title: Gene expression differences in trabecular meshwork cells, grown in culture, from normal and glaucoma-stricken human eyes

status: Public on Feb 04 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Dr. Panjwani's laboratory is focusing on the mechanism by which galectins-3 and 7 mediate corneal epithelial cell migration. We are currently performing studies to: (i) identify and characterize the corneal epithelial cell surface and extracellular matrix (ECM) molecules which serve as counterreceptors of galectin-3 and -7, to establish whether the lectins modulate corneal epithelial cell migration by binding to well known integrins, growth factor receptors, and/or ECM molecules and (ii) determine whether galectin-3 mediates corneal epithelial cell migration indirectly by modulating the expression of key adhesion and/or signal transduction molecules by using small interfering RNA, cDNA microarrays and glycogene arrays.

overall_design:
This study seeks the role of carbohydrate-based recognition system in the pathogenesis of glaucoma.  In this study, RNA preparations of four normal and five glaucoma TM samples harvested over the last year from cadavers were hybridized and analyzed using the GLYCOv2 array.
We have an NIH RO3 grant award to study the role of carbohydrate-based recognition system in the pathogenesis of glaucoma. In particular, it is known that a carbohydrate-binding protein, ELAM, serves as a marker for glaucoma. Other preliminary studies in my lab have shown that galectin-8 plays a role in the adhesion and spreading of trabecular meshwork cells (TM; the cells which modulate ocular pressure) and galectin-3 influences phagocytic capacity of TM cells. These studies suggest that galectins as well as ELAM and their counterreceptors may contribute to the pathogenesis of glaucoma. We would therefore like to compare glycogene expression patterns of normal and glaucomatous TM tissue. To this end, last month we submitted RNA preparations of five each of normal and glaucoma TM tissue harvested over the last year from cadavers. The data of these samples are now being analyzed. Meanwhile, we have analyzed RNA preparations of TM cells grown in culture from five normal and six glaucoma eyes. It is our hope that data from the two projects will enable us conclusively identify glycogenes which are differentially expressed in normal and glaucoma TM cell. Overall, the goal is to shed light on the role of carbohydrate-based recognition system and the carbohydrate-binding proteins in the pathogenesis of glaucoma.

first: Noorjahan

last: Panjwani

middle: R


title: Sex-linked differences in glyco-gene expression in thymocytes

state: CA

country: USA

summary: This laboratory is focusing on to clarify the biologic relevance of a virulence factor known as trans-sialidase from Trypanosoma cruzi, the agent of the Chagas disease (American trypanosomiasis).

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We are working with an enzyme able to directly transfer sialyl residues among macromolecules known as the trans-sialidase. It constitutes a virulence factor from Trypanosoma cruzi, the agent of the Chagas' Disease the American trypanosomiasis. We described the ability of this virulence factor to induce thymocyte apoptosis in vivo that happens after silayl residue mobilization. The apoptosis is mediated by the thymic epithelial cells in the nurse cell complex. By employing the microarray approach we wish to analyze the gene expression induced in the thymus after TS treatment.
Examination of differential expression in thymocytes between male and female mice of genes related to glycosylation. RNA samples (in triplicate) purified from thymocytes were analyzed by Glyco-gene Chip analysis.

first: Oscar

last: Campetella


title: Sod2 KO anemic mice

summary: Gene expression profiling was performed using Anemic Sod 2 Knockout mice and was compared to Gene expression profiles from Sod 2 WT mice.

overall_design:
Background: Our laboratory is interested in the role of oxidative stress in aging and human disease. Currently, a major focus of our efforts is the characterization of a murine hemolytic anemia resulting from oxidative stress, a model for the human disorder Sideroblastic Anemia. This model is based upon transplantation of hematopoietic stem cells from mice that are deficient in the antioxidant protein SOD2 (Friedman J. Exp. Med. 2001 193:925). SOD2 protects against the cytotoxicity of mitochondrial superoxide produced as a byproduct of oxidative phosphorylation (Weisiger J. Biol. Chem. 1973 248:4793). In characterization of the model to date, we have focused upon RBC proteomic analysis to identify 41 proteins differentially expressed when comparing membrane and soluble RBC fractions from SOD2-/- vs. SOD2+/+ mice (Friedman et al. submitted). In addition, we have characterized the in vivo response of animals to a novel catalytic antioxidant (Euk-189) that has b! oth SOD and catalase activities. In addition to proteins involved in mitochondrial function and stress response we find a number of cell surface molecules with significant differential expression. Thrombospondin is found at higher levels in SOD2-/- red cell membrane fractions. This is an extracellular matrix glycoprotein involved in cell adhesion and migration that interacts with glycosaminoglycans (especially the heparan sulfate proteoglycan perlecan) expressed at the endothelial cell surface (Feitsma J. Biol. Chem. 2000 275:9396, Vischer Eur. J. Cell. Biol. 1997 73:332, Sun J. Biol. Chem. 1989 15:2885). Thrombospondin is likely an acquired surface molecule on our red cells, which is of interest as this molecule has been found on the surface of sickle red cells and appears to mediate abnormal adhesion of red cells to vessel wall (Hillery Blood 1996 87:4879, Sugihara Blood 1992 15:2634). CD44 is also found at higher levels in SOD2-/- membrane fractions. CD44 is an adhesion receptor for the high molecular weight polysaccharide hyaluronic acid and has been shown recently to be involved in the trafficking of stem cells to the bone marrow (Avigdor Blood January 2004). Higher expression of these molecules on the surface of SOD2-/- red cells may affect their adhesive interactions with vascular endothelium and may in part explain the early removal of these cells from the circulationóresulting in the observed hemolytic anemia. Some proteins that accumulate on the surface of SOD2 deficient red cells are likely molecular damage sensors, binding to surfaces altered by oxidative damage. The role of specific glycoproteins in such binding remains to be elucidated. Additional surface proteins from red cells show differential expression, many of which are also glycosylated.
Planned Experiment: As the next step in characterization of the anemia model, we will compare the gene expression profile of red cell progenitors isolated from Sod2-/- and Sod2+/+ animals. We have defined cell-sorting conditions for isolation of erythroid progenitor cells from marrow of our mice.

first: Jeff

last: Friedman


title: ArcA- mutant vs. WT

status: Public on Feb 10 2011

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

state: MN

address: 720 4th Ave S

department: Biology

institute: St. Cloud State University

summary:
Background: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control) helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium.
Results: We compared the transcriptional profiles of the virulent wild-type (WT) strain (ATCC 14028s) and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome); of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis) were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV), Gifsy-1 prophage genes, and a few SPI-3 genes (mgtBC, slsA, STM3784). In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Furthermore, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr.
Conclusion(s): We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella biosynthesis, and motility. Furthermore, ArcA and Fnr share in the regulation of 120 S. Typhimurium genes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Anaerobic cultures of the WT or the arcA mutant were used to inoculate three independent flasks for each strain. Every flask contained 150 ml of anoxic LB-MOPS-X. The three independent cultures of each strain were grown to an OD600 of 0.25-0.35, pooled, and treated with RNAlater (Qiagen, Valencia, CA) to fix the cells and preserve the quality of the RNA. Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by the lack of PCR amplification of known genes (i.e.: fnr) and by using agarose-gel electrophoresis. Aliquots of the RNA samples were kept at -80°C for use in the microarray and the qRT-PCR studies.

middle: C

first: Matthew

last: Evans

first: Hosni

middle: M

last: Hassan


title: Gene expression in trabecular meshwork samples from normal and glaucoma eyes

overall_design:
It is known that a carbohydrate-binding protein, ELAM, serves as a marker for glaucoma. Other preliminary studies in my lab have shown that galectin-8 plays a role in the adhesion and spreading of trabecular meshwork cells (TM;the cells which modulate ocular pressure) and galectin-3 influences phagocytic capacity of TM cells. These studies suggest that galectins as well as ELAM and their counterreceptors may contribute to the pathogenesis of glaucoma. We have RNA preparations of five each of normal and glaucoma TM samples harvested over the last year from cadavers.
We have RNA preparations of five each of normal and glaucoma TM samples harvested over the last yeat from cadavers.


title: Renal allograft dysfunction (kidney tissue data set)

status: Public on Feb 02 2011

city: Hangzhou

first: Mao

last: Youying

address: Yuhangtang Road,NO.388

country: China

institute: Zhejiang University

summary: The study comprises various components:  Samples TD:  We aims to screen out different gene expression profile in donor biopsies after revascularization ,  We aims to predict renal allograft dysfunction early after transplantation.  Samples AR, ATN, Tx:  We aim to screen out different gene expression profile in acute rejection on the kidney.  We aim to screen out different gene expression profile in acute tubular necrosis on the kidney.  Results from the various study components can help to diagnose renal allograft dysfunction with different causes by distinct gene expression profile.  Keywords: acute rejection, acute tubular necrosis, donor biopsies, renal allograft dysfunction

overall_design: Samples AR1-AR17: This study has been accomplished with 17 patients of acute rejection on the kidney.Technical replicates: 2 replicates  Samples ATN1-ATN5: This study has been accomplished with 5 patients of acute tubular necrosis on the kidney. Technical replicates: 2 replicates  Samples Tx1-Tx14: This study has been accomplished with 14 patients of stable renal function on the kidney.Tecnical replicates:2 replicates(except Tx12)  Samples TD1-TD12: This study has been accomplished with 12 patients of donor tissue with stable function early after transplantation on the kidney.Technical replicates: 2 replicates  Samples TD13-TD21: This study has been accomplished with 9 patients of donor tissue with renal dysfunction early after transplantation on the kidney.Technical replicates: 2 replicates

first: Y

last: Mao


title: Gene expression in wild type and Mgat3 mouse embryos

summary: Dr. Stanley's laboratory is interested in 1) understanding the biological roles of specific classes of N-glycan in development and immunity through studies of glycosyltransferase mutant mice, 2) identifying complex binding specificities of galectins using a panel of CHO glycosylation mutants, and 3) determining how O-fucose glycans function in Notch receptor signaling and in modulating the interaction of Notch receptors with their ligands.

