title: sncRNAs in E. faecalis V538

city: Caen

first: jean-christophe

last: giard

address: esplanade de la paix

institute: Université de Caen

type: Non-coding RNA profiling by genome tiling array

summary: Small non coding RNA molecules (sncRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sncRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. Enterococcus faecalis. We characterized 11 sncRNAs by tiling microarray analysis, 5’ and 3’ RACE-PCR, and Northern blot analysis. Six sncRNAs were specifically expressed at exponential phase, two sncRNAs were observed at stationary phase, and three were detected during both phases. This is the first experimental genome-wide identification of sncRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen.

overall_design: Identification of sncRNA candidates transcribed by E. faecalis V583 was undertaken with two samples of cells harvested in mid-log growth phase and  stationary phase after 24h of incubation at 37°C in M17 glucose media.

first: Kouki

last: Shioya

first: Charlotte

last: Michaux

first: Carsten

last: Kuenne

first: Torsten

last: Hain

first: Nicolas

last: Verneuil

first: Thomas

last: Hartsch

first: Axel

last: Hartke

first: Jean-Christophe

last: Giard


title: h3k4me2_gw-Establishing a reference epigenome in arabidopsis seedlings

status: Public on Apr 19 2011

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

type: Genome binding/occupancy profiling by genome tiling array

summary: gfe_epigenome - h3k4me2_gw - Epigenomic mapping - Epigenomic mapping of H3K4me2

overall_design: 4 dye-swap - chip-chip

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: Chromosome copy number variation in Cryptococcus neoformans influences virulence and occurs in isolates from AIDS patients

city: Incheon

first: Jaehyuk

last: Choi

address: 119 Academy-ro

country: South Korea

institute: Inceon National Univ

summary: Influence of  copy number changes at several chromosomes to melanin production and virulence of Cryptococcus neoformans

overall_design: Black(B4) and white(W2) strains were compared to each other. Black variant from white strain (W2BA1) is also compared to the black strain(B4).

first: Guanggan

last: Hu

first: Joyce

last: Wang

first: Won

middle: H

last: Jung

first: Iris

last: Liu

first: Ana

last: Litvintseva

first: Tihana

last: Bicanic

first: Rajeev

last: Aurora

first: Tom

last: Mitchell

first: John

last: Perfect

first: James

middle: W

last: Kronstad


title: Embryo seed development: Establishing the network of seed gene expression and analysis of its biodiversity

status: Public on Apr 22 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: gnp3_tri33-arabidoseed. Embryo seed development. WP3: Biodiversity of seed traits: state-of-the-art. Analysis of the expression of small RNAs precursors in the seed development of Arabidopsis thaliana.

overall_design: 12 dye-swaps. Time course.

first: Samira

last: Elftieh

first: Michel

last: Caboche

first: Sandrine

last: Balzergue


title: Circadian regulation of gene expression in the coral algal endosymbiosis

status: Public on Apr 21 2011

city: Ramat Gan

first: Oren

last: Levy

address: Max and Anna Web

department: The Mina and Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

summary: Despite their early evolutionary divergence, reef-building corals exhibit complex circadian responses to diurnal, lunar and annual changes in the conditions around them. Understanding circadian regulation in reef-building corals is, however, complicated by the presence of photosynthetic endosymbionts that have a profound physiochemical influence on the intracellular environment. How corals tune their animal-based clock machinery to respond to external cues while at the same time responding to internal physiological changes imposed by the symbiont is not clear. We explore this issue using microarray analysis to dissect genes governed directly by the circadian machinery from those responding indirectly as a consequence of changing internal oxygen tensions.

overall_design: Three coral colonies were sampled at 4 hr intervals during two consecutive days under an ambient light/dark (LD) cycle and under constant darkness (DD). In total 72 arrays were hybridized, as each array represented a sample from a treatment and a time point (n=3).

