title: Blumeria graminis fsp hordei effects on translation initiation in compatible and incompatible barley

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: The goal of this experiment was to examine the effects of Blumeria gramins f. sp. hordei (Bgh) on the host process of translation initiation in both incompatible and compatible interactions with Hordeum vulgare. This was done by using Bgh isolate 5874 (AVRa6) on the resistant host CI 16151 (Mla6) and fast-neutron derived, loss-of-function mutant m9472 (mla6). Plants were grown 7 days in the greenhouse and then inoculated or non-inoculated and transferred to an 18°C growth chamber with an 8 hr dark, 16 hr light photoperiod. At 32 hours after infection the tissue was harvested and immediately frozen in liquid nitrogen. From the same tissue, total RNA was isolated using a Trizol method, while polysomal RNA was isolated by sucrose density centrifugation. Three biological replications were conducted.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jackson Moeller.  The equivalent experiment is BB72 at PLEXdb.]

overall_design: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA(3-reps);  genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA(3-reps);  genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA(3-reps);  genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA(3-reps);  genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA(3-reps);  genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA(3-reps);  genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA(3-reps);  genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA(3-reps)

first: Jackson

last: Moeller


title: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

status: Public on Mar 07 2011

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary:
Using transcriptomics, the strain-specific metabolism was mapped for two whole-genome sequenced strains of Aspergillus niger
Keywords: Strain comparison

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Two strains grown in controlled bioreactors, three biological replicates each.

first: Margarita

last: Salazar

first: Scott

middle: E

last: Baker

first: Jens

last: Nielsen


title: RNA-Binding Protein targets in Saccharomyces cerevisiae

status: Public on Mar 10 2011

city: Stanford

first: Dan

last: Klass

state: CA

address: 259 Campus Drive Beckman Rm 439

department: Biochemistry

country: USA

institute: Stanford University

summary: The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a key role in discovering these RBPs - most of the known yeast RBPs lack RNA-binding domains that might enable this activity to be predicted. We describe here a new proteome-wide approach to identify RNA-protein interactions based on in vitro binding of RNA samples to yeast protein microarrays that represent over 80% of the yeast proteome. We used this procedure to screen for novel RBPs and RNA-protein interactions. A complementary mass spectrometry technique also identified proteins that associate with yeast mRNAs. Both the protein microarray and mass spectrometry methods successfully identify previously annotated RBPs, suggesting that other proteins identified in these assays might be novel RBPs. Of 35 putative novel RBPs identified by either or both of these methods, 12, including 75% of the eight most highly-ranked candidates, reproducibly associated with specific cellular RNAs. Surprisingly, most of the 12 newly discovered RBPs were enzymes. Functional characteristics of the RNA targets of some of the novel RBPs suggest coordinated post-transcriptional regulation of subunits of protein complexes and a possible link between mRNA trafficking and vesicle transport. Our results suggest that many more RBPs still remain to be identified and provide a set of candidates for further investigation.

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

first: Nikoleta

last: Tsvetanova


title: Combinatorial binding of transcription factors in the pluripotency control regions of the genome

status: Public on Mar 03 2011

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St

department: MCB

institute: Brown University

type: Genome binding/occupancy profiling by genome tiling array

summary: The pluripotency control regions (PluCRs) are defined as genomic regions that are bound by Oct4, Sox2, and Nanog in vivo. We utilized a high-throughput binding assay to record more than 270,000 different DNA/protein binding measurements along incrementally tiled windows of DNA within these PluCRs. This high-resolution binding map is then used to systematically define the context of Oct factor binding and reveals patterns of cooperativity and competition in the pluripotency network. The most prominent pattern is a pervasive binding competition between Oct4 and the forkhead transcription factors. Like many transcription factors, Oct4 is co-expressed with a paralog, Oct1, that shares an apparently identical binding specificity. By analyzing thousands of binding measurements we discover context effects that discriminate Oct1 from Oct4 binding. Proximal Nanog binding promotes Oct4 binding, whereas nearby Sox2 binding favors Oct1. We demonstrate by cross-species comparison and by chromatin immunoprecipitation (ChIP) that the contextual sequence determinants learned in vitro are sufficient to predict Oct1 binding in vivo.

overall_design:
An oligonucleotide pool that tiles through 316 PluCR regions ( a region of simulataneous in vivo Oct4, Sox2 and Nanog ChIP enrichement in human ES cells - Boyer et al. 2005) was incubated in embryonic stem cell extract. Complexes were allowed to form and oligonucletide:protein complexes were immunoprecipitated with one of four antidodies (against Oct4 , Sox2, Nanog, Oct1). The enrichment of oligonucleotides in co-precipitate was analyzed by two color (Cy3/Cy5) microarray strategy using an Agilent custom oligonucleotide array.
MEGAshift (microarray evaluation of genomic aptamers by shift) binding assay protocol based on Tantin et. Al, 2008 and Reid et. Al, 2009.
There are two internal technical replicates.

first: Luciana

last: Ferraris

first: Allan

middle: P

last: Stewart

first: Jinsuk

last: Kang

first: Alec

middle: M

last: DeSimone

first: Matthew

last: Gemberling

first: Dean

last: Tantin

middle: G


title: IPF AEx Series

city: San Francisco

first: Sharon

middle: Chao

last: Wootton

address: Byers Hall, Rm s403c 1700 4th St.

department: Joint Graduate Group in Bioengineering

institute: UC Berkeley and UC San Francisco

summary:
Viruses in acute exacerbations of idiopathic pulmonary fibrosis
Keywords: viral detection

overall_design: BAL from patients with acute exacerbations of IPF and stable IPF were hybridized to a pan-viral cDNA microarray to evaluate the presence of virus during these episodes

middle: C

first: Dong

middle: S

last: Kim

first: Yasuhiro

last: Kondoh

first: Eunice

last: Chen

first: Joyce

last: Lee

first: Jin

middle: W

last: Song

last: Huh

first: Hiroyuki

last: Taniguchi

first: Charles

last: Chiu

first: Homer

last: Boushey

first: Lisa

middle: H

last: Lancaster

first: Paul

middle: J

last: Wolters

first: Joseph

last: DeRisi

first: Don

last: Ganem

first: Harold

last: Collard


title: Extension of glycogene expression pattern analysis in the prefrontal cortical region of Schizophrenic human post-mortem brain samples

status: Public on Mar 02 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
This laboratory focuses on the molecular mechanisms of neuropsychiatric and neurodegenerative disorders
Extension of previous studies investigating Glyco-Gene Expression in Schizophrenia (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27356 ). From previous analyses, a group of 9 genes associated with the biosynthesis of glycosphingolipids were identified as altered in subjects with schizophrenia, with most differences detected in subjects with short DOI and not in chronic illness. The enzyme expression changes are of particular interest as they are important to the synthesis of cerebrosides and sulfatides, which are enriched in membranes making up myelin. There are known deficits in myelin and white matter in schizophrenia so changes in these enzymes may represent a mechanism accounting for these deficits. Furthermore, clusters of co-regulated genes were identified using new software for weighted gene co-networks. This may represent the first molecular definition of different subtypes of schizophrenia, a very heterogeneous psychiatric disorder.

platform_organism:
Homo sapiens
Mus musculus

overall_design: For this follow up study, microarray analyses experiments were  performed on an additional cohort of subjects with schizophrenia in order to, 1) Assess how this group of glycosphingolipid-related genes is altered in disease and control states, and 2) Further determine if co-regulated genes will cluster in the new cohort, which will consist of subjects with a range of durations of illness. For these studies, 32 human samples (16 control and 16 Schizophrenic) were  labeled and hybridized to 26 GLYCOv2 arrays

first: Elizabeth

last: Thomas


title: SF3b155 knock-down by two different siRNA oligos in HeLa cells

status: Public on Mar 08 2011

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary: Analysis of the alternative pre-mRNA procesing after SF3b155 siRNA knock-down in HeLa cells employing a custom microarray platform sensitive to splicing.

overall_design: HeLa cells were transfected with either a scrambled RNA or one of the two different SF3b155 siRNA oligonucleotides (oligo 3: 5’-GACAGCAGAUUUGCUGGAUACGUGA-3; oligo 5: 5’-CCCUGUGGCAUUGCUUAAUGAUAU-3’). Total RNA samples from three biological replicates were labeled in direct and dye-swap hybridizations. Labeled samples were hybridized into our custom splicing-sensitive agilent platform which contains 1804 splicing events from 482 genes.

first: Belen

last: Minana

first: Anna

last: Corrionero

first: Valcarcel

last: Juan


title: Time-of-day-dependent light-induction of gene expression in the chicken pineal gland

city: Tokyo

first: Yoshitaka

last: Fukada

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

summary: Light has a strong effect on whole organism physiology, such as the circadian rhythms that are phase delayed and advanced by light given at early and late subjective night, respectively. Despite the importance of the phase-dependent light responses, little is known about the underlying molecular mechanism. We performed a comprehensive analysis of genes induced by light in a phase-dependent manner in the chicken pineal gland, an organ that represents a unique vertebrate clock system harboring intrinsic light sensitivity.