overall_design:
The bisecting GlcNAc on N-glycans inhibits ricin binding and enhances E-PHA binding. It is expected that mammalian CBP's, including galectins, may have their binding affected positively or negatively by the presence of the bisecting GlcNAc. In fact unpublished experiments have identified reduced binding of at least one galectin to LEC10 CHO cells that express GlcNAc-TIII compared to CHO cells that do not. We have shown that the Mgat3 gene that encodes GlcNAc-TIII, the glycosyltransferase that adds the bisecting GlcNAc, is barely expressed in E9.5 mouse embryos and robustly expressed in E10.5 embryos (J. Biol. Chem. 277, 26300-26309; 2002). We wish to compare glycosylation and lectin genes that are expressed at E10.5 in the brain of embryos from wild type and Mgat3 knockout embryos.
RNA samples were prepared from several embryo heads (3) from Mgat3+/+ and Mgat3-/- E10.5 embryos. We hybridized the RNA to glyco-chips (in triplicate per sample for a total of 6) so we can detect changes in the expression of glyco-genes as well as signaling pathway genes that may be affected.

first: Pamela

last: Stanely


title: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in spleen of Atlantic salmon

status: Public on Feb 03 2011

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Gene expression profiling revealed rapid activation of immunity, both local and systemic, which however did not provide protection of fish against the parasite. Major changes of transcriptome responses wwere observed between days 5 and 10

overall_design: Atlantic salmon was challenged with L. salmonis at the copepod stage. Skin, spleen, and head kidney were sampled from challenged and control fish at 1, 3, 5 dpi (corresponding to the copepod stage); 10 and 15 dpi (chalimus stage). A total of forty samples of spleen and skin form infected salmon (4 individuals from the 5 time points) were used for microarray analyses.. Test samples were labeled with Cy5 and hybridized to pooled control samples labeled with Cy3 from the same time-points. Competitive hybridization to the arrays was followed by washing, scanning, image analysis, and data analysis. Selected genes were analyzed with RT-qPCR.

first: Tariku

last: Tadiso


title: miRNA expression profiling in human mammary epithelial cell (HMEC) CD24-CD44+ and non-CD24-CD44+ cell populations

status: Public on Feb 01 2011

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

summary: To understand the role of p53 in regulating stem cell population (CD24-CD44+) and stemness-associated miRNAs, we first compared miRNA expression profiles between human mammary epithelical cells knocked-down p53 and control cells. We then cross-referenced p53-regulated miRNAs with stemness-associated miRNAs analyzed from expression profiling of sorted CD24-CD44+ and non-CD24-CD44+ cell populations. Further biological experiments were performed with the miRNAs that are altered in CD24-CD44+ stem cell populations and also regulated by p53.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Total RNAs, including miRNAs, extracted from CD24-CD44+ cells (labeled in Hy3) and non-CD24-CD44+ cells (labeled in Hy5) were hybridized on Exiqon miRCURY LNA arrays according to the manufacturer's protocol.

first: M

first: C

middle: J

last: Chang


title: The role of p53 in the regulation of miRNA expression profiling

summary: To understand the role of p53 in regulating stem cell population (CD24-CD44+) and stemness-associated miRNAs, we first compared miRNA expression profiles between human mammary epithelial cells knocked-down p53 and control cells. We then cross-referenced p53-regulated miRNAs with stemness-associated miRNAs analyzed from expression profiling of sorted CD24-CD44+ and non-CD24-CD44+ cell populations. Further biological experiments were performed with the miRNAs that are altered in CD24-CD44+ stem cell populations and also regulated by p53.

overall_design: Total RNAs, including miRNAs, were extracted from cells infected with retrovirus expressing shp53 (labeled in Hy3) and vector control (labeled in Hy5). miRNAs were hybridized on Exiqon miRCURY LNA arrays according to the manufacturer's protocol.


title: Metastatic and Nonmetastatic canine soft tissue sarcoma comparison

city: Raleigh

first: Marlene

last: Hauck

state: NC

address: 4700 Hillsborough Street

department: Clinical Sciences

institute: North Carolina State University

summary: We hypothesize that there is a gene signature which will improve our ability to predict development of metastatic disease in STS patients.  The objective of this study was to determine the feasibility of using cDNA microarray and quantitative real-time PCR (qRT-PCR) analysis to determine gene expression patterns in metastatic versus non-metastatic canine STSs, given the inherent heterogeneity of this group of tumors.  Five STSs from dogs with metastatic disease were evaluated in comparison to eight STSs from dogs without metastasis.  Tumor RNA was extracted, processed and labeled for application to the Affymetrix Canine Genechip 2.0 Array.  Array fluorescence was normalized using D-Chip software and data analysis was performed with JMP/Genomics.  Differential gene expression was validated using qRT-PCR.  Over 200 genes were differentially expressed at a false discovery rate of 5%.  Differential gene expression was validated for five genes upregulated in metastatic tumors.  Quantitative RT-PCR confirmed increased relative expression of all five genes of interest in the metastatic STSs.  Our results demonstrate that microarray and qRT-PCR are feasible methods for comparing gene signatures in canine STSs.  Further evaluation of differences in gene expression between metastatic and non-metastatic STSs is likely to identify genes important in the development of metastatic disease and improve our ability to prognosticate for individual patients.

overall_design: Comparison of metastatic and non-metastatic (defined as no metastasis for at least one year) untreated tumor biopsies.

first: Stacey

last: Snyder

first: Jennifer

last: Mahoney

first: Julie

last: Fisher


title: Agilent Mouse liver gene expression profiling of Cross B6/J x A/J

city: Boston

first: Sergey

last: Lezhnin

state: MA

address: 33 AVENUE LOUIS PASTEUR

department: Molecular Profiling

institute: Merck Research Laboratories

summary: Mapping the genetic architecture of RNA transcript abundances has potential for revealing molecular mechanisms underlying complex traits like disease. Gene expression microarrays allow monitoring genetic control on a whole transcriptome level, but validity and reproducibility of microarray data is a subject of ongoing scientific debate. Here we demonstrate how combining genetic and gene expression data provide a basis for biologically relevant assessment of the current state of microarray technology.  We profile liver samples from a murine F2 intercross population using Agilent microarrays.

overall_design: Tissue profiling in a mouse F2 cross. We analyzed 298 Liver samples.

first: Eugene

last: Chudin

first: Andrew

last: Kasarskis

first: John

last: Castle

first: Amit

last: Kulkarni

first: Serguei

last: Lejnine

first: Eric

last: Schadt


title: Gene expression from null and doubly null mice for 2 sulfotransferases (HED-GlcNAc6ST and GlcNAc6ST-1) compared to WT

first: Steven

last: Head

summary: This laboratory works on selectins and their carbohydrate ligands in lymphocyte homing and inflammation. The lab also studies heparin-degrading endosulfatases and their roles in regulating the interactions of growth factors and morphogens with proteoglycans.

overall_design:
Gene expression profiles from null and doubly null mice for 2 sulfotransferases (HED-GlcNAc6ST and GlcNAc6ST-1) will be compared to WT mice to find impact on L-selectin ligand formation in lymph nodes. RNA was isolated from the lymph nodes of the 2 types of null mice, 1 type of double null mice, and 1 of wild type mice. 3 duplicates of each strain were analyzed by gene expression profiling.
We have null mice and doubly null in two sulfotransferases (HEC-GlcNAc6T and GlcNAc6ST-1) involved in L-selectin ligand formation in lymph nodes. Our functional analysis reveal partial loss (50 and 25%)of lymph node L-selectin ligands in the singly null mice and an 80%loss in the double null mice. We want to identify candidates for the protein scaffolds and underlying posttranslational modifications responsible for the residual L-selectin ligand activity in these mice. We will perform a glycochip analysis with mRNA isolated from lymph nodes of the 3 types of null mice and wild-type mice, all on the C57BL/6 background. Three duplicates from each strain are analyzed, requiring a total of 12 chips. The mice are 8-10 weeks of age and all female.

last: Rosen


title: Thermoanaerobacter sp. X514 in various carbon sources

city: Qingdao

first: Lu

last: Lin

state: Shandong

address: 189 Songling RD

institute: QIBEBT

summary: The sugar metabolic mechanism on glucose, xylose, fructose and cellobiose as the sole or dual carbon source by Thermoanaerobacter sp. X514 was characterized by whole genome cDNA micorarrays.

overall_design: In this study, X514 cell grew in difeined medium supplement with different carbohydrates. Each sample was prepared harvested at early-, mid- and late-log phases respectively. Samples were used to acquire expression profiles of total 2322 unique genes, leading to metabolic mechanism construction.


title: Role of Rok in biofilm structure development of Bacillus subtilis 168

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University of Jena

summary: Comparison of the B subtilis rok mutant vs wild type (sample 1-4) and rok-comK mutant vs comK mutant (sample 5-8)

overall_design: One condition design comparision of (rok vs wt) and (rok-comK vs comK) including a dye swap, 4 biological replicate

first: Oscar

middle: P

last: Kuipers


title: [E-MTAB-5] Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

type: Expression profiling by high throughput sequencing

summary:
Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs.  Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output.  This transcriptional complexity has been sampled mainly using hybridization-based methods under one or a few conditions.  We applied direct high-throughput sequencing of cDNAs, complemented with different expression data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe, independently from available gene annotations.  We interrogated transcriptomes under multiple conditions, including exponential proliferation, meiotic differentiation and environmental stress, and in RNA processing mutants, to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental, and genetic factors.  High-throughput sequencing proved to be a powerful and quantitative method to deeply sample transcriptomes at unprecedented resolution.  Unlike hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90% of the genome, including traces of RNAs that were not actively transcribed or rapidly degraded.  The combined sequencing and strand-specific array data provided rich information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus refining the existing genome annotation.  Sequence trans-reads spanning exon-exon or exon-intron junctions gave unique insight into a surprising variability in splicing efficiency across introns and genes.  Splicing efficiency was largely coordinated with transcriptional efficiency, and hundreds of introns showed regulated splicing as a function of cellular proliferation or differentiation.