first: David

last: Miller


title: Carboxypeptidase of glutamate-like gene as a tumor suppressor in pancreatic cancer cells and a prognostic marker for resected pancreatic cancer patients

city: Bethesda

first: Jih-Hsiang

last: Lee

state: MD

address: 9000 Rockville Pike, building 10 8N254

department: Medical oncology branch

country: USA

institute: National Cancer Institute

summary: Pancreatic cancer is the fourth leading cancer-related death in United States. The clinical relevance of genomic imbalances in pancreatic cancer is uncertain. We performed array-comparative genomic hybridization (aCGH) in 44 resected pancreatic cancer specimens from a Korean cohort. We observed recurrent copy number gains were observed in chromosome 1q, 11q, 18q11.1-11.2, and 20q13.13; and losses in chromosome 2p, 9p, 10q, 14q, 15q, 18q12.2-23, 19q, 20q11.1, 21p, and 22q. High copy number gains, with log2 ratio >2.0, were observed in 4 cytobands, encoding genes such as G protein-coupled receptor 48, c-myc and gamma-catenin. By comparing the aCGH results of long survivors and short survivors, determined according to the median survival, we observed that loss of cytoband 18q22.3, encoding 5 genes, was the only alteration with significantly different frequencies. The copy number of the CPGL (Carboxypeptidase of glutamate-like) gene in cytoband 18q22.3 was found to be significantly associated with overall survival in univariate analyses (p=0.019 by log-rank test). This was subsequently assessed in the Italian cohort: 41 out of the 61 specimens carried deletion of the CPGL gene. Patients with deletion of the CPGL gene also had shorter overall survival (p=0.003 by log-rank test). Multivariate analysis of the two cohorts combined showed that loss of 18q22.3 / deletion of the CPGL gene was an independent poor prognostic factor for overall survival after adjusting for other factors which were found to impact the outcome (hazard ratio 2.72, p=0.0007). overexpression of the CPGL or its alternating splicing isoform CPGL-B in a pancreatic cancer cell lines resulted in slower proliferation of cells, G1 cell cycle arrest, and reduced migration activity. In conclusion, through aCGH analysis, we identified loss of 18q22.3 / deletion of the CPGL gene as potentially being an independent poor prognostic factor in resected pancreatic cancer. We further identified the CPGL gene as a potential tumor suppressor for pancreatic cancer cell lines.

overall_design: Array-comparative genomic hybridization was performed in 44 resected pancreatic cancer specimen from a Korean cohort. Genomic alteration relating to prognosis of the Korean cohort was further validated in a Italian cohort containing 61 resected pancreatic cancer specimens.

first: Elisa

last: Giovannetti

first: Jih-Hyeok

last: Hwang

first: Iacopo

last: Petrini

first: Qiuyan

first: Johannes

last: Voortman

first: Yonghong

first: Seth

middle: M

last: Steinberg

first: Niccola

last: Funel

first: Paul

last: Meltzer

first: Yisong

first: Giuseppe

last: Giaccone


title: h3k4me3_gw-Establishing a reference epigenome in arabidopsis seedlings

first: François

last: ROUDIER

summary: gfe_epigenome - h3k4me3_gw - Epigenomic mapping - Epigenomic mapping of H3K4me3

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: h3k27me3_gw-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k27me3_gw - Epigenomic mapping - Epigenomic mapping H3K27me3


title: Expression data from Caulobacter crescentus starved for carbon

status: Public on Apr 20 2011

city: Stanford

first: Leticia

last: Britos

state: CA

address: 279 Campus Dr.

institute: Stanford University

summary: Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of C. crescentus to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis.

overall_design: Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures, and total RNA was extracted after 30 and 60 minutes of incubation. The controls are cells growing in complete media.


title: Expression data from WT, DSigT and DSigU Caulobacter crescentus (syn. C. vibrioides) starved for carbon

summary: Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of C. crescentus to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. We explored the differential gene expression changes in wild type cells and cells carrying deletions of two alternative extracytoplasmic function sigma factors, SigT and SigU.