overall_design: Newborn chicks were entrained to 12-h light/12-h dark cycle for 7 days then transferred to constant darkness for a day to be exposed to light for 1 h from CT (circadian time) 6 (representing subjective day), CT14 (early subjective night) or CT22 (late subjective night). Control animals were kept in the dark without light pulse. The pineal glands were isolated at the end of the 1-h light pulse for gene expression analysis by Affymetrix GeneChip. Each condition contains 2 biological samples.

first: Megumi

last: Hatori

first: Tsuyoshi

last: Hirota

first: Koichi

last: Kokame

first: Toshiyuki

last: Miyata


title: Determinants of heat resistance in Escherichia coli AW1.7

city: Edmonton

first: Michael

last: Gänzle

address: 4-10 Ag/For Centre

department: AFNS

country: Canada

institute: University of Alberta

summary: Microarray hybridization of cDNA libraries obtained from exponentially growing or heat-shocked AW1.7 or GGG10 cultures was performed to compare gene expression of these two strains. Expression of selected genes from different functional groups was quantified by quantitative PCR (q-PCR). DnaK, 30S and 50S risobomal subunits were overexpressed in E. coli GGG10 relative to E. coli AW1.7 upon heat shock at 50°C, indicating improved ribosome stability. The outer membrane porin NmpC and several transport proteins were overexpressed in exponentially growing E. coli AW1.7.

overall_design: Gene expression of a heat resistant strain, E. coli AW1.7, was compared to gene expression in a heat sensitive strain, E coli GGG10. RNA was isolated from late exponential cultures, or from late exponential cells heat-shocked by exposure to 50°C for 15 min. Three independent biological repeats were analyzed, and technical repeats (dye-swap) were performed for two of three biological repeats.

first: Lifang

last: Ruan

first: Lynn

last: McMullen


title: Microarray-based Characterization of Microbial Community Functional Structure and Heterogeneity Associated with Acid Mine Drainages

city: changsha

first: xueduan

last: liu

address: lushan south road

country: China

institute: central south university

summary: To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities.  In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them.

overall_design: This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).

first: Guanzhou

last: Qiu

first: Huaqun

last: Yin

first: Li

last: Shen

first: Jizhong

last: Zhou

first: Zhili

last: He

first: Ye

last: Deng

first: Sanghoon

last: Kang

first: Yun

last: Fang

first: Xueduan

last: Liu


title: Short and long term cold responses in a winter barley

first: PLEXdb Curator

summary: Gene expression changes in a winter cultivar of barley in response to short and long term cold treatments   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ben Trevaskis.  The equivalent experiment is BB94 at PLEXdb.]

overall_design: treatment: Non-vernalized (3-replications); treatment: Short-term cold (3-replications); treatment: Vernalized (3-replications); treatment: 1 day post-vernalized (3-replications)

first: Ben

last: Trevaskis


title: Long term cold responses in a winter barley

summary: Gene expression changes maintained after vernalization   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ben Trevaskis.  The equivalent experiment is BB95 at PLEXdb.]

overall_design: treatment: Non-vernalized(3-replications);  treatment: Post-vernalized(3-replications)


title: Microarray screening of RNA samples from two human myeloma and two human lymphoma cell lines

first: Steven

last: Head

summary:
This laboratory studies the T cell recognition of glycolipid antigens, including the biochemical characterization of glycolipid antigens, the cell biology of glycolipid antigen presenting machinery, the chemical synthesis of self and foreign glycolipids, and the cellular immunology that might shed light on finding glycolipid targets for adjuvant and vaccine development.
In myeloid patients, the suppression of NKT cells has been reported. This suppression is mediated by endogenous glycolipid antigens presented by CD1d, a non-classic MHC molecule. Tumor B cells express CD1d molecule and preserve the capacity in presenting glycolipid antigens to NKT cells. However, the identity of the tumor glycolipid antigens remain unknown. We recently identified isoglobotrihexosylceramide (iGb3), as one endogenous ligand for human NKT cells. We have also purified iGb3 from thymuses of pediatric patients. Thus we hypothesize that iGb3 might be directly linked to the NKT suppression in myeloma patients. The processing of iGb3 requires the “assembly line” of glycosyltransferases, the glycosidases and sphingolipid activator proteins. The loading of iGb3 antigen is dependent on lipid transfer proteins such as saposins, and the more recently characterized CD1e molecule. Thus we used the Glyo-chip approach to have a systemic survey of the above enzyme and protein components. We hope to find clues to help us in understanding the glycolipid antigen presentation in tumor B cells.

overall_design: EXPERIMENT: We purified RNA from 2 myeloma cell lines (U226 and 8226) by the RNAqueous kit from Ambion, TX. RNA was also purified from 2 lymphoma cell lines (Daudi and RL). 4 samples were provided to Core E of Consortium of Functional Genomics for Glyco-chip version 2 array.

first: Dapeng


title: Interorgan coordination of the murine adaptive response to fasting

status: Public on Mar 09 2011

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: The effects of fasting have been studied extensively, predominantly on isolated processes, within a specific organ. No comprehensive study of the adaptations was available for different organs, let alone interrelating them, which left the understanding of the body’s orchestration of fasting response limited.  The gene expression profiles of brain, small intestine, kidney, liver and skeletal muscle were therefore studied in mice subjected to short, moderate and prolonged fasting. Functional category enrichment, network, and text-mining analyses were employed to scrutinize the overall adaptive response, aiming to identify responsive pathways, processes and networks, and their regulation.  The implicated processes did not follow the accepted carbohydrate-lipid-protein succession of energy substrates expenditure. Instead, they were activated simultaneously in different organs during the whole duration of fasting. The most prominent changes occurred in lipid and steroid metabolism, especially in the liver and kidney, which showed biochemically similar, orchestrated responses. They were accompanied by suppression of the immune response and cell turnover, particularly in the small intestine, tied in with increased proteolysis in the muscle. Enhanced defence against oxidative damage, obvious in all the organs, was the top reaction of the brain, otherwise shown to be extremely well protected from starvation. The major transcription regulators of fasting response in different organs were FoxO transcription factors, AP-1, p53, cMyc, Sp1, EGF and HNF4α.  The revealed interorgan interactions between metabolic, inflammatory and cell turnover responses are essential when designing strategies to treat the starvation affected individuals, while stressing the significance of using complimentary bioinformatics tools in the high-throughput data analysis.

overall_design: 6 week-old male FVB mice were fasted for 0, 12, 24, 48 or 72 hours before sacrifice (N = 5 per group). From each mouse total RNA was isolated from five organs - liver, small intestine, kidney, brain, and calf muscle.  Five microarrays per experimental condition (five tissues, five timepoints) were performed. We used a common reference design. The single common-reference sample was a pool of equal amounts of RNA from all the samples investigated, including additional samples from 5 mice that were fasted for 48 hours and supplemented with vitamin B complex after 24 and 36 hours of fasting.

first: M

last: Sokolović

first: P


summary:
Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation.
Gene expression in F9 teratocarcinoma cells: Study of the differential expression of glycosyltransferases, sulfotransferases and proteoglycan core proteins in F9 teratocarcinoma cells before and after differentiation with retinoic acid/theophylline/cAMP. Published data indicated that differentiation of the cells induces the synthesis of anticoagulant heparin-like compounds and a large increase in overall glycosaminoglycan synthesis.

overall_design: Glyco-gene Chip microarray analysis of RNA samples (in triplicate) from the cells before and after differentiation to reveal factors that regulate the assembly process and how it leads to the generation of binding sites for glycan-binding proteins.

first: Jeffrey

last: Esko


title: Coordinate regulation of galectins in GAL3 deficient mouse keratinocytes exposed to UVB irradiation

summary:
Dr. Liu's research group is interested in studying the expression and functions of galectin-3, -7 and -12, in particular the roles of these proteins in inflammation and neoplasm.
Members of the galectin family are known to participate in cellular homeostasis by modulating cell growth, controlling cell cycle progression, and inducing or inhibiting apoptosis. It is known that some galectins have similar functions. However, it is not fully understood whether they work cooperatively or not. Recent reports suggest that gal-3 deficiency may induce changes in cellular homeostatic mechanisms, leading to changes in expression of other galectins and galectin-related proteins.

overall_design: To analyze the coordinate regulation of galectins in the face of gal-3 deficiency, gene expression patterns of gal-3 / and gal-3 -/- keratinocytes exposed to UVB were compared. Murine epidermal keratinocytes from gal-3 / and gal-3 -/- mice will be irradiated with 200 J/m2 of UVB. Total RNA will be extracted at 0, 6, 12 and 24 h after irradiation. Classes were prepared in triplicate for a total of 24 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

first: Fu-Tong

last: Lui


title: Differential expression of glycosyltransferases in P19 mouse embryonal carcinoma cells with or without differentiation by retinoic acid

summary:
The project is aimed at understanding the role of the Lex-containing L5 carbohydrate epitope in the developmental process of neural induction. We plan to identify 1) the protein to which the L5 glycan is attached, 2) glycosyltransferases upregulated during neural induction, 3) the corresponding L5 carbohydrate binding protein (CBP), 4) the mechanism of interaction between L5 and its CBP, and 5) the spatiotemporal regulation of L5 and L5-CBP expression during neural induction.
There is evidence, by Westernblot and immunofluorescence, that the expression of the Lewis-x-like L5 carbohydrate epitope shows dramatic differences in expression between undifferentiated cells and cells differentiated with retinoic acid. We wish to know which enzyme(s) involved in the biosynthetic pathway may be up/downregulated under these experimental conditions.