ArrayExpress Release Date: 2008-12-03

Publication Title: Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution
Publication Author List: Brian Wilhelm, Samuel Marguerat, Stephen Watt, Falk Schubert, Valerie Wood, Ian Goodhead, Christopher J. Penkett, Jane Rogers and Jurg Bahler

Person Roles: submitter
Person Last Name: Wilhelm
Person First Name: Brian
Person Mid Initials:
Person Email: btw@sanger.ac.uk
Person Phone:
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Bahler
Person First Name: Jurg
Person Mid Initials
Person Email: jurg@sanger.ac.uk
Person Phone
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: growth_condition_design
Experimental Design: replicate_design
Experimental Design: co-expression_design
Experimental Factor Name: MEDIA
Experimental Factor Name: TIME
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: TEMPERATURE
Experimental Factor Name: CULTURE_DENSITY
Experimental Factor Type: media
Experimental Factor Type: time
Experimental Factor Type: growth_condition
Experimental Factor Type: temperature
Experimental Factor Type: culture_density
Quality Control Type: biological_replicate


title: Expression data from cultured chicken primordial germ cells (PGCs)

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: The growth factors and signaling pathways that are essential for the inducing proliferation of chicken PGCs is unclear. We investigated the effect of basic fibroblast growth factor (bFGF) on the survival and proliferation of PGCs under feeder-free conditions.

overall_design: We used microarrays to examine the genes regulated by bFGF treatment in chicken PGCs. Cultured PGCs were collected before and after withdrawal of bFGF for 24 h, and 24 h after bFGF replacement. The RNA was extracted and hybridized on Affymetrix microarrays. Three replicates each.

first: Jin

middle: W

last: Choi

first: Gwonhwa

last: Song

first: Jae

middle: Y

last: Han


title: Array CGH characterization of esophago-gastric adenocarcinoma

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

institute: Cambridge Research Institute

summary: The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival.

overall_design: Total RNA isolated from human tissue sections was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide. Briefly, 4 µg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 7.0, Rosetta Biosoftware, Seattle, WA).

first: X

last: Goh

first: J

last: Rees

first: S

middle: F

last: Chin

last: Marioni

first: V

last: Save

first: M

last: O’Donovan

first: P

last: van den Ijessel

first: D

last: Alderson

first: B

last: Ylstra

first: C

last: Caldas

first: R

last: Fitzgerald


title: Subpopulation-specific transcriptome analysis of cytometrically sorted Streptococcus mutans cells: Analysis of CSP-mediated intrapopulation diversity

city: Braunschweig

first: Andre

last: Lemme

address: Inhoffenstr. 7

department: Cell Biology

institute: Helmholtz Centre for Infection Research

summary:
Transcriptional profiling of the competence-stimulating peptide (CSP) response in Streptococcus mutans of FACS-separated subpopulations and mixed cells of a clonal culture.

CSP-mediated competence development in S. mutans is a transient and biphasic process since only a subpopulation induces expression of ComX in the presence of CSP and activation of the DNA uptake machinery in this fraction shuts down ~3-4 hours post induction. Here we combine, for the first time in bacteria to our knowledge, flow cytometric sorting of cells and subpopulation-specific transcriptome analysis of both the competent and non-competent fractions of CSP-treated S. mutans cells. Sorting was guided by a ComX-GFP reporter and the transcriptome analysis demonstrated the successful combination of both methods because a strong enrichment of transcripts for comX and its downstream genes was achieved. Three two-component systems were expressed in the competent fraction, among them ComDE. Moreover, the recently identified regulator system ComR/S was expressed exclusively in the competent fraction. By contrast, expression of bacteriocin-related genes was at the same level in all cells. GFP reporter strains for ComE and mutacin V confirmed this expression pattern on the single cell level. Fluorescence microscopy revealed that some ComX-expressing cells committed autolysis in an early stage of competence initiation. In viable ComX-expressing cells, uptake of DNA could be shown on the single cell level. This study demonstrates that all cells in the population respond to CSP through activation of bacteriocin-related genes but that two subpopulations segregate, one becoming competent and another one that lyses, resulting in intrapopulation diversity of the clonal culture.

overall_design: Two conditions: induced and not induced with CSP. Three induced cell populations: competent subpopulation, incompetent subpopulation, all cells. Two biological replicates each population.

first: Lothar

last: Gröbe

first: Micheal

last: Reck

first: Jürgen

last: Tomasch

first: Irene

last: Wagner-Döbler


title: Affymetrix Mouse liver gene expression profiling of Cross B6/J x A/J

first: Sergey

last: Lezhnin

summary: Summary Mapping the genetic architecture of RNA transcript abundances has potential for revealing molecular mechanisms underlying complex traits like disease. Gene expression microarrays allow monitoring genetic control on a whole transcriptome level, but validity and reproducibility of microarray data is a subject of ongoing scientific debate. Here we demonstrate how combining genetic and gene expression data provide a basis for biologically relevant assessment of the current state of microarray technology.  We profile liver samples from a murine F2 intercross population using Affymetrix microarrays.

overall_design: Tissue profiling in a mouse F2 cross. We analyzed 294 Liver samples.

first: Eugene

last: Chudin

first: Andrew

last: Kasarskis

first: John

last: Castle

first: Amit

last: Kulkarni

first: Serguei

last: Lejnine

first: Eric

last: Schadt


title: Transcriptional profile of ecdysoneless mutants and Wild Type controls

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

summary: Comparisons of temperature sensitive mutants (ecdysoneless) at permissive and restrictive temperatures to identify genes under control of ecdysone hormone. Also, Wild Type Strain (Canton S), controls for temperature sensitive genes, are included at the temperature used for restrictive temperatures.

overall_design: Modified Round Robin design with dual colors and direct hybridization comparison between each strain and temperature variable. A representative dye swap was conducted for the Wildtype strains to determine whether dye intensity posed a significant/confounding artifact.

first: Kevin

last: White

first: Michael

last: Bender


title: JIL kinase – marker of active chromatin and sensor of dosage compensation

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip profiles of JIL-1, H3S10phK14ac and H4K16ac in Drosophila S2 cells

overall_design: JIL-1, H3S10phK14ac and H4K16ac ChIP in Drosophila S2 cells. 2-4 biological replicates per experiment. dye-swaps as indicated in sample description

first: C

last: Regnard

first: T

first: A

last: Mitterweger

first: I

last: Dahlsveen

first: P

last: Becker


title: S. oneidensis MR-1 with electrode, Fe(III)citrate and oxygen as electron acceptor

city: Ithaca

first: Miriam

last: Rosenbaum

state: NY

address: 325 Riley-Robb Hall

department: Biological and Environmental Engineering

institute: Cornell University

summary: S. oneidensis MR-1 was grown with different electron acceptors: an electrode at 0.4 V vs. SHE, 50 mM Fe(III)citrate, and oxygen. The gene expression pattern for each experiment was analyzed and the differences in gene expression for the different experimental conditions were compared.

overall_design: For two samples S. oneidensis was grown with a graphite anode electrode (at 0.4 V. vs. SHE) as the only electron acceptor - one sample was directly fed with 20 mM lactate, one sample was fed with lactate produced during fermentation of glucose by Lactococcus lactis. Four samples were grown anaerobically with 50 mM Fe(III)citrate as the only electron acceptor, and 20 mM lactate for 20 h. Three samples were grown aerobically with 20 mM lactate for 20 h. The same modified M4 medium was used for all samples. For RNA extraction, the biofilm was scraped off the frozen (-80°C) carbon electrode with a sterile razor blade. Biofilm-carbon sludge was combined with 7 mL ice-cold phosphate buffer saline (PBS), vortexed, sonicated at 7 W for 30 s on ice (3 repetitions), and centrifuged. For the liquid cultures, 2 mL of each culture were combined with 2 mL RNA protect, vortexed, and centrifuged at 5,500g for 10 min. The pellets were resuspended in NAES buffer (50 mM sodium acetate buffer, 10 mM EDTA and 1 % SDS at pH 5). RNA was isolated with a phenol:chloroform extraction protocol.