overall_design: Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures (wild-type (strain LS101), DSigT (strain LS3554) and DSigU (strain LS3547)). Total RNA was extracted after 15 minutes of incubation. Controls are cells that were mock washed and incubated in parallel in complete media.


title: Natural genetic variation caused by small insertions and deletions in the human genome

city: Baltimore

first: Scott

middle: E.

last: Devine

address: 801 W. Baltimore Street

institute: Institute for Genome Sciences

type: Genome variation profiling by genome tiling array

summary: We identified 1.96 million small insertions and deletions (INDELs) in the genomes of 79 diverse humans.  10,003 of these INDELs were probed on a custom INDEL genotyping array.

overall_design: A custom Affymetrix array was developed to genotype 10,003 small human INDEL polymorphisms ranging from 1 bp to 100 bp in length.  These arrays were used to genotype the 10,003 INDELs in 158 diverse humans.  These humans included: 1) the 24 humans from the polymorphism discovery panel (PDR; Coriell), 2) Yoruban trios from the HapMap project (YRI), 3) Han Chinese from the HapMap project (CHB), and 4) the HuRef genome (Venter).  Technical replicates were included for some samples.

middle: E


title: Transcriptome analyses using the Chen Lab Cotton 25k oligo microarray

status: Public on May 06 2011

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: The chip of cotton oligonucleotide microarrrays, which contain ~23,000 UniGenes from our own ESTs sequence project (Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) ) and open resources, was developed. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected (LCM) fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to (-2DPA), right at (0DPA), and shortly after the initiation of fiber cells (2DAP and 7DPA). Many genes in various molecular functions or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development.

overall_design: For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.

first: Jinsuk

middle: J

first: Foo

last: Cheung

first: Christopher

last: Town

first: Jeffrey


title: Using Gene Expression to Assess the Status of Fish from Anthropogenically Influenced Estuarine Wetlands

city: Berkeley

first: Don

last: Pham

address: 238 Morgan Hall

institute: University of California, Berkeley

summary: The diverse mixture of contaminants frequently present in estuarine wetlands complicates their assessment by routine chemical or biological analyses.  We investigated the use of gene expression to assess contaminant exposure and the condition of southern California (USA) estuarine fish.   Liver gene expression, plasma estradiol concentrations and gonad histopathology were used to investigate the biological condition of longjaw mudsuckers (Gillichthys mirabilis).  A wide array of metals, legacy organochlorine pesticides, PCBs and contaminants of emerging concern were detected in sediments and whole fish.  Overall gene expression patterns were characteristic to each of four sites investigated in this study.  Differentially expressed genes belonged to several functional categories including xenobiotic metabolism, detoxification, disease and stress responses.  In general, plasma estradiol concentrations were similar among fish from all areas.   Some fish gonads had pathologic changes (e.g. infection, inflammation) that could indicate weakened immune systems and chronic stress.  The differential expression of some genes involved in stress responses correlated with the prevalence of histologic gonad lesions.   This study indicates that sentinel fish gene expression data is a promising tool for assessing the biological condition of fish exposed to environmental contaminants.  Key Words: Gene expression, fish, contaminants, estuaries.  This abstract belongs to a manuscript that has been submitted to Environmental Science and Technology.  The manuscript has been invited as part of an especial Omics Issue which is expected to be published in 2012.

overall_design: In this study, we used hepatic gene expression in wild longjaw mudsuckers (Gillichthys mirabilis) to assess biological responses from anthropogenically influenced wetlands.  We investigated the relationships among gene expression responses, chemical exposure and additional biological responses in this species.  We studied estuarine wetlands that had diverse contaminant characteristics and received three main types of contaminant inputs in different proportions: agricultural runoff, urban runoff and municipal wastewater.