overall_design: Two classes of p19 mouse embryonal carcinoma cell RNA were analyzed: undifferentiated and differentiated with retinotic acid. Classes were prepared in triplicate for a total of 6 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

first: Bridgitte

last: Schmitz


title: Broad epigenetic signature of maternal care in the brain of adult rats (expression)

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

type: Expression profiling by genome tiling array

summary: Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. However, epigenetic changes at a single gene promoter are unlikely to account for the range of responses to the early life environment and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Here we show that natural variations in maternal care are associated with coordinate changes in DNA methylation, chromatin, and gene expression spanning over a hundred kilobase pairs in the hippocampus of adult rats. The offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends and higher transcriptional activity across many genes, suggesting that a broad epigenetic regulation of gene expression may form part of a coordinated response to early maternal care.

overall_design: We obtained hippocampal samples from adult offspring of rat mothers that differed in the frequency of pup licking/grooming in the first week of life, 4 from high frequency and 4 from low frequency mothers.  Using custom-designed microarrays with probes tiling the 7 million base pair region of rat chromosome 18 centered at the NR3C1 gene at 100 bp spacing, we obtained transcription profiles by hybridizing cDNA to microarrays.  Each profile was generated in duplicate.

first: Patrick

last: McGowan

first: Matthew

last: Suderman

first: Michael

last: Meaney


title: Conjugated linoleic acid inhibits hyphal growth in Candida albicans by modulating Ras1 cellular levels and down-regulating TEC1 expression

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

summary: The polymorphic yeast Candida albicans exists in blastospore and filamentous forms. The switch from one morphological state to the other coincides with the expression of virulence factors, which makes the yeast-to-hypha transition an attractive target for the development of new antifungal agents. Because an untapped therapeutic potential resides in small molecules that hinder C. albicans filamentation, we characterized the inhibitory effect of conjugated linoleic acid (CLA) on hyphal growth and addressed its mechanism of action. CLA inhibited hyphal growth in a dose-dependent fashion, in both liquid- and solid-inducing media. The fatty acid blocked germ tube formation and impeded hyphal elongation. Global transcriptional profiling revealed that CLA downregulated the expression of hypha-specific genes and abrogated the induction of several morphogenesis regulators, including RAS1, TEC1 and UME6. CLA’s repressive effect on TEC1 expression was Ras1-dependent, but Efg1-independent. CLA treatment resulted in the delocalization of Ras1 and its degradation, resulting in the downregulation of the Ras1-cAMP-PKA signaling pathway. This study provides the biological and molecular explanations that underlie CLA’s ability to inhibit hyphal growth in C. albicans.

overall_design: Two-color experimental design that consistently used growth in Spider Media at 30℃ as the control. We tested the effect of high temperature as well as the effect of adding 100 mµ CLA at either low or high temperature. RNA from each replicate came from independent cultures.

first: Julie

last: Shareck

first: Pierre

last: Belhumeur


title: Differential expression of microRNA profiles from the peripheral blood of type 1 and type 2 diabetic patients

status: Public on Mar 05 2011

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

country: Singapore

institute: National University of Singapore

summary:
Using microarray, we compared the expression of miRNAs from the peripheral blood of male subjects with T1DM and T2DM with healthy controls. Healthy male controls used were age-matched to the T2DM group patients with mean(SD) 37.3 (7.1) years. Subjects with T1DM were younger [23.3(1.6) years]. Expression was compared and validated using quantitative real-time PCR. Statistical testing (ANOVA, P-value <0.05) was performed and fold changes with respect to the control were calculated
Systolic BP, fasting glucose, HbA1c, total cholesterol and LDL-cholesterol levels were significantly higher in T2DM subjects compared with controls (P-value <0.05). Compared with controls, we identified 37 differentially regulated miRNAs in DM subjects. Among them, 21 miRNAs were upregulated (2-5 fold change, p-value < 0.05) and 16 miRNAs were downregulated (1.5-2 fold change, p-value < 0.05). These miRNAs had gene putative targets primarily involved in regulating pancreatic development and functions, adipocyte differentiation, insulin signaling and glucose-dependent insulin secretion.

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

first: Arunmozhiarasi

last: Armugam

first: Dwi

last: Karolina

first: Chin

last: Khoo


title: Differential expression profiling between two maize internodes identifies genes involved in cell wall biogenesis

status: Public on Mar 06 2011

city: Aberystwyth

first: Maurice

last: Bosch

address: Gogerddan

department: Institute of Biological, Environmental & Rural Sciences

country: United Kingdom

institute: Aberystwyth University

summary:
Despite the economic importance of grasses as food, feed and energy crops, little is known about the genes that control their cell wall synthesis, assembly and remodelling.  Here we provide a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis.

Differential gene-expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material.

This is one of only few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall-related processes in grasses. The results suggest that many proteins involved in cell wall-related processes during normal development are also recruited during defence-related cell wall remodelling events.

The data presented provide a platform for future studies in which candidate genes can be tested for involvement in cell wall processes through forward and reverse genetic-based approaches, contributing towards a better understanding of cell wall biogenesis and its regulation in grasses.

overall_design: The experiment consisted of six biological replicates (internode 9 and internode 13 were harvested from six maize plants). Dye-swaps were performed (in 3 slides, internode 9 RNA was labelled with Cy3 and internode 13 RNA was labelled with Cy5; in 3 other slides, internode 13 RNA was labelled with Cy3 and internode 9 RNA was labelled with Cy5).

first: Claus-Dieter

last: Mayer

first: Alan

last: Cookson

first: Iain

last: Donnison


title: Identification of glycosyltransferases and glycosydases responsible for the synthesis/degradation of mucin O-glycans at the human ocular surface epithelium

first: Steven

last: Head

summary: The major focus of Dr. Argueso's research is to characterize the carbohydrate portion of the different mucins expressed by the ocular surface epithelia as well as the enzymes involved with their synthesis, and to determine whether the alteration of mucin glycosylation is associated with ocular surface disease.

overall_design:
Highly glycosylated mucins on the ocular surface (cornea and conjunctiva) are the first line of defense of the eye against injury and infection. Changes in O-glycosylation of mucins may cause ocular surface disorders, such as dry eye. Gene expression patterns in the conjunctival epithelium of three normal subjects were analyzed.
The three subjects have the same ABO-blood-group. For each donor, conjunctival cells were obtained by impression cytology. Conjunctival impression cytology was performed on each eye two times with a one-week interval. Conjunctival cells obtained from each individual were pooled and the RNA isolated. All three samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

first: Pablo

last: Argueso


title: Gene expression analysis in T cells from spleens of mice that provide a model for systemic lupus erythematosus

summary: This laboratory focuses on the interactions of murine CD4+CD25+ regulatory T cells (Tregs) with CD4+CD25- T cells, both from a fundamental biological point of view, and in the context of a murine model of lupus.

overall_design:
This study characterized the surface glycans expressed by CD25 and CD25- CD4 T cells selected from lupus-prone (systemic lupus erythematosus or SLE) mouse strains MRL/Mp and NZB/W F1 and two control strains, CBA/Ca (haplotype-matched with the MRL/Mp; H-2k) and BALB/c.
A transcriptomic survey of freshly isolated and bead-activated CD25 and CD25- CD4 T cells selected from mouse spleens was conducted using these four strains. Three replicate samples of each condition were hybridized to the GLYCOv2 array, for a total of 48 samples.

first: Oliver

last: Garden


title: Spliceostatin treatment on HeLa cells

first: BELEN

last: MINANA

summary: HeLa cell line treated with Spliceostatin or methanol

overall_design: Three biological replicates and one technical replicate were labeled in direct and dye-swap experiments.

first: Belen

last: Minana


title: Up regulation of lactosamine containing glycans

summary: Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets.

overall_design:
We have a mutant mouse (b3GNT2 KO) that up-regulates the expression of lactosamine containing glycans in a subset of olfactory neurons.
Gene expression profiling was performed using control and mutant mice that up-regulate the expression of lactosamine containing glycans in a subset of olfactory neurons. Glycosyltransferase expression that differed between control and mutant mice were identified.

first: Gerald

last: Schwarting


title: Technical comparison of qRT-PCR experiments with the GLYCOv2 custom array

summary: Gene expression patterns were surveyed using RNA from 4 different murine sources.

overall_design:
Four classes of RNA were analyzed: undifferentiated embryonic stem cells, differentiated ES cells, kidney and liver tissues.
Classes were prepared in triplicate for a total of 12 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array. Analysis results were used for comparison with parallel experiments using qRT-PCR.

first: Kelley

last: Moremen


title: Influence of inflammation on the expression and activity of glycosyltransferases in human bronchial mucosa

summary: Bronchial inflammation is common in patients suffering from Cystic Fibrosis (CF) and is commonly responsible for mortality from CF. It is known that this inflammation has an influence over glycosylation events in bronchial mucins and abnormal glycosylation has been described in CF. These abnormalities can not be directly linked to CF, as the cells that secrete bronchial mucins do not express CFTR.