first: Haim

last: Bar

first: Qasim

last: Beg

first: Lars

last: Angenent


title: Comparative genomic hybridization of BRCAX breast tumors

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

summary:
Only about 25% of familial breast cancer is explained by mutations in BRCA1 and BRCA2, fewer by moderate penetrance genes like P53, PTEN, CHEK2, ATM and PALB2 and an unknown fraction by common variants of genes with low penetrance. Evidence suggests that additional dominant breast cancer genes exist and these are referred to as BRCAX.
Clinical presentation of families with highly increased incidence of breast cancer that are non-BRCA1/BRCA2, suggests dominant inheritance of such high penetrance breast cancer genes. Because cancer genes often confer a specific clinical presentation (e.g. age of onset, sex-ratio, tissue spectrum) it seems useful to initiate their discovery by such clinical criteria. An earlier linkage study of BRCAX / non-BRCA1/2 breast cancer families aimed to enrich for a common genetic defect by setting stringent inclusion criteria, failed to identify new breast cancer susceptibility loci.
Motivated by results of BRCA1 and BRCA2 breast tumors that have characteristic genomic signatures (array-CGH 'phenotypes'), we present the largest dataset to date showing the genomic profiles of 58 BRCAX primary breast tumors by array-CGH and show by unsupervised hierarchical clustering that they form a heterogeneous group with 4 distinct subtypes that are different from (n = 48) sporadic controls.
This provides a possible explanation for the lack of high LOD scores in linkage studies. The presence of more than one BRCAX sub-type suggests the existence of more than one BRCAX gene. We propose approaches that can be employed to stratify BRCAX families based on array-CGH data.

overall_design: 58 primary breast carcinomas from non-BRCA1/2 hereditary breast cancer families (HBC) compared to 48 sporadic tumors

first: E

middle: H

last: van Beers

first: S

middle: A

last: Joosse

first: R

last: Oldenburg

last: Verhoef

last: Devilee


title: Molecular and metabolic effects of norUDCA in Abcb4 knockout mice

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: To identify (i) target genes relevant for the disease development (WT vs. Abcb4-/- mice) and (ii) to gain insights into mechanisms leading to the reversal of chronic cholestatic liver injury in Abcb4-/- mice treated with the side-chain modified bile acid "norUDCA" (Abcb4-/- mice vs. norUDCA treated Abcb4-/- mice).

overall_design: Samples were analyzed in duplicates for each genotype and treatment.

first: Tarek

last: Moustafa

last: Trauner

first: Christian

last: Guelly


title: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in skin of Atlantic salmon

first: Aleksei

last: Krasnov

summary: Gene expression profiling revealed rapid activation of immunity, both local and systemic, which however did not provide protection of fish against the parasite. Major changes of transcriptome responses wwere observed between days 5 and 10

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon was challenged with L. salmonis at the copepod stage. Skin, spleen, and head kidney were sampled from challenged and control fish at 1, 3, 5 dpi (corresponding to the copepod stage); 10 and 15 dpi (chalimus stage). A total of forty samples of spleen and skin form infected salmon (4 individuals from the 5 time points) were used for microarray analyses.. Test samples were labeled with Cy5 and hybridized to pooled control samples labeled with Cy3 from the same time-points. Competitive hybridization to the arrays was followed by washing, scanning, image analysis, and data analysis. Selected genes were analyzed with RT-qPCR.

first: Tariku

last: Tadiso


title: Comparative transcriptomic analysis of in vivo and in vitro produced bovine 4-cell stage and 8-cell stage embryos

status: Public on Jan 31 2011

city: Charlestown

first: Petr

last: Vodicka

state: Massachusetts

address: 114 16th Street

department: Department of Neurology

institute: Massachusetts General Hospital

summary: Pre-implantation embryos derived by in vitro fertilization differ in their developmental potential from embryos obtained in vivo. In order to characterize changes in gene expression profiles caused by in vitro culture environment, we employed microarray constructed from bovine embryo-specific cDNAs (BlueChip v., Université Laval, Québec) to compare in vitro cultured and in vivo derived bovine embryos at 4-cell and 8-cell stage.

overall_design: Analysis directly compared RNA samples from pool of 20 in vivo derived 4-cell stage embryos to RNA samples from pool of 20 in vitro cultured 4-cell stage embryos and RNA samples from pool of 20 in vivo derived 8-cell stage embryos to RNA samples from pool of 20 in vitro cultured 8-cell stage embryos.  Three technical replicates, including one dye-swap array were prepared for each developmental stage (4-cell stage, 8-cell stage, respectively) .

first: Katerina

last: Vodickova Kepkova

first: Tereza

last: Toralova

first: Miloslava

last: Lopatarova

first: Svatopluk

last: Cech

first: Radovan

last: Dolezel

first: Vitezslav

last: Havlicek

first: Urban

last: Besenfelder

first: Anna

last: Kuzmany

first: Marc-Andre

last: Sirard

first: Jozef

last: Laurincik

first: Jiri

last: Kanka


title: Expression data from batch cultivations of Aspergillus niger wild type and adrA, facB and creA deletion mutants

city: Göteborg

first: Margarita

last: Salazar Peña

address: Kemigården 4

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources.
Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger.

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.

last: Salazar

first: Javier

last: Calzada-Funes

first: Kenneth

last: Bruno

first: David

last: Culley

first: Scott

last: Baker

first: Jens

last: Nielsen


title: Global Reactivation of Epigenetically Silenced Genes in Prostate Cancer

city: Philadelphia

first: Ilsiya

last: Ibragimova

state: PA

address: 333 Cottman ave, w350

department: ICR

institute: Fox Chase Cancer Center

summary: Transcriptional silencing associated with aberrant promoter hypermethylation is a common mechanism of inactivation of tumor suppressor genes in cancer cells.

overall_design: To profile the genes silenced by hypermethylation in prostate cancer, we screened an expression microarray for genes reactivated in the LNCaP, DU-145, PC-3 and MDA2b prostate tumor cell lines after treatment with the demethylating drug 5-aza-2 deoxycytidine (5Aza-dC) and histone deacetylation inhibiting drug trichostatin A (TSA).

first: Michael

last: Ochs


title: Comparative gene expression profile  of Ngn3-overexpressing cultured hippocampal neurons vs the corresponding control populations

status: Public on Jan 27 2011

city: madrid

first: Ana

last: Dopazo

address: Melchor Fdez Almagro

department: Genomics Unit

country: Spain

institute: CNIC

summary: Gene expression profiles of Ngn3-overexpressing cultured hippocampal neurons was compared to the profile of the corresponding control populations.  (neurons expressing GFP). Neurogenin3, a proneural transcription factor controlled by Notch receptor, is involved in hippocampal neuron differentiation and synapses, but little is known about the molecular bases of Ngn3 activity in neurons. Microarray analysis indicated that overexpression of Ngn3 upregulated a number of genes related with cytoskeleton dynamics. One of then was Fmn1 whose protein is associated with actin and microtubule cytoskeleton. Overexpression of the isoform Fmn1-Ib in cultured hippocampal neurons induced an increase in the number of primary dendrites and in the number of glutamatergic synaptic inputs without affecting GABAergic synapses resulting in a modification in the balance between excitation and inhibition. The same changes were provoked by overexpression of Ngn3. In addition downregulation of Fmn1 by the use of Fmn1-siRNAs impaired such morphological and synaptic changes induced by Ngn3 overexpression in neurons. These results reveal a previously unknown involvement of Formin1 in dendritic and synaptic plasticity as a key protein in the Nng3 signaling pathway that contributes to understanding of molecular mechanisms of the neuronal differentiation.

overall_design: Cultured hippocampal neurons were transduced using Sindbis virus bearing myc-tagged Ngn3 or GFP as control. Cells were lysed and total RNA was extracted.Gene expression profiles were obtained for each sample and compared

first: Maria-Angeles

last: Arevalo

first: Alfredo

last: Rodriguez-Tebar


title: A small RNA controls expression of the chitinase ChiA  in Listeria monocytogenes

status: Public on Jan 26 2011

first: Teresa

last: Bergholz

address: 405 Stocking Hall

department: Food Science

summary: In recent years, more than 60 small RNAs (sRNAs) have been identified in the gram-positive human pathogen Listeria monocytogenes, but their putative roles and mechanisms of action remain largely unknown. The sRNA LhrA was recently shown to be a post-transcriptional regulator of a single gene, lmo0850, which encodes a small protein of unknown function. LhrA controls the translation and degradation of the lmo0850 mRNA by an antisense mechanism, and it depends on the RNA chaperone Hfq for efficient binding to its target. In the present study, we sought to gain more insight into the functional role of LhrA in L. monocytogenes. To this end, we determined the effects of LhrA on global-wide gene expression. We observed that nearly 300 genes in L. monocytogenes are either positively or negatively affected by LhrA. Among these genes, we identified lmo0302 and chiA as direct targets of LhrA, thus establishing LhrA as a multiple target regulator. Lmo0302 encodes a hypothetical protein with no known function, whereas chiA encodes one of two chitinases present in L. monocytogenes. We show here that LhrA acts as a post-transcriptional regulator of lmo0302 and chiA by interfering with ribosome recruitment, and we provide evidence that both LhrA and Hfq act to down-regulate the expression of lmo0302 and chiA. Furthermore, in vitro binding experiments show that Hfq stimulates the base pairing of LhrA to chiA mRNA. Finally, we demonstrate that LhrA has a negative effect on the chitinolytic activity of L. monocytogenes. In marked contrast to this, we found that Hfq has a stimulating effect on the chitinolytic activity, suggesting that Hfq plays multiple roles in the complex regulatory pathways controlling the chitinases of L. monocytogenes.