first: Doris

last: Vidal-Dorsch

first: Steve

last: Bay

first: Monica

middle: A

last: Mays

first: Darrin

last: Greenstein

first: Diana

last: Young

first: Jeff

last: Wolf

first: Alex

last: Loguinov

first: Vulpe

last: Chris


title: h2bub-Establishing a reference epigenome in arabidopsis seedlings

first: François

last: ROUDIER

summary: gfe_epigenome - h2bub - Epigenomic mapping - Epigenomic mapping of H2Bub

first: Vincent

last: Colot

first: Francois

first: Marie-Laure


title: Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon

first: Leticia

summary: Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of specific developmental stages of C. crescentus -swarmer and stalked cells- to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis.


title: h3k27me2-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k27me2 - Epigenomic mapping - H3K27me2 ChIP-chip

overall_design: 2 dye-swap - chip-chip

last: Roudier

last: Martin-Magniette


title: h3k56ac-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k56ac - Epigenomic mapping - H3K56Ac ChIP-chip


title: h3k36me3-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k36me3 - Epigenomic mapping - H3K36me3


title: h3-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3 - Epigenomic mapping - H3 ChIP-chip


title: VIPR: A probabilistic algorithm for analysis of microbial detection microarrays

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

summary: The development of rapid and sensitive assays capable of detecting a wide range of infectious agents is critical for the effective diagnosis of diseases that have multiple etiologies.  In recent years, many microarray-based diagnostics have been developed to identify viruses present in clinical specimens in a highly parallel fashion.  Unfortunately, the rate of development of algorithms to interpret data generated from such platforms has not been commensurate.  In particular, none of the existing interpretive algorithms is capable of utilizing empirical training data in a Bayesian framework.  We have developed an interpretive algorithm, VIPR (Viral Identification using a PRobabilistic algorithm), to capitalize on our ability to generate positive control data for analysis of microbial diagnostic arrays.  To illustrate this approach, we have focused on the analysis of viruses that cause hemorrhagic fever (HF).  To assess the efficacy of VIPR, we hybridized 33 viruses to 100 microarrays and applied our algorithm to this dataset.  A microarray composed of nearly 15,000 oligonucleotides was designed using a custom viral taxonomy-based strategy.  The performance of VIPR was assessed by performing a leave-one-out cross validation.  VIPR was able to identity the infecting virus with an accuracy of 94%.  VIPR outperformed previously described algorithms for the set of HF viruses tested.  Bayesian interpretative algorithms such as VIPR should be considered for diagnostic microarray applications.

sample_organism:
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
Yellow fever virus
La Crosse virus
Rift Valley fever virus
Toscana virus
Omsk hemorrhagic fever virus
unidentified
Kyasanur Forest disease virus
California encephalitis virus
Rocio virus
Ebola virus - Gabon (1994-1997)
Zaire ebolavirus
Reston ebolavirus
Sudan ebolavirus
Ngari virus
Lake Victoria marburgvirus - Angola2005
Mammarenavirus juninense
Mammarenavirus amapariense
Mammarenavirus brazilense
Mammarenavirus choriomeningitidis
Mammarenavirus guanaritoense
Mammarenavirus ippyense
Mammarenavirus lassaense
Mammarenavirus machupoense
Mammarenavirus mopeiaense
Mammarenavirus praomyidis
Mammarenavirus tacaribeense
Orthohantavirus hantanense
Orthohantavirus puumalaense
Orthohantavirus seoulense
Orthonairovirus haemorrhagiae

platform_organism: Flaviviridae Filoviridae Arenaviridae Peribunyaviridae

overall_design: In this study, 33 viruses including virtually every known hemorrhagic fever virus and a selection of their close relatives were grown in culture and hybridized to 102 microarrays.  In addition, 8 uninfected samples were hybridized (110 total hybridizations).  These hybridizations were used to test a novel algorithm for diagnosing the infecting virus from a hybridization pattern.

first: David

last: Wang


title: Transcriptional response of an azole-resistant Candida parapsilosis isolate [voriconazole].

status: Public on Apr 18 2011

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary: Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of voriconazole. Whole genome microarrays were used to compare the transcriptional response of the voriconizole-resistant and susceptible isolates.