overall_design:
This study is to determine if bronchial inflammation could be responsible for abnormal glycoslylation in CF. Pro-inflammatory cytokines TNF, IL6, and IL8, as well as anti-inflammatory cytokine IL10 are present and seem to have active roles in the respiratory tree of CF patients.
In this study, the effects of these cytokines on the expression of glycosyl- and sulfotransferases involved in the biosynthesis of O-glycans in the bronchial cell line Calu-3 were analyzed. Three replicates for each cytokine treated group and controls were hybridized to GLYCOv2 array.

first: Sophie

last: Groux-Degroote


title: Developmental gene expression differences between neonatal and adult mouse atria and ventricles

summary:
We study the role of glycosylation in ion channel function. Specfically, we are focusing on how ion channel glycosylation modulates, controls, and impacts cardiac, skeletal muscle, and neuronal electrical activity.
We wish to determine differences in gene expression through development and between the atria and ventricles of the mouse heart. Our data indicate differential sialylation directly affects voltage-gated sodium channel function through the developing heart in a chamber-specific manner. We wish to expand our findings to include other ion channels involved in the cardiac action potential, and to eventually create a map of the cardiac conduction system that details the role of differential glycosylation in cardiac excitability. Determining differential expression of the genes that regulate ion channel glycosylation is vital to these goals.

overall_design: We analyzed four sets of pooled RNA to be run in triplicate: one each from neonatal and adult mouse atria and ventricles.

first: Eric

last: Bennett


title: FGF2 sustains NANOG and switches the outcome of BMP4 induced human embryonic stem cell differentiation

city: madison

first: James

last: Thomson

state: Wisconsin

address: 425 Henry Mall

department: Regenerative Biology

institute: Mogridge Institute for Research

summary: NANOG has emerged as a central gatekeeper of pluripotency. Here we show that as human embryonic stem (ES) cells exit the pluripotent state, NANOG can play a key role in determining lineage outcome. It has previously been reported that BMPs can induce differentiation of human ES cells into extraembryonic lineages. Here we report that FGF2 switches BMP4 induced differentiation outcome to mesendoderm, characterized by the uniform expression of T (brachyury) and other primitive streak markers. Blocking the MEK-ERK pathway either by chemical inhibitors or by an ERK-specific phosphatase (DUSP6) blocks the FGF2-mediated lineage switch. Active MEK-ERK signaling prolongs NANOG expression during BMP-induced differentiation. Forced NANOG expression results in FGF independent BMP4 induction of mesendoderm, and knockdown of NANOG greatly reduces T induction. Together, our results demonstrate that FGF2 signaling switches the outcome of BMP4 induced differentiation of human ES cells by maintaining NANOG levels through the MEK-ERK pathway.

overall_design: There are three sets of expression data. Set 1 (14 samples) is 5day human ES cells (H1) differentiated with different concentrations of BMP4, in the presence or absence of FGF2. Set 2 (14 samples) is 50ng/mL of BMP4 induced H1 cells differentiation time course, with or without FGF2. Set 3 (22 samples) is 5ng/mL of BMP4 induced H1 cells differentiation time course, with or without FGF2.

first: P

last: Yu

first: R

last: Stewart

first: S

last: Tian

first: J


title: Elucidating mechanisms by which regulated expression of proteoglycans and glycosylation-related genes in the striatum contribute to Huntington disease

summary:
This laboratory focuses on the molecular mechanisms of neuropsychiatric and neurodegenerative disorders
Our goal is to elucidate mechanisms by which regulated expression of proteoglycans and glycosylation-related genes contribute to neurodegenerative diseases involving the striatum. A number of studies have demonstrated that neural proteoglycans are involved structural organization of the striatum and formation of dopaminergic connections to and from the striatum. Several proteoglycans are also associated with neuronal regeneration and some have been shown to be components of filamentous inclusions found in neurodegenerative disorders. In addition, the localization and proper function of dopamine receptors, which are predominantly expressed in the striatum, are governed by N-linked glycosylation events. Huntingtonís Disease (HD), a progressive neurodegenerative disorder, results in selective degeneration of the striatum. This is caused by a mutation in the protein, huntingtin, however, the mechanisms responsible for neuronal degeneration remain unknown. Similar to the brains of HD patients, HD transgenic mice exhibit huntingtin protein aggregation and nuclear inclusions, selective degeneration of dopamine neurons in the striatum and dopamine receptor dysfunction.

overall_design: In this study, the gene expression patterns of HD transgenic mice were analyzed. Four groups, pre-symptomatic HD mice (6 weeks old), WT control (6 weeks), post symptomatic HD (16 weeks), and WT control (16 weeks), were hybridized and analyzed using the GLYCOv2 array. Each group was hybridized in triplicate.

first: Elizabeth

last: Thomas


title: TLR3, TLR7, and TLR9 stimulation in murine dorsal root ganglion neurons

city: Bethesda

first: O M Zack

last: Howard

state: MD

address: 6701 Rockledge Dr.

department: DBIB

institute: NIH/CSR

summary: TLR3, TLR7, and TLR9 stimulation induces many mouse inflammatory and autoimmune cytokines or immune receptors

overall_design: DRGN were cultures 5 days prior to a 16 hour stimulation - Three separate studies were analyzed for inflammatory response

first: Jia

last: Qi

first: O

middle: Z


title: High Resolution Array CGH Identifies Common Mechanisms that Drive Embryonal Rhabdomyosarcoma Pathogenesis

status: Public on Mar 01 2011

city: Dallas

first: Vera

middle: Ashley

last: Paulson

state: TX

address: 5323 Harry Hines Blvd

department: Pediatric Hematology-Oncology

institute: UT Southwestern

type: Genome variation profiling by genome tiling array

summary:
gDNA was obtained from 26 frozen ERMS tumors for aCGH and copy number analysis
Tumors compared to nimblegen pooled male reference, using 2.1 Million probe Nimblegen array CGH Build 18 NCBI36

overall_design: 26 ERMS tumors compared to nimblegen pooled male reference

first: John

last: Cameron


title: Counteractive balancing of transcriptome expression involving CodY and CovRS in Streptococcus pyogenes

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

summary:
Streptococcus pyogenes (group A Streptococcus, GAS) responds to environmental changes in a manner that results in an adaptive regulation of the transcriptome. Global transcriptional regulators are able to integrate important extracellular and intracellular information and are responsible for modulation of the transcriptional network. The roles of several global transcriptional regulators in adaptation and virulence gene expression have been described.
In this study we used microarray to investigate the regulatory roles of CodY and CovRS played in Streptococcus pyogenes.
keywords: genetic modification

overall_design: Streptococcus pyogenes NZ131 wild-type cells, ΔcodY, ΔcovRS and ΔcodYcovRS strains were grown in C-medium until mid-exponential phase or early-stationary phase. The transcriptional profile of the whole genome was examined with microarray.

first: Zhiyun

last: Chen

first: Joseph

last: Ferretti

first: Horst

last: Malke


title: Global Profiling of Activin Target Genes in Mouse Granulosa Cells

city: Evanston

first: Jingjing

last: Kipp

state: IL

address: 2205 Tech Dr.

institute: Northwestern University

summary: In order to understand the mechanisms and pathways by which activin regulates follicle function, we performed a microarray study and identified activin regulated genes in mouse ovarian granulose cells.

overall_design: Primary cultured ovarian granulosa cells collected from day 21-23 old immature mice were treated with Activin A (A), Activin A plus its antagonist follistatin (AplusF), and PBS (P, vehicle) for 24 h. RNA from each treatment group was isolated and the experiments were repeated four times. Samples from experiment one were assigned as P1, A1 and A+F1, samples from experiment two as P2, A2 and A+F2, and so on.  About 100 ng of each RNA sample was amplified using a modified Eberwine T7-based amplification protocol and hybridized to the Illumina Sentrix Mouse-6 Expression BeadChip (Illumina, Inc., San Diego, CA) that contains 48,000 sets of oligonucleotides.

middle: L

first: Kelly

last: Mayo


title: Change in gene expression in Chlamydomonas reinhardtii upon heat shock

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

summary: This was an accompanying experiment. Previously, the expression of genes hsp70A and hsp70B had been established as being tetrapyrrole-dependent (Kropat et al., 1997, 2000). Since both are well-known heat-shock proteins, we performed a one-step heat shock treatment by shifting the temperatures from 23°C to 42°C for 45 min. Moreover, this experiment served as an additional global control to further test the reliability of the microarray and our general conditions since the heat shock response in general is quite well investigated. 3988 responding genes were identified. Among them are 22 genes known to be regulated by HS, selected examples are: the heat shock proteins 22A, 22B and 22C, here leading the list of top-regulated genes on place 1 with a FC of 91297 (22A), place 3 with a FC of 45023 (22B) and place 5 with a FC of 6570 (22C). Other examples are several DnaJ-like proteins or the ClpB chaperone, from the Hsp100 family.

overall_design: In total the analysis comprises 8 samples.  For heat shock, a 20 ml culture with ~4 × 106 cells per ml in a 100 ml Erlenmeyer flask was incubated at 42°C for 45 min in the light with shaking. Control cultures were incubated in the light at 23°C (von Gromoff et al., 1989; Kropat et al., 2000). For harvest, cultures were chilled immediately by pouring them onto crushed ice, centrifuged (5 min, 3000 g, 4°C) and resuspended in 1 ml TAP. This procedure was repeated three times, resulting in 3 biological replicates.