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: cDNA from 4 independent replicates of wild type EGD was directly compared to cDNA from 4 independent replicates of EGD delta LhrA

first: Jesper

middle: S

first: Birgitte

last: Kallipolitis


title: Expression data for human epithelium from subjects with atopic dermatitis, psoriasis and nonatopic controls

status: Public on Jan 29 2011

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary: The expression and function of tight junction genes, in particular claudin-1, was studied in order to further understanding of the biology underlying atopic dermatitis.

overall_design:
Gene expression profiling was performed on total RNA from nonlesional epidermal samples from 5 subjects with atopic dermatitis, 4 subjects with
psoriasis, and 5 nonatopic controls using the Illumina Sentrix HumanRef-8 Expression BeadChip.  There were duplicate (technical replicate) arrays run for 2 of the nonatopic control samples (the normalized transformed expression values of replicate pairs were averaged before performing data analysis, also, for each probe, the combined value for replicate pairs of Detection Pvalues was taken to be their minimum - so a Present call for one of the replicate pair of expression values results in a Present call for the combined (average) expression value).
Details of the design and the results found are given in the paper associated with this GEO Series.

first: Anna

last: De Benedetto

first: Nicholas

last: Rafaels

first: Laura

last: McGirt

first: Andrei

middle: I

last: Ivanov

first: Steve

middle: N

last: Georas

first: Chris

last: Cheadle

middle: E

first: Kunzhong

last: Zhang

first: Sadasivan

last: Vidyasagar

first: Takeshi

last: Yoshida

first: Mark

last: Boguniewicz

first: Tissa

last: Hata

first: Lynda

last: Schneider

first: Jon

last: Hanifin

first: Richard

middle: L

last: Gallo

first: Natalija

last: Novak

first: Stephan

last: Weidinger

first: Terri

last: Beaty

first: Donald

last: Leung

first: Kathleen

last: Barnes

first: Lisa

last: Beck


title: lin-35(n745) mutants vs. lin-35(n745), mes-4(RNAi) (below referred to as reference sample and test sample respectively)

status: Public on Jan 25 2011

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and lin-35(n745) treated with mes-4(RNAi) at 26 degrees.

overall_design: One-condition experiment, mutant (lin-35) vs. mutant plus RNAi (lin-35, mes-4RNAi).  Biological replicates 4 mutant, 4 mutant plus RNAi harvested indepedently.  One lin-35 replicate and one lin-35, mes-4(RNAi) replicate per array.

first: Wenchao

last: Wang

last: Petrella

first: Caroline

last: Spike

first: Andreas

last: Rechsteiner

first: Valerie

last: Reinke


title: Genome-wide expression profiling of Fusarium graminearum in response to azole fungicide treatment

city: Halle/Saale

first: Rayko

last: Becher

address: Betty-Heimann-Str. 3

department: Department of Phytopathology and Plant Protection

institute: Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences

summary: In this study, a newly developed 8x15K Fusarium graminearum Agilent microarray was applied to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles from treated versus untreated fungal liquid cultures uncovered 1058 genes that were significantly differentially expressed. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the most significantly responding category, providing statistical confirmation of the mode-of-action of azole fungicides. Transcriptional profiling of 54 genes, which encode ABC transporters in F. graminearum, suggested that several of these might be involved in reducing intracellular fungicide concentration. In addition, several genes encoding transcription factors with similarity to yeast genes known to co-ordinate fungicide responses exhibited significant differential expression.

overall_design: Hybridization was performed with cRNA samples either derived from three independent untreated or three independent azole-treated liquid cultures (12 h at 5 mg/l tebuconazole).

first: Fabian

last: Weihmann

first: Holger

last: Deising

first: Stefan

middle: G

last: Wirsel


title: Expression data from batch cultivations with the acidogenic Aspergillus niger wild type strain ATCC 1015 and the areB complete deletion strain constructed using ATCC 1015 as background strain with glucose or glycerol as carbon sources.

first: Margarita

last: Salazar Peña

summary: This approach aims at searching unidentified regulatory roles of the AreB transcription factor in the overall carbon metabolism of A. niger. A full areB gene deletion mutant was constructed and characterized in A. niger ATCC 1015. Both strains were grown on glucose or glycerol using ammonia as nitrogen source in batch cultivations and the transcriptome was analyzed using three biological replicated transcriptome experiments. Two areB gene deletion replicates, one on glucose and one on glycerol were discarded due to bad quality and therefore not included in the analysis. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for three Aspergillus species including A. niger.

overall_design: Triplicate batch fermentations with the two Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and the areB complete gene deletion strain were carried out and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.

last: Salazar

first: Kenneth

last: Bruno

first: David

last: Culley

first: Scott

last: Baker

first: Jens

last: Nielsen


title: Gene expression profiles of the aerenchy maformation in maize using laser microdissection

status: Public on Jan 28 2011

city: Tokyo

first: Hirokazu

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo

department: Graduate school of agricultural and life Science

country: Japan

institute: University of Tokyo

summary: To adapt to waterlogging in soil, some gramineous plants, such as maize (Zea mays), form lysigenous aerenchyma in the root cortex. Ethylene, which is accumulated during waterlogging, promotes aerenchyma formation.  Aerencyma is formedonly in cortex in maise root. Therevore, aerenchyma is one of the model of programmed cell death. However, the molecular mechanism of aerenchyma formation is not understood. Therefore we isolated only cortex cells in maize primary root using laser microdissection. And microarray analysis was perforemed to identify the arechyma formation related genes. For  microarray analysis, we designed 4 different experiments. Basal part and apical part of root were used for 1st experiment because arenchyma was formed in basal part of root, but not in apex. In second experiment, basal part of root with 6 hours waterlogged treatment  and without treatment were used. And, as aerenchyma was induced by ethylene,  ethylene and 1-MCP (inhibitor of ethylen perception) were used for experiment3 and 4.

overall_design: Gene expression analysis in 4 kinds of samples (cortex in basal reagion of maize primary root which were treated with waterlogged condition, aerobic condition, ethylene and 1-MCP and cortex in apical reagion of maize primary root which were treated with waterlogged conditio)

first: Tieming

last: Ji

first: Katsuhiro

last: Shiono

first: Imene

last: Rajhi

first: Ryosuke

last: Watanabe

first: Kazuhiro

last: Ohtsu

first: Akira

last: Kanno

first: Patrick

last: Schnable

first: Nobuhiro

last: Tsutsumi

first: Naoko

middle: K

last: Nishizawa

first: Mikio

last: Nakazono

first: Dan

last: Nettleton


title: Transcriptomic response of murine liver to severe injury and hemorrhagic shock: CodeLink portion of dual platform

status: Public on Jan 24 2011

city: Pittsburgh

first: Joyeeta

last: Dutta-Moscato

address: 450 Technology Drive, Suite 300

department: Surgery

institute: University of Pittsburgh

summary: A dual platform microarray analysis was used to characterize the temporal transcriptomic response in the mouse liver following trauma and hemmorhagic shock

overall_design: Mice were divided into five groups, anesthetized and surgically treated to simulate a time course and trauma severity model: non-manipulated animals (C), minor trauma (MT), 1.5 hour of hemorrhagic shock and severe trauma (HS/T), 1.5 hour HS/T followed by 1 hour resuscitation (HS/T+1.0R), 1.5 hour HS/T followed by 4.5 hours resuscitation (HS/T+4.5R)

first: Rebecca

middle: D

last: Edmonds

first: Yoram

last: Vodovotz

first: Claudio

last: Lagoa

first: Yawching

last: Yang

first: Mitchell

last: Fink

first: Ryan

middle: M

last: Levy

first: Jose

last: Prince

middle: J

last: Kaczorowski

first: George

middle: C

last: Tseng

first: Timothy

middle: R

last: Billiar


title: aCGH analysis of Palb2GT/+;p53-/- and Palb2+/+;p53-/- lymphomas

status: Public on Jan 21 2011

first: Rinske

last: Drost

type: Genome variation profiling by genome tiling array

summary:
Palb2 interacts with BRCA1 and BRCA2 in supercomplexes involved in DNA repair via homologous recombination. Heterozygous germline mutations in PALB2 confer a moderate risk of breast cancer while biallelic PALB2 mutations are linked to a severe form of Fanconi anaemia characterized by early childhood solid tumours and severe chromosomal instability. In contrast to BRCA1- or BRCA2-associated cancers, breast tumours in heterozygous PALB2 mutation carriers do not show loss of the wild type allele, suggesting PALB2 might be haploinsufficient for tumour suppression.
To study the role of PALB2 in development and tumourigenesis, we have generated Palb2GT mouse mutants using a gene trap approach. Whereas Palb2GT/GT homozygous mutant embryos died at mid-gestation due to massive apoptosis, Palb2GT/+ heterozygous mice were viable and did not show any obvious abnormalities. Deletion of p53 alleviated the phenotype of Palb2GT/GT embryos, but did not rescue embryonic lethality. In addition, loss of p53 did not significantly collaborate with Palb2 heterozygosity in tumourigenesis in heterozygous or homozygous p53 knockout mice. Tumours arising in Palb2GT/+;p53+/– or Palb2GT/+;p53–/– compound mutant mice retained the wild type Palb2 allele and did not display increased genomic instability.

overall_design: Comparison of 15 Palb2GT/+;p53-/- and 11 Palb2+/+;p53-/- lymphomas. Spleen/liver DNA of the same animal was used as reference material.