overall_design: Transcriptional profile of an in vitro derived voriconazole-resistant isolate of C. parapsilosis (BC014VRC) compared to the susceptible isolate (BC014S). Cell were grown in YPD medium in normoxia at 35 degrees. Each strain was labelled with Cy3 or Cy5. Overall, 4 independent biological replicates were compared; 2 dye swaps were performed to normalize dye effects.

first: Ana

middle: T

last: Silva

first: Isabel

last: Miranda

first: Alessandro

last: Guida

first: John

last: Synnott

first: Rita

last: Rocha

first: Cidália

middle: I

last: Pina-Vaz

first: Acácio

last: Rodrigues


title: MicroRNA expression profiling on formalin-fixed paraffin-embedded (FFPE) tissue blocks of human adrenal pheochromocytomas

city: Budapest

first: Zsófia

last: Tömböl

address: Szentkirályi u. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

summary: MicroRNAs are involved in the pathogenesis of several tumors, however, there have been no data on microRNA expression in pheochromocytomas to date.  In this study we have performed microRNA expression profiling in sporadic benign, hereditary benign (multiplex endocrine neoplasia type 2-related and von Hippel-Lindau syndrome-related pheochromocytomas), and sporadic recurring adrenomedullary tumors. Due to the rarity of these neoplasms, the retrieval of sufficient quantities of fresh or immediately snap frozen tumor samples is difficult, therefore the applicability of formalin-fixed paraffin-embedded tissue samples for the analysis of microRNA expression in pheochromocytomas was examined.

overall_design: In this study microRNA expression pattern of sporadic benign, sporadic recurring, MEN2-related and VHL-related hereditary adrenal pheochromocytomas has been reported. For microRNA expression profiling, total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks. Biological replicates: 6 sporadic benign, 5 sporadic recurring, 5 MEN2-related and 5 VHL-related pheochromocytoma FFPE tissues has been investigated (n=21). To prove the applicability of FFPE blocks for microRNA microarray analysis, the microRNA expression data of three matched frozen and FFPE pheochromocytoma samples derived from the same patients were compared. MicroRNA expression analysis of 21 FFPE and 3 frozen samples was performed on Agilent Human miRNA Microarray Rel12.0  (v3.0) (8x15k) containing probes corresponding to 866 human and 89 human viral miRs.

first: Katalin

last: Éder

first: András

last: Falus

first: Károly

last: Rácz

first: Peter

last: Igaz


title: h3k27me3-Establishing a reference epigenome in arabidopsis seedlings

first: François

last: ROUDIER

summary: gfe_epigenome - h3k27me3 - Epigenomic mapping - H3K27me3 ChIP-chip

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure


title: Transcriptional response of an azole-resistant Candida parapsilosis isolate [fluconazole].

first: Geraldine

summary: Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of fluconazole. Whole genome microarrays were used to compare the transcriptional response of the fluconazole-resistant and susceptible isolates.

overall_design: Transcriptional profile of in vitro derived fluconazole resistant isolate of C. parapsilosis (BC014FLC) compared to susceptible isolate (BC014S). Cell were grown in YPD medium in normoxia at 35 degrees. Each strain was labelled with Cy3 or Cy5. Overall, 4 independent biological replicates were compared; 2 dye swaps were performed to normalize dye effects.


title: Transcriptional response of an azole-resistant Candida parapsilosis isolate [posaconazole].

summary: Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of posaconazole. Whole genome microarrays were used to compare the transcriptional response of the posaconazole-resistant and susceptible isolates.

overall_design: Transcriptional profile of an in vitro derived posaconazole-resistant isolate of C. parapsilosis (BC014PSC) compared to the susceptible isolate (BC014S). Cell were grown in YPD medium in normoxia at 35 degrees. Each strain was labelled with Cy3 or Cy5. Overall, 3 independent biological replicates were compared; 1 dye swap was performed to normalize dye effects.

first: Ana


title: h3k4me2-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k4me2 - Epigenomic mapping - H3K4me2 ChIP-chip

last: Martin-Magniette


title: Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

status: Public on Apr 17 2011

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

summary: Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming.