first: Wolfgang

last: Hess


title: SYSTEMATIC TRANSCRIPTIONAL PROFILING OF THE LIVER, HEART, SKELETAL MUSCLE, AND ADIPOSE TISSUE IN INSULIN RESISTANT, DIET-INDUCED OBESE C57BL/6J MOUSE

city: Calgary

first: Jane

last: Shearer

state: AB

address: 2500 University Drive NW

department: Kinesiology

institute: University of Calgary

summary: Following 20wk of either chow or high fat feeding, tissues were collected from C57BL/6J mice. Gene expression in four tissues that have been associated with obesity-related metabolic complications: white adipose tissue (WAT), skeletal muscle, the liver, and the heart were examined.  Data suggest that some tissues may be attempting to reduce the metabolic perturbations that occur in the early stages of obesity. Also, many identified genes were associated with a variety of disorders, thereby serving as potential links between obesity and related health risks.

overall_design: After 3 wk of weaning, male C57BL/6J littermates were randomly separated into control (n=6) and treatment (n=6) groups for each tissue. After an acclimatization period of 1wk, animals were given free access to a chow diet (23% protein, 21% fat, and 55% carbohydrate) or a high fat (HF) diet (15% protein, 59% fat, and 26% carbohydrate) for 20wk. Following the feeding period, animals were fasted for 6h, anesthetized with pentobarbital, and weighed. Blood glucose was assessed in anesthetized mice. Non-esterified fatty acids and immunoreactive insulin was assayed with a double antibody method. Samples of WAT, the liver, gastrocnemius muscle and heart were obtained, frozen with liquid nitrogen, and stored at -80oC until subsequent use. Tissue samples were homogenized at short intervals of time and total RNA was isolated using cold TRIzol (Invitrogen, Ontario, Canada)  to prevent RNA degradation. Cdna was prepared to perform the microarrays. For every treatment sample and its corresponding control, two microarrays were performed in a dye-swap normalization experiment. Mouse M7K microarray chip from the Southern Alberta Microarray Facility (University of Calgary, Calgary, AB) were used (GEO Accession: Platform GPL3965).

first: Robyn

middle: K

last: Lee

first: Su

last: Lin

first: Vongai

last: Nyamandi

first: Mayi

last: Arcellana-Panlilio

first: Dustin

last: Hittel

first: Christoph

last: Sensen


title: Examination of DPY-30, DPY-27, SDC-3, DPY-26, MIX-1, SMC-4, ASH-2, RNA Polymerase II binding in wild type and DCC mutant embryos

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

institute: HHMI/UCB

summary: Here we exploit the essential process of X-chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome-wide binding, and function of gene  regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. The DCC binds to two categories of sites on X: rex sites that recruit the DCC in an autonomous, sequence- dependent manner, and dox sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DCC mutants that abolish rex-site binding do not eliminate dox-site binding, but instead reduce it to the level observed at autosomal binding sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex-site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites exhibit similar binding properties. Our data support a model for DCC binding in which low-level DCC binding at dox and autosomal sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then greatly elevates DCC binding to dox sites in cis, which lack intrinsically high DCC affinity on their own. We also show here that the C. elegans DCC achieves dosage compensation through its effects on transcription.

overall_design: ChIP-chip experiments using antibodies against DPY-27, SDC-3, DPY-30, DPY-26, MIX-1, SMC-4, ASH-2 in wild-type embryos.  ChIP-chip experiments using antibodies against SDC-3, DPY-27, DPY-30, ASH-2, and IgG in different DCC mutants.  ChIP-chip experiments using antibodies against RNA Pol II (hypophosphorylated and S2 and S5) in wild type and sdc-2 partial loss of function mutants.

first: Rebecca

last: Pferdehirt

first: William

last: Kruesi


title: An antibody to Streptococcus pneumoniae capsular polysaccharide enhances quorum sensing

city: Bronx

first: Masahide

last: Yano

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: The primary mechanism by which pneumococcal capsular polysaccharide-based vaccines are believed to mediate protection is by induction of serotype-specific opsonic antibodies that facilitate bacterial killing by phagocytes (opsonophagocytosis).  However, antibodies that are protective against experimental pneumococcal pneumonia in mice but do not promote opsonophagocytic killing in vitro have also been identified 1-3.  Such non-opsonic antibodies are associated with bacterial clearance in vivo, but the mechanism by which this occurs is unknown.  In this letter, we demonstrate that a protective, non-opsonic serotype 3 pneumococcal capsular polysaccharide-specific monoclonal antibody (MAb) enhances quorum sensing, which results in competence induction and fratricide of serotype 3 pneumococcus.  Gene expression profile analysis revealed that the MAb together with the pneumococcal autoinducer, competence stimulating peptide 2 (CSP2), augments differential expression of competence (com) related bacteriocin-like peptide (blp) genes that are known to be involved in pneumococcal fratricide. Taken together, these findings reveal a previously unsuspected mechanism of antibody action, namely, enhancement of quorum sensing and bacterial fratricide.  Given that this activity does not require phagocytes, antibodies that function accordingly may hold promise as adjuncts to current vaccines or as desired products of next generation pneumococcal vaccines.

overall_design: 6 samples

first: Shruti

last: Gohil

first: Liise-anne

last: Pirofski


title: The Effect of GATA6 on miRNA in Lung Development

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 421 Curie Blvd

department: Medicine

institute: Univeristy of Pennsylvania

summary: Gata6 regulates lung epithelial stem cell development and airway regeneration.  Here, the expression profile of microRNA was investigated when Gata6 was depleted during lung development.

overall_design: Analysis used total RNA from Sftpc-rtTA:tetO-cre lungs at E14.5 as control samples (WT) for comparison to the experimental samples of total RNA from Gata6flox/flox: Sftpc-rtTA: tetO-Cre mutant lungs at E14.5.

first: Edward

last: Morrisey

first: Yuzheng

last: Zhang


title: Change in gene expression in Chlamydomonas reinhardtii upon feeding with hemin and Mg-protoporphyrin

first: Bjoern

last: Voss

summary: The tetrapyrroles Mg-protoporphyrin IX (MgProto) and heme, in Chlamydomonas reinhardtii only synthesized within the chloroplast, have been implicated in retrograde control of nuclear gene expression in this unicellular green alga. However, feeding of the two tetrapyrroles to Chlamydomonas cultures growing in the dark has previously been shown to transiently induce 5 nuclear genes, among them three genes coding for the chloroplast heat shock proteins HSP70A, B and E. Here, we measured the impact of MgProto and hemin feeding in the dark on changes in gene expression at the genomic level. About 10% of the 10000 genes represented on the microarray showed a transient up or down regulation with a fold change of 4 or more (p ≤0.05). The two most prominent groups of regulated genes were those where both MgProto and heme caused either an up or down regulation. Minor regulatory groups consisted of genes which were either down- or up-regulated by one of the tetrapyrroles but not by the other. In contrast, feeding of protoporphyrin IX had no regulatory effect on a number of selected genes. Interestingly, 499 of the 982 responding genes were also regulated by heat shock; 85% of those showed the same response (up or down) as seen after MgProto/heme feeding, indicating a previously not anticipated role of MgProto and heme in stress response. Indeed, most prominent among the functional groups of annotated genes up or down regulated by the tetrapyrroles were those whose gene products are involved in protein folding and/or protein degradation. Striking is the virtual absence of regulated genes that encode constituents of the photosynthetic apparatus. This and the transient nature of changes in gene expression observed upon feeding of the tetrapyrroles suggest a signaling role of these plastid compounds in the adaptation of the alga to alterations in the environment.

overall_design: In total the analysis comprises 32 samples. A starter culture grown in the light with ~2 × 10e6 cells per ml was subdivided into 25 ml aliquots in 100 ml Erlenmeyer flasks and incubation continued in the dark for 16 h. At time 0, MgProto or hemin (final concentration 9 μM each) was added to the cultures in the dark and incubation in the dark was continued until harvest. Control cultures were treated the same way but did not receive the tetrapyrroles. Cells were harvested at time points 0 min, 60 min, 120 min and 180 min. This procedure was repeated one time, resulting in 1 biological replicate.

first: Wolfgang

middle: R

last: Hess


title: Spatial transcriptomic analysis of the Arabidopsis thaliana - Botrytis cinerea interaction

city: Cape Town

first: Joseph

middle: Mary Kusasira

last: Mulema

state: Western Cape

address: Private Bag, Rondebosch

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

summary: A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores.

overall_design: Three Biological replicates were done of which the third replicate was a dye-swap. In total 12 samples were analyzed. Each array constituted one replicate making six arrays for the whole experiment.

first: Katherine

last: Denby


title: Transcriptional profile of EHEC O157 TUV93-0 overexpressing PsrA or PsrB

status: Public on Apr 03 2011

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: PsrA and PsrB were found to repress Type III secretion (T3S) when provided in multicopy. Total RNA was extracted at late exponential phase in T3S permissive media (MEM-HEPES). Transcriptional profiles were expressed relative to the vector control (pGEM).

overall_design: Dual colour design. Cy5 labelled cDNA from TUV93-0 pPsrA or pPsrB cultures were hybridised against TUV93-0 pGEM Cy3 labelled cDNA. Data were normalised using the Genespring GX 7.3.1 analysis package.


