sequenced over 95,000 ESTs from this library, and with request of upland cotton ESTs from other laboratories, we acquired a gene pool of more than 30,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 29,000 high-quality cotton cDNAs (each sequence length>400bp, average length > 600bp) and external controls.
Keywords: repeat samples for transcriptome analysis

overall_design:
Data for 8 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt0-Cy5 wt-3-Cy3
Set 1 (dye swap): wt-3-Cy3 wt0-Cy5
Set 2: wt0-Cy5 wt-3-Cy3
Set 2 (dye swap): wt-3-Cy3 wt0-Cy5
Set 3: wt0-Cy5 wt-3-Cy3
Set 3 (dye swap): wt-3-Cy3 wt0-Cy5
Set 4: wt0-Cy5 wt-3-Cy3
Set 4 (dye swap): wt-3-Cy3 wt0-Cy5

GSM209619, GSM209620, GSM209621, GSM209622, GSM209623, GSM209624, GSM209625, GSM209626,

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

GSM209627, GSM209628, GSM209629, GSM209630, GSM209631, GSM209632, GSM209633, GSM209634,

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

GSM209635, GSM209636, GSM209637, GSM209638, GSM209639, GSM209640, GSM209641, GSM209642,

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

GSM209643, GSM209644, GSM209645, GSM209646, GSM209647, GSM209648, GSM209649, GSM209650,

Data for 6 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: fl+3-Cy5 wt-3-Cy3
Set 1 (dye swap): wt-3-Cy3 fl+3-Cy5
Set 2: fl+3-Cy5 wt-3-Cy3
Set 2 (dye swap): wt-3-Cy3 fl+3-Cy5
Set 3: fl+3-Cy5 wt-3-Cy3
Set 3 (dye swap): wt-3-Cy3 fl+3-Cy5

GSM209455, GSM209456, GSM209608, GSM209609, GSM209610, GSM209612,

Data for 6 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: fl-3-Cy5 wt-3-Cy3
Set 1 (dye swap): wt-3-Cy3 fl-3-Cy5
Set 2: fl-3-Cy5 wt-3-Cy3
Set 2 (dye swap): wt-3-Cy3 fl-3-Cy5
Set 3: fl-3-Cy5 wt-3-Cy3
Set 3 (dye swap): wt-3-Cy3 fl-3-Cy5

GSM209613, GSM209614, GSM209615, GSM209616, GSM209617, GSM209618


title: Transcription of ectopic DNA in E.coli

city: Vancouver

first: Rene

middle: Louis

last: Warren

state: British Columbia

address: 570 West 7th avenue Suite 100

department: Genome Sciences Centre

institute: BC Cancer Agency

type: Expression profiling by genome tiling array

summary:
To assess the degree of transcription in E.coli of ectopic DNA from related gamma proteobacteria, we designed a custom NimbleGen array containing highly redundant and substantially complete oligonucleotide probe sets for E. coli, H. influenzae and P. aeruginosa annotated genes.  We transformed E. coli, in separate experiments, with individual BAC clones and probed arrays with cDNA derived from DNase treated RNA isolated from the overnight culture of the transformants.
Keywords: cross-regulation on genomic scale

platform_organism:
Pseudomonas aeruginosa
Escherichia coli
Haemophilus influenzae
Homo sapiens

overall_design: We analyzed 10 samples, including 3 normal (native cells), one control (Human), 2 H. influenzae BACs transfromed in E. coli, 3 P. aeruginosa BACs transformed in E. coli and 18 H. influenzae BACs representing most of the H. influenzae genome.

first: Doug

last: Freeman

first: Roger

middle: C

last: Levesque

first: Duane

last: Smailus

first: Stephane

last: Flibotte

first: Robert

last: Holt


title: Gene expression for Integrative epigenomic study in leukemia samples

first: Maria

last: Figueroa

summary:
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation is a hallmark of cancer and plays a central role in determining tumor phenotype.  We predicted that integration of different genome-wide epigenetic regulatory marks along with gene expression levels would provide greater power in capturing biological differences between leukemia subtypes. Gene expression, cytosine methylation and histone H3 lysine 9 (H3K9) acetylation were measured using high-density oligonucleotide microarrays in primary human acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) specimens. We found that DNA methylation and H3K9 acetylation distinguished these leukemias of distinct cell lineage, as expected, but that an integrative analysis combining the information from each platform revealed hundreds of additional differentially expressed genes that were missed by gene expression arrays alone. This integrated analysis also enhanced the detection and statistical significance of biological pathways dysregulated in AML and ALL. Integrative epigenomic studies are thus feasible using clinical samples and provide superior detection of aberrant transcriptional programming than single-platform microarray studies.
Keywords: Gene expression

overall_design: 5 acute leukemia samples (2 ALL and 3 AML) in duplicate.


title: H3K9acetyl ChIP on chip for integrative epigenomic study in leukemia samples

summary:
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation is a hallmark of cancer and plays a central role in determining tumor phenotype.  We predicted that integration of different genome-wide epigenetic regulatory marks along with gene expression levels would provide greater power in capturing biological differences between leukemia subtypes. Gene expression, cytosine methylation and histone H3 lysine 9 (H3K9) acetylation were measured using high-density oligonucleotide microarrays in primary human acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) specimens. We found that DNA methylation and H3K9 acetylation distinguished these leukemias of distinct cell lineage, as expected, but that an integrative analysis combining the information from each platform revealed hundreds of additional differentially expressed genes that were missed by gene expression arrays alone. This integrated analysis also enhanced the detection and statistical significance of biological pathways dysregulated in AML and ALL. Integrative epigenomic studies are thus feasible using clinical samples and provide superior detection of aberrant transcriptional programming than single-platform microarray studies.
Keywords: ChIP-chip

overall_design: 5 acute leukemia samples (2 ALL and 3 AML) in duplicate, without dye swap. Replicate #2 for samples ALL2 and AML3 were excluded due to poor hybridization.


title: Investigation of Prognostic Markers in Soft tisse Sarcoma by Gene Expression and Tissue Profiling

status: Public on Mar 31 2008

city: Sydney

first: Paromita (Romi)

last: Das Gupta

state: NSW

address: High St, Randwick

department: Dept Surgery

country: Australia

institute: Prince of Wales Hospital

summary:
Gene expression profiling of sarcoma cell lines of increasing metastatic potential: SW684 (low grade), HT1080 (high grade), GCT (metastatic). Differential gene expression may elucidate biomarkers of tumour progression and metastasis.
Keywords: disease state analysis

overall_design: Common reference design. Reference cell line: Pooled Normal fibroblast cell line MRC5, labelled with Alexa Fluor 555 (Cy3) in every experiment. Samples: Sarcoma cell lines labelled with Alexa Fluor 647 (Cy5). At least 3 replicates for each tumour grade.

first: Paromita