overall_design: iPS cells were produced from melanocytes, fibroblasts, and hepatocytes, representing the three germ layers. Expression levels were profiled in the differentiated cells and their matched iPS cells, as well as 3 human ES cell lines (H1, H7 and H9) and their embroid bodies.

first: Yuki

last: Ohi

first: Han

last: Qin

first: Chibo

last: Hong

first: Laure

last: Blouin

first: Jose

last: Polo

first: Tingxia

last: Guo

first: Zhongxia

last: Qi

first: Sara

middle: L

last: Downey

first: Philip

middle: D

last: Manos

first: Derrick

last: Rossi

first: Jingwei

last: Yu

first: Matthias

last: Hebrok

first: Konrad

last: Hochedlinger

first: Joseph

last: Costello

first: Miguel

last: Ramalho-Santos


title: h3k4me3-Establishing a reference epigenome in arabidopsis seedlings

first: François

last: ROUDIER

summary: gfe_epigenome - h3k4me3 - Epigenomic mapping - H3K4me3 ChIP-chip

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: h3k9me2-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k9me2 - Epigenomic mapping - H3K9me2 ChIP-chip


title: h3k9me3-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k9me3 - Epigenomic mapping - H3K9me3 ChIP-chip


title: h4k20me1-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h4k20me1 - Epigenomic mapping - H4K20me1 ChIP_chip


title: Gene expression data for the budding yeast mutants pol30-8, dot1Δ and pol30-8 dot1Δ

city: Cold Spring Harbor

first: Bruce

last: Stillman

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary:
The mutation in the budding yeast gene PCNA, pol30-8, as well as deletion of DOT1 (dot1Δ), encoding the only histone H3 K79 methyltransferase in budding yeast, have been implicated in telomeric silencing. To further analyze these mutants, we used microarrays to study whether either pol30-8, dot1Δ or the double mutant leads to changes in gene expression levels when compared to isogenic wild-type strains.
ABSTRACT:                                                                                Telomere-associated position effect variegation (TPEV) in budding yeast has been used as a model for understanding epigenetic inheritance and gene silencing. A widely used assay to identify mutants with improper TPEV employs the URA3 gene at the telomere of chromosome VII-L that can be counter-selected with 5-fluoroorotic acid (5-FOA). 5-FOA resistance has been inferred to represent lack of transcription of URA3 and therefore to represent heterochromatin-induced gene silencing. For two genes implicated in telomere silencing, POL30 and DOT1, we show that the URA3 telomere reporter assay does not reflect their role in heterochromatin formation. Rather, an imbalance in ribonucleotide reductase (RNR), which is induced by 5-FOA, and the specific promoter of URA3 fused to ADH4 at telomere VII-L are jointly responsible for the variegated phenotype. We conclude that metabolic changes caused by the drug employed and certain mutants being studied are incompatible with the use of certain prototrophic markers for TPEV.

overall_design: 3 replicates each of the S. cerevisiae MATalpha wild-type, pol30-8, dot1Δ and pol30-8 dot1Δ strains carrying the epigenetic silencing reporter genes hmr::ADE2 and URA3-VIIL (in the W303 genetic background; the ade2-1 and ura3-1 alleles normally present in this background were deleted) were grown to mid-logarithmic phase and harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Marlies

middle: P

last: Rossmann

first: Weijun

last: Luo


title: Global Transcriptional Analysis of Stress-Response Strategies in Acidithiobacillus ferrooxidans ATCC 23270 Exposed to Organic Extractant - Lix984n

status: Public on Apr 14 2011

city: changsha

first: xueduan

last: liu

address: lushan south road

country: China

institute: central south university

summary: Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.

overall_design: In this work, the whole-genome array was employed to conduct the time-course transcriptome analysis of A. ferrooxidans ATCC 23270 in response to 1% (v/v) Lix984n for 5, 20, 40, and 80 min.