title: Temporal transcriptomic analysis of the Arabidopsis thaliana - Botrytis cinerea interaction

summary: Transcriptional profiling of Arabidopsis leaves comparing mock-treated leaves with Botrytis cinerea infected leaves over a time-course (12 and 24 hrs).

overall_design: Two-condition experiment, Mock-treated vs infected leaves. Biological replicates: 5 Mock-treated, 5 infected, independently grown and harvested. One replicate per array.


title: Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNAs by HIV-1

city: Columbus

first: Amy

middle: M

last: Hayes

state: OH

address: 1925 Coffey Rd

department: Veterinary Biosciences

institute: Ohio State University

summary:
Herein expression trends of host miRNA were measured in CEMx174 lymphocytes infected with HIV-1NL4-3 or derivative strains deficient in Tat RSS activity (RSS) or vif-/vpr (VV), or unexposed to virus.  As expected from previous studies, miRNA trends were different in naive and HIV-1 infected cells.   Moreover, miRNA expression trends were similar for HIV-1 and vif-/vpr-deficient HIV-1, but diverged for RSS.  Rather than generalized changes in miRNA levels, HIV-1 bearing the Tat K51A RSS mutation changed the steady state of a subset of miRNAs. The results are attributable to reduction in miRNA stability or change in miRNAs activity that altered steady state expression.  Comparison of the miRNA expression trends in patient PBMC and the CEMx174 lymphocytes determined >50% overlap with a subset of miRNAs identified in patients, supporting the utility of HIV-1 cell culture model to refine experimental design with patient samples, which represent miRNA profiles of co-isolated infected and uninfected cells.
Our results indicate that ablation of Tat RNA silencing suppressor activity in HIV-1 changes the steady state of a subset of host mature miRNA. The observation reinforces the concept of active HIV-1 interplay with host small RNAs that modulate replication and spread. The study validated the utility of derivative HIV-1 strains to explore the interface of viral genes with host small RNA activity.

overall_design: In this study the microRNA profiles of CEMx174 cells infected with HIV-1 NL4-3 or derivative viruses deficient in Vif/Vpr or Tat RNA silencing suppressor activity were compared to mock infected cells.  The samples were analyzed in duplicate.

first: Shuiming

last: Qian

first: Wu

last: Li

first: Kathleen

last: Boris-Lawrie


title: Novel biomarkers for high grade T-cell lymphoma

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Mature NK and T-cell lymphomas are occasionally encountered in Asia but are very rare in Western populations. In part due to its rarity, little is known about this group of neoplasms, and despite being rather different disease entities, they are all treated similarly but with diverse clinical outcomes. Novel biomarkers (at both the genetic and protein levels) are needed to resolve diagnostic difficulties, improve prognostication and develop targeted therapies. To rectify this deficiency, we interrogated the transcriptome of several NK and mature T-cell lymphomas by whole-genome expression profiling for new markers that may further stratify this diverse group of conditions. Our initial efforts have identified a promising candidate marker that appears to differentiate NKTL lymphoma from other forms of T-cell neoplasms, and this finding has been validated by immunohistochemistry on archival material in a large number of patient cases.

overall_design:
Correlating gene expression status with tumor type.
Gene expression profiling was performed on 8 cases of angioimmunoblastic T-cell lymphoma (AITL), 4 cases of natural killer T-cell lymphoma (NKTL), and 6 cases of peripheral T-cell lymphoma - unspecified (PTCL-U). In addition, expression profiling was performed on one xenograft tumor, which was derived from a primary NKTL, and its cultured line.


title: Sex-different hepatic glycogen content, glucose and amino acid output in rats.

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

summary:
In the present study we tested the hypothesis that male and female rat livers respond differently to a change in nutrient availability or to insulin treatment. We compared hepatic gene expression, hepatic glycogen and glucose output, insulin sensitivity and amino acids, using healthy rats.

Keywords: Hepatic gene expression, sex-differences

overall_design: Two-condition experiment. Biological replicates: 4 male rat livers from rats on a standard diet and 4 female rat livers from rats on a standard diet.  One replicate per array.

middle: E

first: Kamal

last: Yassin

first: Louisa

last: Cheung

first: Moira

last: Lewitt

first: Kerstin

last: Brismar

first: Claes-Göran

last: Östenson

first: Gunnar

last: Norstedt

first: Petra

last: Tollet-Egnell


title: Global changes of gene expression during scleroglucan synthesis in Sclerotium rolfsii

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

institute: Technische Universität München

summary:
Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads earlier. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases.
Our first transcriptomic analysis, comparing an early stage of scleroglucan synthesis in high-level and low-level producing media, uncovered that most differentially expressed unigenes belong to the functional categories ‘metabolism’ and ‘transport’ (Schmid et al., 2010). In order to get more insights into transcriptional regulation of scleroglucan production, we extended in this study our transcriptomic analyses. We determined transcriptomic profiles for a later stage of cultivation in both media, thus giving us the opportunity to study temporal phenomena under high- and low-level producing conditions.

overall_design: Tailor-made microarrays (44K multiplex chip, Agilent) were designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the 454 unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene.   For comparative expression profiling, total RNA was isolated from S. rolfsii, cultured for 61 h in EPSmax13 (biological triplicate) and EPSmin17 media (biological triplicate). RNA quality control, synthesis of Cy3-labeled cRNA including cRNA purification and cRNA quality control, microarray hybridization, scanning and data extraction (Agilent´s feature extraction software) were performed by imaGenes GmbH. Expression data were analyzed by imaGenes GmbH using an in-house developed data analysis pipeline. After quantile normalization, genes were defined as differentially expressed if their expression levels varied at least 2 fold in EPSmax13 samples compared to EPSmin17 samples and if the difference was statistically significant (Student’s t-test, P-value cut-off of 0.05).

first: Boris

last: Winter

first: Dirk

last: Müller-Hagen

first: Ulf

last: Stahl

first: Volker

last: Sieber

first: Vera

last: Meyer


title: Expresion analyses of red1∆

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Investigation of whole genome gene expression level changes in red1∆, compared to the wild-type strain.

overall_design: A chip study using total RNA recovered from two separate wild-type cultures of fission yeast and two separate red1∆ cultures of fission yeast.  Each chip measures the expression level of 1997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.


title: Mixing Experiment - Mouse Kidney and Spleen

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: The design of this experiment was based on the assumption that transcript levels will change linearly while going from 100 percent of one tissue to 100 percent of the other. This assumed linear data set could be used to evaluate various issues related to low-level microarray data analysis.

overall_design:
Hybridization cocktails from two mouse tissues, kidney and spleen, were prepared and mixed in a range of ratios and applied to 4-5 replicate GLYCOv1 chips for analysis.
The mixture ratios were as follows: 100 percent kidney, 75 percent Kidney/25 percent spleen, 50 percent kidney/50 percent spleen, 25 percent kidney/75 percent spleen, and 100 percent spleen.


title: eQTL mapping in 57 F1 diversity lines of Arabidopsis thaliana

city: Chicago

first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

summary: eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions

overall_design: 57 F1 lines without replicates, the 5th or 6th true leaf

first: Xu

last: Zhang

first: Andy

last: Cal

middle: O


title: Comparison of DPY-27 binding in embryos and fed L1 larvae

first: Barbara

department: MCB

summary:
Here we exploit the essential process of X-chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome-wide binding, and function of gene  regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. The DCC binds to two categories of sites on X: rex sites that recruit the DCC in an autonomous, sequence- dependent manner, and dox sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DCC mutants that abolish rex-site binding do not eliminate dox-site binding, but instead reduce it to the level observed at autosomal binding sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex-site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites exhibit similar binding properties. Our data support a model for DCC binding in which low-level DCC binding at dox and autosomal sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then greatly elevates DCC binding to dox sites in cis, which lack intrinsically high DCC affinity on their own. We also show here that the C. elegans DCC achieves dosage compensation through its effects on transcription.
The processed data files available here were used in Figure 6 of the paper which references this data.

overall_design: ChIP-chip experiments using antibodies against DPY-27 in wild type mixed embryos and fed L1 larvae.

first: Rebecca

last: Pferdehirt

first: William

last: Kruesi


title: Genome-wide analysis of Dnmt3L heterozygous and wildtype spermatocytes and spermatids

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Comparison of gene expression differences between Dnmt3L heterozygous and wildtype pachytene spermatocytes, and similarly between Dnmt3L heterozygous and wildtype round spermatids which were isolated from the Dnmt3L knockout mouse line. This array was conducted to address the hypothesis that Dnmt3L heterozygosity results in deregulated gene expression within spermatocytes and spermatids. Results show that Dnmt3L heterozygosity causes numerous genes to be differentially regulated on a genome-wide level, showing that DNMT3L has an important role in regulating gene expression within these male germ cells.

overall_design: Three preparations each of Dnmt3L purified wildtype spermatocytes, wildtype spermatids, heterozygous spermatids, and two preparations of heterozygous spermatocytes were isolated for a total of 11 samples. Each preparation was made up of cells isolated from 10 mice.

first: Natasha

last: Zamudio

first: Moira

last: O'Bryan

first: Charity

last: Law


title: Hierarchical regulation in a KRAS-dependent transcriptional network revealed by a reverse-engineering approach