first: Peter

last: Bouwman

first: Christiaan

last: Klijn

first: Mark

last: Pieterse

first: Hanneke

last: van der Gulden

first: Ji-Ying

last: Song

first: Karoly

last: Szuhai

first: Jos

last: Jonkers


title: Transcriptional profiling of wild-type vs Perp-null mice during tooth development

status: Public on Jan 22 2011

city: San Francisco

first: Andrew

last: Jheon

address: 513 Parnassus Ave HSE1501

institute: UCSF

summary: Little is known about the role of cell-cell adhesion in the development of mineralized tissues. Here we report that PERP, a tetraspan membrane protein essential for epithelial integrity, is a critical regulator of enamel formation. Perp is necessary for proper cell attachment and gene expression during tooth development, and its expression is controlled by P63, a master regulator of stratified epithelial development. During enamel formation, PERP is localized to the interface between the enamel-producing ameloblasts and the stratum intermedium (SI), a layer of cells subjacent to the ameloblasts. Perp-null mice display dramatic enamel defects, which are caused, in part, by the detachment of ameloblasts from the SI. Microarray analysis comparing gene expression in teeth of wild-type and Perp-null mice identified several differentially expressed genes during enamel formation. Analysis of these genes in ameloblast-derived LS8 cells upon knock down of PERP confirmed the role for PERP in the regulation of gene expression. Together, our data show that PERP is necessary for the integrity of the ameloblast-SI interface and that the lack of Perp causes downregulation of genes that are critical for proper enamel formation.

overall_design: Two-condition experiment, RNA isolated from WT vs. Perp-null lower 1st molars. Biological replicates: 3 control replicates, 3 mutant replicates.

first: Ophir

last: Klein


title: The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome: expression

first: Bas

last: van Steensel

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that of these five proteins, only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens LAD – NL interactions by a local antagonistic effect. Our results provide insights into the evolution of LAD organization and reveal a role for SU(HW) in the regulation of genome – NL interactions.

overall_design: RNA was isolated from three independent Drosophila Kc167 cell cultures. Expression profiles were made of self-self hybridizations on spotted INDAC long oligo arrays. The three replicates were averaged.

first: Joke

last: van Bemmel

first: Ludo

last: Pagie

first: Ulrich

last: Braunschweig

first: Wim

last: Brugman

first: Wouter

last: Meuleman

first: Ron

last: Kerkhoven


title: Nitrate Stress in Desulfovibrio vulgaris Hildenborough (Fur knockout : JW707)

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary:
Using data from microarray experiments, we investigated the effects of excess sodium nitrate on D. vulgaris.

Keywords: stress response, time course

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with 105 mM sodium nitrate to untreated cells at times of 0, 30, 60, 120, and 240 min.


title: Altered expression of microRNAs in bone metastasis compared with human prostate cancer

city: guangzhou

first: David

last: Guo

address: zhongshan 2 road

institute: SYSU

summary: The principal problem arising from prostate cancer (PCa) is its propensity to metastasize to bone. MicroRNAs (miRNAs) play a crucial role in many tumor metastases.The importance of miRNAs in bone metastasis of PCa has not been elucidated to date. We investigated whether the expression of certain miRNAs was associated with bone metastasis of PCa.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We examined the miRNA expression profiles of 6 primary and 7 bone metastatic PCa samples by miRNA microarray analysis. Total RNA was taken from the specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3.0 biochip  representing about 924 microRNA.

first: Xingsheng

last: Peng

first: Wei


title: Comparison of steady state mRNA levels between equine articular cartilage and ten other equine tissues

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary: A tissue survey of gene expression was conducted using microarray-based transcriptional profiling to compare equine articular cartilage to 10 other normal adult horse tissues.  The ten comparative tissues were bladder, cerebellum, kidney, liver, lung, lymph node, muscle, placental villous, spleen, and testis.

overall_design: Messenger RNA transcriptome comparisons were conducted between equine articular cartilage and ten other body tissues using a 9413 element equine-specific cDNA microarray and a two-color dye-swap experimental design.  After scanning, the median intensities adjusted for background were entire chip Lowess-normalized for each individual slide.  Quantile regression was used to estimate the conditional quantile of the M and A log ratios given the observed average log intensity.  Briefly, a nonparametric approach was used to reveal the relationship between percentiles of M and A, where M is log2 (R/G) and A is 0.5 log2 (RG) with R representing expression in articular cartilage and G representing expression in the comparative tissue.  The quantile regression was fit using a B-spline with 5 fixed nodes.  The 1st, 5th, 10th, 20th, 50th, 80th, 90th, 95th, and 99th conditional quantiles were estimated.  For each observed gene intensity in a given tissue comparison, the normal quantile was used as the cartilage-specificity in place of the corresponding estimated regression quantile.

first: Wenying

last: Zhu

first: Liping

last: Huang

first: Kadie

last: Vanderman

first: Marlene

last: Tremblay

first: Christopher

middle: P

last: Saunders

first: Stephen

last: Coleman

first: Mai

last: Zhou

first: Mihoko

last: Shimojo

first: Arnold

last: Stromberg

first: Arne

last: Bathke

first: James

last: MacLeod


title: Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig loci in activated B cells

city: Worcester

first: Richard

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: After immunization or infection, activation-induced cytidine deaminase (AID) initiates diversification of immunoglobulin (Ig) genes in B cells, introducing mutations within the antigen binding V regions (somatic hypermutation, SHM) and double-strand DNA breaks (DSBs) into switch (S) regions, leading to antibody class switch recombination (CSR). Using a candidate approach, AID has been shown to initiate mutations at numerous non-Ig genes in B cells in Peyer’s patches. However, it is not known if during B cell activation, AID also induces DNA breaks at genes other than IgH genes, which would lead to genomic instability and malignancy. Using a non-biased genome-wide approach, we have identified hundreds of reproducible AID-dependent DSBs in mouse splenic B cells shortly after induction of CSR in culture.  Most interestingly, AID induces DSBs at sites syntenic with sites of translocations, deletions, and amplifications found in human B cell lymphomas, including within the oncogene B cell lymphoma11a (bcl11a)/evi9.  The AID-dependent DSBs are not restricted to transcribed regions, and they frequently occur within repeated sequence elements, including CA and non-CA repeats, and SINEs.

overall_design: Comparison of Nbs1 binding sites in wild-type vs. aid-/- splenic B cells induced to undergo CSR; aid-dependent Nbs1 sites correlated with gene transcription (RNA Pol2).

first: Ori

last: Staszewski

first: Anna

last: Ucher

first: Raygene

last: Martier

first: Janet

last: Stavnezer

first: Jeroen

last: Guikema


title: Alternative splicing signatures in apoptosis related genes of human HeLa cells with RNAi targeting p68 RNA helicase-DDX5

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary:
Alternative splicing profiling of apopotosis related genes in human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs targetting p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5) cloned into the pSuper expression vector compared to empty vector.

Keywords: treated vs. untreated comparison; alternative splicing

overall_design: Two-condition experiment, where the p68 DDX5 gene product levels was inhibited by siRNA transfection and compared to transfection with the negative control (scrambled siRNA). Biological replicates: 2, all independently grown and harvested. A dye swapping technical duplicate was performed for each biological replicate. Samples were hybridized onto a 44290 feature array designed by ExonHit to detect splicing events in apopotosis related genes  and manufactured by Agilent using in situ synthesis of oligonucleotides by SurePrint technology.

first: Mariette

last: Kokolo

first: Montse

last: Bach-Elias


title: Time course of Streptomyces coelicolor: M145 Control vs. wblA deletion mutant

city: Norwich

first: Govind

last: Chandra

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

institute: John Innes Centre

summary: The basic experiment is a comparison of gene transcript levels of Streptomyces coelicolor M145 and its wblA deletion mutant at 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation on solid medium. The wblA mutant is morphologically defective, most of its aerial hyphae failing to show any sign of sporulation-directed attributes, and also overproduces some antibiotics. The microarray analysis was aimed to reveal the major transcriptional changes underpinning or associated with this pleiotropic phenotypic change. Using a fairly stringent cut-off, 291 genes were found to be affected, including developmental genes, antibiotic biosynthetic genes, and genes for primary metabolism. Some genes were over-expressed and others under-expressed in the mutant. Although the largest effects were mostly at timepoints corresponding to aerial growth and early sporulation, some genes were most strongly influenced at earlier timepoints.

overall_design: M145 vs wblA deletion mutant. 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation, were analysed.  Each timepoint comprised 2 technical replicates each of 3 biological replicates. RNA was isolated from triplicated cultures grown on cellophane overlays on MM + mannitol after 24, 36, 48, 60, 72 and 84 hours of incubation.  Samples of the RNA were converted to Cy3-labelled cDNA in vitro, and mixed with Cy5-labelled genomic DNA. Each mixture was hybridised to two glass slide microarrays each carrying oligonucleotide probes corresponding to 99% of the genes in the annotated S. coelicolor genome. Thus RNA from each timepoint was compared to the same batch of genomic DNA and the comparison used to arrive at expression values of genes. These expression values were then used to arrive at differential expression between M145 and the wblA deletion mutant for all genes at all six timepoints.

first: Keith

middle: F

last: Chater

first: Kay

last: Fowler


title: Gene expression analysis of dendritic cells from normal or tumor bearing prostates

status: Public on Jan 20 2011

city: Frederick

first: Stephanie

middle: Kaye

last: Watkins

address: 1050 Boyles St.