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite

summary: Mutations in RAS proteins occur in 30% of human tumours and have a high relevance in tumor progression. Despite the importance of the underlying genetic network that governs the effects of oncogenic RAS, it is still poorly understood. We developed and applied a reverse-engineering approach in order to reconstruct the network structure of the signaling and gene-regulatory network downstream of RAS from perturbation experiments. We performed microarray, RT-PCR and Western Blot analysis to detect mRNA and protein levels of cytoplasmatic and nuclear targets downstream of RAS after systematic perturbation of the signaling pathways and knock-down of selected transcription factors in KRAS-transformed ovarian surface epithelium cell lines. The reconstructed model shows that the investigated components are connected through a complex network. The transcription factors decomposed into two hierarchically arranged groups. While knock-down of all investigated transcription factors showed a partial reversion of the malignant phenotype, different growth assays show that these two groups of transcription factors control different functions in the malignant anchorage-independent growth and cell cycle regulation of the ROSE cells. Furthermore, the model showed strong regulatory interplay of inhibitory and activating interactions between the RAS-dependent trancriptional network and cytoplasmatic signaling components.

overall_design: Overall the study contains 32 samples. We studied the influence of seven transcription factors (Fosl1, Gfi1, Hmga2, Junb, Klf6, Otx1, Rela) being knocked down by means of RNA interference. Two independent siRNA duplexes (N1, N2) against the same gene were used. All experiments were done with Cy3/Cy5 dye-swaps. As a negative control, we used scrambled siRNAs. Off-target effect was estimated by comparison of the scrambled siRNA treatment and an unterated cell line ROSEA 25.

first: Iwona

last: Stelniec


title: Inflammatory gene expression in response to sublethal phosgene exposure in Balb/c mice

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

institute: Dstl

summary: Phosgene is a lung damaging chemical warfare agent which can cause death by the inhalation route. In this study the inflammatory response to phosgene was mapped over a 96h time-course using a custom microarray in the Balb/c mouse.

overall_design: Three groups of six mice were exposed to phosgene and a three groups exposed to an air only control. Following exposure mice were culled at 6 timepoints (1, 4, 7, 24, 48 and 96h). RNA was extracted and run on the custom array.

first: Gareth

last: Griffiths


title: Expression patterns of cancer-related genes and their putative antisense transcripts in normal and colon cancer tissues

city: Fujisawa

first: Rintaro

last: Saito

state: Kanagawa

address: 5322 Endo

institute: Keio University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Background: Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type.
Results: To discover novel antisense transcripts encoded in the antisense strand of important genes, such as cancer-related genes, we conducted expression analyses of antisense transcripts using our custom microarray platform along with 2376 probes designed specifically to detect the potential antisense transcripts of 501 well-known genes suitable for cancer research. Using colon cancer tissue and normal tissue surrounding the cancer tissue obtained from 6 patients, we found that antisense transcripts without poly(A) tails are expressed from approximately 80% of these well-known genes. This observation is consistent with our previous finding that many antisense transcripts expressed in a cell are poly(A)-. We also identified 101 and 71 antisense probes displaying a high level of expression specifically in normal and cancer tissues respectively. Some of these probes showed characteristic expression patterns which are anti-correlated with the expression patterns of the sense genes.
Conclusion: Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation.

overall_design: 501 probes targeting well-known genes suitable for cancer researches were designed. Additionally 2,376 probes targeting putative transcription units on the antisense strand of these genes were designed. Samples were obtained from colon cancer tissues and normal tissues surrounding cancer tissues of six patients.

first: Keisuke

last: Kohno

first: Yuki

last: Okada

first: Yuko

last: Osada

first: Koji

last: Numata

first: Chihiro

last: Kohama

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Akio

last: Kanai

first: Hiroshi

last: Yasue

first: Soichiro

last: Murata

first: Kuniya

last: Abe

first: Masaru

last: Tomita

first: Nobuhiro

last: Ohkohchi

first: Hidenori

last: Kiyosawa


title: Tasquinimod, a Quinoline-3-Carboxamide Anti-Angiogenic Agent, treated Prostate Cancer Cell Line in-vivo and in-vitro

city: Lund

first: Johan

last: Vallon-Christersson

address: Lund University

department: Department of Oncology, Clinical Sciences

institute: Lund University

summary:
The quinoline-3-carboxamide ABR-215050 (Tasquinimod (INN)), exhibits anti-tumor activity via inhibition of tumor angiogenesis in human and rodent tumors. To further explore the mode of action of ABR-215050, in vivo experiments with gene microarray analysis were performed using samples of LNCaP prostate tumors excised from nude mice exposed to ABR-215050 for 24h at 10 mg/kg(ad.lib.). The array data were validated by real-time PCR (sqRT-PCR), as well as by protein expression experiments. Among several significant differentially expressed gene after exposure to ABR-215050, were cytokine receptor CXCR4, cytochrome P450 1A1 (CYP1A1), thrombospondin-1 (THBS1) and Lysyloxidase  preprotein (LOX).

To further explore the mode of action of ABR-215050, in vitro experiments with gene microarray analysis were performed using LNCaP prostate tumor cells. The array data were validated by real-time PCR (sqRT-PCR), as well as by protein expression experiments. One of the most significant differentially expressed genes after exposure to ABR-215050, was thrombospondin-1 (THBS1).

overall_design: 2-color treatment vs. control microarray experiment comprising four biological replicates. Each biological replicate was hybridized with dye-swap; resulting in eight hybridizations for each dataset (in vitro and in vivo), for a total of 16 hybridizations.

first: Anders

last: Olsson

last: Björk

first: John

middle: T

last: Isaacs

first: Tomas

last: Leanderson


title: Expression patterns of sense-antisense transcripts in normal and cancer tissues

first: Rintaro

last: Saito

summary: We characterized the expression patterns of sense-antisense transcripts, based on available cDNA sequences, in colon (colorectal) cancer tissues and in normal tissues surrounding the cancer tissues. Although expression balances (ratios) of most of sense and antisense transcript pairs did not change between patients or between normal and cancer tissues, we found 68 sense-antisense transcripts whose expression balances were altered specifically in colon cancer tissues.

overall_design: We conducted DNA microarray analyses by using the same set of probes designed for 2621 sense-antisense pairs to detect transcripts expressed in colon cancer tissues. These probes comprise 2358 pairs for the detection of protein-coding transcripts only, 250 pairs for the detection of protein-coding transcripts paired with non-protein-coding transcripts, and 13 pairs for the detection of non-protein-coding transcripts only.

first: Keisuke

last: Kohno

first: Yuki

last: Okada

first: Yuko

last: Osada

last: Numata


title: Definition, conservation and epigenetics of housekeeping and tissue-enriched genes

city: Seattle

first: Xinwei

last: She

state: WA

address: 401 Terry Ave. N

department: Molecular Informatics

institute: Rosetta Inpharmatics, Merck

summary:
Background
Housekeeping genes (HKG) are constitutively expressed in all tissues while tissue-enriched genes (TEG) are expressed at a much higher level in a single tissue type than in others.  HKGs serve as valuable experimental controls in gene and protein expression experiments, while TEGs tend to represent distinct physiological processes and are frequently candidates for biomarkers or drug targets.  The genomic features of these two groups of genes expressed in opposing patterns may shed light on the mechanisms by which cells maintain basic and tissue-specific functions.
Results
Here, we generate gene expression profiles of 42 normal human tissues on custom high-density microarrays to systematically identify 1,522 HKGs and 975 TEGs and compile a small subset of 20 housekeeping genes that can be used as experimental reference and are superior to many commonly used HKGs.  Cross-species comparison shows that both the functions and expression patterns of HKGs are conserved. TEGs are enriched with respect to both segmental duplication and copy number variation, while no such enrichment is observed for HKGs, suggesting the high expression of HKGs are not due to high copy numbers. Analysis of genomic and epigenetic features of HKGs and TEGs reveals that the high expression of HKGs across different tissues is associated with decreased nucleosome occupancy at the transcription start site as indicated by enhanced DNase hypersensitivity.  Additionally, we systematically and quantitatively demonstrated that the CpG islands' enrichment in HKGs transcription start sites (TSS) and their depletion in TEGs TSS.  Histone methylation patterns differ significantly between HKGs and TEGs, suggesting that methylation contributes to the differential expression patterns as well.
Conclusions
We have compiled a set of high quality HKGs that should provide higher and more consistent expression when used as references in laboratory experiments than currently used HKGs. The comparison of genomic features between HKGs and TEGs shows that HKGs are more conserved than TEGs in terms of functions, expression pattern and polymorphisms.  In addition, our results identify chromatin structure and epigenetic features of HKGs and TEGs that are likely to play an important role in regulating their strikingly different expression patterns.

overall_design: PolyA+ purified RNA pooled from multiple donors of a single human tissue type (e.g. cerebellum) were amplified with random primers and hybridized on a two-color ink-jet oligonucletodie microarray  against a common reference pool, comprising ~20 normal adult tissue pools, on custom microarray patterns. Total 42 normal human tissues were testes against the pools.