department: CIP/LMI

institute: NCI-Frederick

summary:
Tumors cause the induction or repression of many genes associated with inflammation. To investigate the up and down regulation of genes associated with immune stimulation or immune tolerance RNA was isolated from dendritic cells from normal or tumor bearing prostate for microarray analysis.
Using the TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) model and a fold change comparison system we identified genes that are associated with immune tolerance to be up-regulated and genes associated with immunity to be down regulated in tumor associated dendritic cells.
Keywords: Comparative gene expression, prostate cancer, dendritic cells

overall_design: Prostatic dendritic cells were isolated from 4 normal and 6 tumor bearing mice for comparison of gene expression.

first: S

first: A

middle: A

last: Hurwitz


title: Mast cell microRNAs regulated by KIT signaling

first: Cliff

last: Takemoto

address: 720 Rutland Ave/Ross 1125

department: Pediatric Hematology

institute: The Johns Hopkins University

summary: Objective is to identify microRNAs regulated by KIT signaling in mast cells.  miRNA profiles of murine bone marrow derived mast cells with and without SCF treatment were compared.  In addition, miRNA profiles of the P815 mutant KIT cell line with and without the KIT inhibitor, imatinib, were compared.  We identified miRNAs that were differentially regulated by KIT signals.

overall_design: Two systems were used to identify microRNAs regulated by KIT.  RNA was collected from primary murine bone marrow derived mast cells (BMMC) treated and not treated with KIT ligand (SCF).  In addition, RNA was harvested from the P815 (activating KIT mutation positive) cell line treated and not treated with the KIT inhibitor, imatinib. Samples were harvested after 24 hours of treatment


title: Role for ISGF3II in the Antiviral Activity of IFN-gamma

status: Public on Jan 19 2011

city: Bethesda

first: Angel

last: Morrow

address: 9000 Rockville Pike

institute: NIH/NIAID

summary: Type-I (e.g. IFN-alpha, IFN-beta) and type-II IFNs (IFN-gamma) have antiviral, antiproliferative, and immunomodulatory properties. Both types of IFN signal through the Jak/STAT pathway to elicit antiviral activity, yet IFN-gamma is thought to do so only through STAT1 homodimers while type-I IFNs activate both STAT1- and STAT2-containing complexes such as ISGF3. Here we show that ISGF3II - composed of phosphorylated STAT1, unphosphorylated STAT2, and IRF9 - also plays a role in IFN-gamma-mediated antiviral activity in humans. Using phosphorylated STAT1 as a marker for IFN signaling, western blot analysis of IFN-alpha2a treated human A549 cells revealed that pSTAT1 (Y701) levels peaked at 1h, decreased by 6h, and remained at low levels for up to 48h. Cells treated with IFN-gamma showed a biphasic pSTAT1 response with an early peak at 1-2h and a second peak at 15-24h. Gene expression microarray following IFN-gamma treatment for 24h indicated an induction of antiviral genes that are induced by ISGF3 and associated with a type-1 IFN response. Induction of these genes by autocrine type-I and type-III IFN signaling was ruled out using neutralizing antibodies to these IFNs in biological assays and by qRT-PCR. Despite the absence of autocrine IFNs, IFN-gamma treatment induced formation of ISGF3II. This novel transcription factor complex binds to ISRE promoter sequences, as shown by ChIP analysis of the PKR promoter. STAT2 and IRF9 knockdown in A549 cells reversed IFN-gamma-mediated ISRE induction and antiviral activity - implicating ISGF3II formation as a significant component of the cellular response and biological activity of IFN-gamma.

overall_design: Two treatments using three biological replicates each were performed using three million A549 cells. Each was seeded overnight in 10mL complete RPMI and treated. Three were treated with alpha-IFN and three treated with gamma-IFN for 24h. Control samples were left untreated.


title: Systematic meta-analysis and replication of genome-wide expression studies identifies molecular pathways of Parkinson’s disease

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

summary: Analysis of human dopamine (DA) from postmortem brains of 8 patients with Parkinson’s disease (PD). Results provide insight into the molecular processes perturbed in the PD substantia nigra.

overall_design: Human dopamine (DA) neurons from 8 PD and 9 control subjects were obtained. Double-stranded complementary DNA was made with a biotinylated T7(dT)-24 primer. Biotinylated complementary RNA was fragmented and hybridized to Affymetrix human genome U133_X3P microarrays. The Affymetrix .CEL files were normalized to “all probe sets” in a standardized matter, and scaled to 100 by the MAS5 algorithm implemented in the Bioconductor package.

first: Ippolita

last: Cantuti-Castelvetri

first: Clemens

last: Scherzer


title: Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses

city: Newark

first: Nicole

last: Donofrio

state: DE

address: 531 S. College Ave

department: Plant and Soil Sciences

institute: University of Delaware

summary: Rice blast is the most threatening disease to cultivated rice worldwide. Magnaporthe oryzae, its causal agent is likely to encounter environmental challenges during invasive growth in the host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that M. oryzae have similar gene expression patterns in planta, versus during in vitro stresses.  Gene expression data was collected from in vitro experiments of heat shock, oxidative burst, and three different types of nutrient starvation. These data were compared to fungal gene expression during the invasive growth phase in compatible interactions on two grass hosts, rice and barley. We have identified 4,973 differentially expressed genes, from which 1,909 genes showed similar regulation patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which growth in planta conditions closely grouped with the starving nutrient conditions. Out of these 1,909 genes, 55 and 129 genes were induced and repressed in all seven treatments, respectively. The functional categorization of those 55 induced genes revealed that most of them are either related to carbon metabolism, membrane proteins, or are involved in oxidoreduction reactions. The 129 repressed genes are putatively involved in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport. These findings indicated that M. oryzae is likely coping with nutrient deprived environments in its hosts during the invasive growth stage about 72 hours post-inoculation, and not as much with host defense responses, or a temperature stress.

overall_design: Eight M. oryzae treatments: mycelia grown in liquid complete medium (set as the control); 72 hours post-incoulation (hpi) in rice leaves; 72 hours post-incoulation in barley leaves; mycelia under heat shock; mycelia under oxidative stress; mycelia under minimal medium; mycelia under nitrogen starvation; mycelia under carbon starvation. Three biological replicates had their total RNA pulled after RNA extraction. Dye-swaps used as technical replicates.

first: Sandra

last: Mathioni

first: André

last: Beló

first: Christopher

last: Rizzo

first: Ralph

last: Dean


title: Whole genome expression profile of dsap18 mutant Drosophila melanogaster embryos

status: Public on Jan 18 2011

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

institute: Universitat de Barcelona

summary: SAP18 is a highly evolutionarily conserved protein found in all eukaryotic organisms from Saccharomycces cerevisiae to humans. It has been proposed to be involved in multiple cellular processes, from gene regulation to mRNA processing, playing different cellular functions, such as cell fate control during development or regulation of apoptosis or salt stress responses. Previous studies found SAP18 capable of repressing transcription when tethered directly to a promoter region. To gain further insight into the role of Drosophila SAP18, we performed genome-wide expression profiling of a dSAP18 mutant allele and found that dSAP18 is required for the expression of several immune-related genes, amongst others.  To provide an updated view of the transcriptome, the probe sequences from the platform used (GPL3797) were matched to FlyBase Genome Release 5.5 and the corresponding gene names and identifiers were obtained. In the cases where one probe matched more than one gene, all of them were obtained.

overall_design: A total of four microarrays were hybridized in biological replicate pairs, such that the total RNA from dsap18 mutant animals (dsap18^117/Df(3R)sbd^45 0-24h staged embryos) and control animals (rescued dsap18^117/Df(3R)sbd^45 0-24h embryos containing a dsap18-HA transgene) used as starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

first: Elisabet

last: Costa

first: Maria

last: Espinàs


title: Transcriptome comparision in ovaries between sexual and apomictic plants of Brachiaria using cDNA microarrays

city: Thuwal

first: Eduardo

middle: Andres

last: Gorron Gomez

address: KAUST, Thuwal, Saudi Arabia

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Some flowering plants exhibit a phenomenon called apomixis, defined as the ability to produce seeds asexually and with the same genetic constitution as the mother plant. The existence of a genetic basis for apomixis is evident, but the molecular mechanisms that underlie it remain unclear. The search for “the master apomixis gene” had led to the isolation of diverse candidate transcripts. However, neither of them could be clearly confirmed. The techniques employed so far have been based on differential-display PCR and have not allowed detecting transcripts with low levels of expression or low differential expression. For all these reasons, in this study we employed cDNA microarrays combined with subtractive libraries in order to isolate transcripts with differential expression between sexual and apomictic plants of the genus Brachiaria. We used ovaries corresponding to two developmental stages: i) stage I, appearing of initial aposporic cell in apomictic plants; and ii) stage II, degeneration of meiotic-derived tetrad and establishment of diploid embryo sac in apomictic plants. Subtractive libraries revealed some differential bands, which were spotted over glass slides together with clones from non-subtractive libraries, and with amplicons associated to apomixis obtained using degenerate PCR. A total of 26 distinct sequences showed differential expression, only 1 of them was overexpressed in apomictic plants, and the majority was related to stage I. Bioinformatic analyses confirmed meiosis-related roles for some of the genes, a result consistent with a higher level of expression in sexual ovaries. Nevertheless, for some sequences a clear function could not be assigned. Some of them appear to be related to the polyploid stage of apomictic plants, in one hand, and to putative transcription factors, on the other hand. The implications of these results under a molecular model of apomeiosis are discussed.

sample_organism:
Urochloa brizantha
Urochloa decumbens
Urochloa ruziziensis

overall_design: We employed RNA from ovaries from sexual plants as a control, and RNA from ovaries of apomictic plants as experiment. Four different sexual and four apomictic genotypes were employed. A sexual genotype was compared against a given apomictic genotype, for a total of 4 comparisions. Each comparision were performed ifor two developmental stages, for a total of eight comparisions. In each comparision, a dye swap was done.

last: Gorrón

first: Diana

last: Bernal

first: Silvia

last: Restrepo

first: Joe

last: Tohme


title: Development of microRNA expression signatures for gastric cancer

status: Public on Jan 15 2011

city: Shanghai

first: Hong

middle: Xia

last: Wang

state: Shanghai

address: 1630# Dongfang Road

institute: Shanghai Renji Hospital

summary: To further investigate of microRNA expression profile of gastric cancer, we have employed whole microRNA gene chip as a discovery platform to identify gene differential expression between gastric cancer tissues with mormal gastric tissues.Expression of four microRNAs (miR-125b,miR-451,miR-192b,miR-200b) from this signature was quantified and verified in the same RNA samples by real-time PCR.

overall_design: A total of 4 consecutive patients with gastric cancer undergoing elective surgery were entered into this study. After obtaining informed consent from the patients and after receiving the approval of the ethics committee, the following tissue samples were collected: tumor (3 × 3 × 5 mm) and adjacent normal tissues (3 × 3 × 5 mm).

first: Hongxia

first: Yingchun

last: Xu

first: Lei

last: Tang


title: Copy number variation in the genomes of Caenorhabditis elegans end-to-end fusion strains

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: End-to-end chromosome fusions that occur in the context of telomerase deficiency can trigger genomic duplications. These duplications are suggested to arise via Breakage-Fusion-Bridge cycles. To test this hypothesis, we examined end-to-end fusions isolated from C. elegans telomere replication mutants. Genome level rearrangements revealed fused chromosome ends possessing interrupted terminal duplications accompanied by template switching events. These features are very similar to disease-associated duplications of interstitial segments of the human genome. A model termed Fork Stalling and Template Switching has been proposed previously to explain such duplications, where promiscuous replication of large, non-contiguous segments of the genome occurs. Thus, a DNA synthesis-based process can create duplications that seal end-to-end fusions, in the absence of Breakage-Fusion-Bridge cycles.

overall_design: Numerous C. elegans mutant samples were studied with comparative genomic hybridization. There were no replicates or dye-swap hybridizations.

first: Mia

last: Lowden

first: Donald

last: Moerman

first: Shawn

last: Ahmed


title: Role of Hog1 in oxygen regulation of gene expression

status: Public on Jan 13 2011

city: Princeton

first: Mark

last: Hickman

state: NJ

address: Washington Road

department: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

summary: Expression microarrays of WT vs. hog1D cells in aerobic or 5 hours of hypoxic growth (100% nitrogen gas).

overall_design: Two strains (WT vs. hog1 deletion), two conditions (aerobic vs. 5 hours hypoxic), two biological replicates each strain/condition.

first: Fred

last: Winston


title: Analysis of microRNA expression during Epstein-Barr virus encoded LMP1 and LMP2A transfected in TW03 cells

city: Stockholm

first: ZiMing

last: Du

address: Nobels vagen

institute: Karolinska Institutet

summary: Epstein-Barr virus has been reported to  regulate cellular microRNA expression in B cells. In the present study, we investigated  the differential microRNAs modulated by Epstein-Barr virus in Naspharyngeal Carcinoma, using CapitalBio corporation's mammalian miRNA arrays.

overall_design: Three cellular models were used in this study: the human naspharyngeal carcinoma cell line TW03 as a blank control; TW03 transfected with Epstein-Barr virus encoded LMP1; TW03 transfected with Epstein-Barr virus encoded LMP2A

first: Zi-Ming

first: Jian-Yong

last: Shao


title: Differentially expressed miRNAs between HepG2.2.15 and HepG2 cells

status: Public on Jan 14 2011

city: Beijing

first: Hongyan

last: Guo

address: Chengfu

department: School of Medcine

institute: Tsinghua University

summary: MiRNAs are important posttranscriptional regulators in various physiological processes and their dysregulations have been found in diseases such as infection, imflammation and cancer. Here we compared the miRNA profilings between HBV-producing HepG2.2.15 and its non-HBV maternal HepG2 cell to find potential miRNAs involving in HBV expression. The result indicated that some of the deregulated miRNAs in HepG2.2.15 have been implicated in viral infection and the processes of the immune regulation.

overall_design: HepG2.2.15 vs. HepG2

first: Mingyong

last: Luo


title: The stress kinase MKK7 couples oncogenic stress to p53 stability and tumor suppression

city: Vienna

first: Daniel

last: Schramek

address: Dr. Bohrgasse 3

institute: IMBA

summary: Transcriptional profiling of control and MKK7-deficient  primary mouse pneumocytes after oncogenic KRasG12 induction

overall_design: Two-condition experiment, MKK7 proficient vs.  MKK7 deficient pneumocytes. 3 Biological replicates: 3 control, 3 knock out, independently grown and harvested. 3 technical replicates per array (each sample was hybridized to 3 in-house arrays (47MM, 51MM and 46MM - see HybridisationInfo.xls) for a total of 54 hybridizations).

first: Athanassios

last: Kotsinas

first: Arabella

last: Meixner

first: Teiji

last: Wada

first: Ulrich

last: Elling

first: J

last: Pospisilik

first: G

last: Neely

first: Ralf-Harun

last: Zwick

first: Verena

last: Sigl

first: Guido

last: Forni

first: Manuel

last: Serrano

first: Vassilis

last: Gorgoulis

first: Josef

last: Penninger


title: The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome: DamID

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that of these five proteins, only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens LAD – NL interactions by a local antagonistic effect. Our results provide insights into the evolution of LAD organization and reveal a role for SU(HW) in the regulation of genome – NL interactions.

overall_design:
DamID experiments for Lamin, CTCF, SU(HW), GAF, DWG, and BEAF-32, and for Lamin after overexpression and after knockdown of SU(HW), were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation.

The supplementary file 'GSE20311_DamID_norm_mean.txt' contains the mean log2(Dam-fusion/Dam-only) values of two replicates.

first: Joke

last: van Bemmel

first: Ludo

last: Pagie

last: Braunschweig

first: Wim

last: Brugman

first: Wouter

last: Meuleman

first: Ron

last: Kerkhoven


title: Not gene expression based, methylation detection using cDNA array

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

summary: genomic DNA hybridized to gene spots on the cDNA array was used for methylation detection using antibodies against 5methyl cytosine

overall_design: DNA from control and irradiated C57BL/6 mouse were used for the study


title: Host imprinting on bacterial genomes-rapid, divergent evolution in individual hosts

city: Wuerzburg

first: Jaroslaw

last: Zdziarski

address: Josef-Schneider Str. 2/Bau D15

department: Institut fuer Molekulare Infektionsbiologie

institute: Universitaet Wuerzburg

summary: Transcriptional profiling of Asymptomatic Bacteriuria (ABU) Escherichia coli strain 83972 comparing the progenitor wild type strain ABU83972 with its re-isolates from human bladder colonization (PI-2, PII-4, PIII-4) and in vitro cultivation experiment (4.9).

overall_design: Wild type vs. re-isolate cells. Biological replicates: 3 wild type, 3 re-isolates, independently grown and harvested. One replicate per array.

first: Elzbieta

last: Brzuszkiewicz

first: Björn

last: Wullt

first: Heiko

last: Liesegang

first: Dvora

last: Biran

first: Birgit

last: Voigt

first: Jenny

last: Grönberg-Hernandez

first: Michael

last: Hecker

first: Eliora

last: Ron

first: Rolf

last: Daniel

first: Gerhard

last: Gottschalk

first: Jörg

last: Hacker

first: Catharina

last: Svanborg

last: Dobrindt


title: New schwann cell markers identified by gene profiling analysis after axonal contact

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

summary: Elucidating the genes regulated during cell-cell communication remains fascinating considering the importance of cell recognition and downstream signaling through development and in many diseases. In the peripheral nervous system, the interaction between Schwann cells (SCs) and axons is crucial as it allows their survival and induces SCs to differentiate and engage a process of myelination. To get further insight the molecular mechanisms resulting from this cell interaction, comparative gene analysis between SCs and SCs co-cultured with DRG neurons were performed and led us to identify a set of 32 genes regulated in SCs in the early stage of neuron-SC contact. Expression of several candidates were analyzed by QPCR during development and we demonstrate using a blocking antibody approach in an in vitro myelination assay that one candidate was not only upregulated in response to axonal contact but also controls peripheral myelination.

overall_design: Three biological replicates each in dye swap for 22k slides and two biological replicates each in dye swap for NeuroDev2

first: Decker

last: Laurence

first: Blugeon

last: Corinne

first: Stephane

last: Le Crom


title: Cell type specificity of chromatin organization mediated by CTCF and cohesin

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression, whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function.

overall_design: Comparison of CTCF binding in K562 and 293T cells using ChIP-chip. 3 replicates each cell type, ChIP and input DNA for each replicate.

first: Ann

last: Dean