title: Chromosome length influences replication-induced topological stress

status: Public on Feb 28 2011

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary: During chromosome duplication the parental DNA molecule becomes over-wound, or positively supercoiled, in the region ahead of the advancing replication fork. To allow fork progression this superhelical tension has to be removed by topoisomerases, which operate by introducing transient DNA breaks. Positive supercoiling can also be diminished if the advancing fork rotates along the DNA helix, but then sister chromatid intertwinings form in its wake. Despite these insights it remains largely unknown how replicationinduced superhelical stress is dealt with on linear, eukaryotic chromosomes. Here we show that this stress increases with the length of budding yeast chromosomes. This opens for the possibility that superhelical tension is handled on a chromosome scale and not only within topologically closed chromosomal domains as the current view predicts. We found that inhibition of type I topoisomerases leads to a late replication delay of longer, but not shorter chromosomes. This phenotype is also displayed by cells expressing mutated versions of the cohesin- and condensin–related Smc5/6 complex. The chromosomal association of the Smc5/6 complex is shown to increase in response to chromosome lengthening, chromosome circularization, or inactivation of Topoisomerase 2, all having the potential to increase the number of sister chromatid intertwinings 3. Furthermore, non-functional Smc6 reduces the accumulation of intertwined sister plasmids after one round of replication in the absence of Topoisomerase 2 function. Our results demonstrate that the length of a chromosome influences the need of superhelical tension release in Saccharomyces cerevisiae, and allow us to propose a model where the Smc5/6 complex facilitates fork rotation by sequestering nascent chromatid intertwinings which form behind the replication machinery.

overall_design: Smc6、Nse4, and Scc2 profiles with or without topological tension was analyzed (in top2 mutant, cells with circular chromosome, and fragmented chromosome) . 17 ChIP samples and corresponding WCE fractions have been analyzed.


title: Role of the prophages in the Staphylococcus aureus pathogenesis

city: Rockville

first: Sarah

last: Akkoush

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

summary: Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA).  It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of ϕNM3, the hlb-converting phage in S. aureus Newman,  reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes.  In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process.

overall_design:
Following strains were grown in TSA broth:

Staphylococcus aureus USA300 (reference)
Staphylococcus aureus USA300 with deletion of ϕSa2usa (Query)
Staphylococcus aureus USA300 with deletion of ϕSa3usa (Query)
Staphylococcus aureus USA300 Prophage-free mutant (Query)
Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa2mw (Query)
Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa3usa (Query)
strain: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa (Query)

RNA samples were harvested at early log, midlog and stationary phase.Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

middle: B

last: Jones

first: Rosslyn

last: Maybank

first: Kenneth

last: Shatzkes

first: Fei

last: Sun

first: Taeok

last: Bae

first: Scott

middle: N

last: Peterson


title: Whole-genome in vitro expression analysis of F. tularensis isolates grown to mid log phase

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary:
This study was aimed to perform comparative expression analysis of both virulent and avirulent strains of F. tularensis with a goal to possibly identify genes unique to low and high virulent strains to understand their role, if any in virulence features of an isolate. Initially, thirty strains were selected representing both type A and type B clades of F. tularensis. Five strains failed to grow on Chamberlain's medium (Chamberlain 1965) and were excluded from the study. All the isolates were grown to mid-log phase in Chamberlain’s medium and the total RNA was collected by standard protocols for expression analysis. The samples were analyzed in duplicates. F. tularensis Schu S4, a known virulent strains was used as a reference strain for this study.

Chamberlain RE (1965) "Evaluation of Live Tularemia Vaccine Prepared in a Chemically Defined Medium," Applied Microbiology, 13(2): 232-5

overall_design: Twenty four query strains and one reference strain (FRAN016 Schu S4) were used in the hybridizations. Most of the hybridizations have more than one biological replicates, resulting in a total of fifty five samples analyzed.

first: Robert

last: Fleischman

first: Gagan

last: Pandya

first: Mark

last: Wolcott

first: David

last: Rozak

first: Bryan

last: Frank

first: Ming

last: Bu

first: Matt

last: Lewis

last: Braisted

first: Vasily

last: Sharov


title: Transcriptomic Response of Listeria monocytogenes throughout the Life Cycle

status: Public on Feb 24 2011

city: Summit Argo

first: Zengxin

last: LI

address: 6502 S Archer Rd

institute: NCFST

summary: A long-term-survival (LTS) phase in Listeria monocytogenes was recently discovered.  Cells in this phase are coccoid in shape, survive for at least 30 d without any decrease in viable cell numbers, and are very resistant to heat and high pressure.  However, how cells of L. monocytogenes transition to this long-term-survival phase is little understood.  Therefore, a whole-genome expression analysis was conducted to study the transcription profile of L. monocytogenes as it enters the LTS phase.  Transcription profiles at log, stationary and death phases were analyzed since differential gene expressions at these phases may contribute to the eventual transition to the LTS phase.  Specifically, cells of L. monocytogenes F2365 at log, stationary, death and LTS phases were obtained by incubating cultures in TSBYE at 35°C for 13 h, 17 h, 24 h and 168-336 h, respectively.  Also, to study cells transitioning from the LTS phase back to the log phase, 1 ml of the LTS-phase culture at 336 h was reinoculated into 100 ml of fresh TSBYE with incubation at 35°C for 8 h.  Total RNAs of all samples were extracted, reverse transcribed into cDNAs and then hybridized to the L. monocytogenes expression microarray (Roche NimbleGen).  During the transition from log phase to stationary phase, differential changes in gene expression involved genes associated with cell envelope, cell division, stress response, energy metabolism, protein synthesis and material transport.  During the transition from stationary to death phase, differential changes were observed in genes related to cell envelope, detoxification, pathogenesis, energy metabolism, protein synthesis and material transport.  When cultures transitioned from death phase to 168-h LTS phase, significant downregulation of genes associated with amino acid and protein biosynthesis, as well as stress responses, were observed (P < 0.05), while multiple genes related to cell envelope, energy production and material transportation were significantly upregulated (P < 0.05).  High similarity of transcription profiles (r = 0.93) within LTS phase was observed when comparing transcriptomes at 168 h and 336 h.  RNA quality measurement revealed a high level of degradation of ribosomal RNA during the LTS phase.  The transcription profile at 8-h (log-phase) after re-inoculation of LTS cells also resembled that at 13 h (r = 0.94).  We hypothesize that the upregulation of some compatible solute transporters during the LTS phase may result in accumulation of these solutes, which may lower intracellular water activity and thus enhance resistance of L. monocytogenes to heat and high pressure.  Dormancy may be induced at the LTS phase which is suggested by the downregulation of genes associated with transcription and translation.  Once fresh nutrients are provided, LTS cells may quickly exit dormancy and become metabolically active as they transition to the log phase.

sample_organism: Listeria monocytogenes serotype 4b str. F2365

overall_design: Based on the annotated genome of L. monocytogenes F2365 (GenBank accession# NC_002973) (Donaldson et al., 2009), a gene expression microarray was designed to target 2821 protein-coding genes (including putative protein-coding genes).  Each of the 2821 genes was targeted by 12 unique 60-mer oligonucleotide probes.  Each unique probe was printed in duplicates on the microarray.   The microarrays were in a format of 4 × 72 k (4 microarrays per slide, with each microarray containing 72,000 probes) and provided by Roche NimbleGen (Roche NimbleGen, WI).

first: Jia

last: Wen

first: Xiangyu

last: Deng

last: Li

first: Edward

middle: G

last: Dudley

first: Ramaswamy

middle: C

last: Anantheswaran

first: Stephen

last: Knabel

first: Wei

last: Zhang


title: miRNA expression in NK cells

status: Public on Feb 23 2011

city: San FRANCISCO

last: Steiner

address: 513 Parnassus Ave UCSF Box 0414 HSE 201

institute: UCSF

summary: The goal of this study is to characterize the miRNA expression in both freshly isolated and cultured NK cells from both mice and humans. (2 samples from mouse cells (naive and cultured), 2 from human cells (naïve and cell line), 4 samples total)

sample_organism:
Homo sapiens
Mus musculus

overall_design:
At this point, this experiment involves one replicate of each of the samples using dual channels to analyze freshly isolated cells and cultured cells on the same custom printed slide. (intended only to gain preliminary insight into miRNA expression in NK cells for further analysis)

SUPPLEMENTARY FILE:
File includes normalized total intensity and log2 ratio (representing RNA from freshly isolated cells-Cy5/cultured cells-Cy3[mouse] or freshly isolated cells-Cy5/cell line-Cy3[human]).


title: MicroRNA expression contributes to the poor prognosis of human small cell lung cancer

status: Public on Feb 22 2011

city: Beijing

last: bi

address: Panjiayuannanli 17#

institute: Cancer Hospital and Cancer Institute

summary: MicroRNAs are important cellular components and their dysfunctions are associated with various disease.Small-cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, but little is know about the underlying machinery that leads to rapid tumor growth and early metastases.In this study, clinical outcome prediction miRNAs were successfully found  through expression profiling of a total of 924 miRNA genes in 42 SCLC cases.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 42 patients with respectable very limited disease (training set) were enrolled. All the patients underwent surgical resection followed by adjuvant chemotherapy according to the standard of care.   Total RNA was extracted from formalin-fixed paraffin-embedded （FFPE）specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3 biochip representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.

first: Jianzhong

last: Cao

first: Yongmei

last: Song

last: Bi

first: Luhua

last: Wang

first: Qiming

last: Zhan