first: Qihou

last: Li

first: Yun

last: Fang

first: Huaqun

last: Yin

first: Wenqing

last: Qin

first: Zhijun

last: Zhou

first: Yili

last: Liang

first: Qian

first: Nuo

first: Xinxing

last: Liu

first: Guanzhou

last: Qiu

first: Xueduan


title: Lifespan extension via eIF4G inhibition is mediated by post-transcriptional remodeling of stress response gene expression in C. elegans

status: Public on Apr 16 2011

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Reducing protein synthesis slows growth and development but can increase adult lifespan. We demonstrate that knock-down of eukaryotic translation initiation factor 4G (eIF4G), which is down-regulated during starvation, results in differential translation of genes important for growth and longevity in C. elegans. Genome-wide mRNA translation state analysis showed that inhibition of IFG-1, the C. elegans ortholog of eIF4G, results in a relative increase in ribosomal loading and translation of stress response genes. Some of these genes are required for lifespan extension when IFG-1 is inhibited and are new determinants of longevity. Furthermore, enhanced ribosomal loading of certain mRNAs upon IFG-1 inhibition was correlated with increased mRNA length. This association was supported by changes in the proteome assayed via quantitative mass spectrometry. Our results support a role for IFG-1 in mediating the antagonistic effects on growth and somatic maintenance by modulating translation of a specific class of mRNA based on transcript length.

overall_design: 24 experimental samples were analyzed using custom oligo microarrays. A wild type sample pool was used as the Cy3 reference/control for all experimetal samples. All extracted RNA prior to array analysis was fractioned (via a sucrose gradient) based on ribosomal loading and pooled into ribosomal and free RNA (Fraction1), light polysomes (Fraction2) and heavy polysomes (Fraction3) as described in the experimental procedures. The control RNAi is ‘empty’ vector L4440 RNAi feeding vector plasmid (1999 Firelab vector kit) transformed HT115(DE3), which was obtained from the Caenorhabditis Genetics Center (University of Wisconsin).

first: Aric

middle: N

last: Rogers

first: Di

last: Chen

first: Gaiwan

last: McColl

first: Krysta

last: Felkey

first: Bradford

last: Gibson

first: Alan

last: Hubbard

first: Gordon

last: Lithgow

first: Pankaj

last: Kapahi


title: The Microbial Detection Array Combined with Random Phi29-Amplification used as a Diagnostic Tool for Unbiased Virus Detection in Clinical Samples

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples.

overall_design: 19 clinical samples were analyzed for presence of virus using the MDA microarray. One of the samples is a negative control (water). One HCV-positive serum sample is included twice (HCV+1 and HCV+2).

first: Lena

last: Erlandsson

first: Maiken

last: Rosenstierne

first: Crystal

last: Jaing

first: Anders

last: Fomsgaard


title: Development and evaluation of a 60-mer oligonucleotide microarray for profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems

status: Public on Apr 15 2011

city: Lucknow

first: Natesan

last: Manickam

state: Uttar Pradesh

address: Mahatma Gandhi Marg

department: Department Environmental Biotechnology Division

country: India

institute: Indian Institute of Toxicology Research

summary: We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph),  biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected.  Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.

sample_organism:
Escherichia coli K-12
Rhodococcus jostii RHA1
Sphingomonas sp. NM05
soil metagenome
Escherichia coli BL21
freshwater sediment metagenome
Escherichia coli DH5[alpha]
Bordetella sp. IITR-02

overall_design: Agilent one-color CGH experiment,Organism: Genotypic designed Agilent-17159  Genotypic designed  Agilent  Multibacterial 8x15k Array , Labeling kit:  Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)

first: Ashutosh

last: Pathak


title: MicroRNA expression profiles of interstitial lung disease (ILD) patients

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary:
The mechanisms and molecular pathways underlying interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches were used to identify perturbed networks in these disease states to gain a better understanding of the underlying mechanisms of disease. Through profiling genes and miRNAs, we found subsets of genes and miRNAs that distinguish different disease stages, ILDs from controls, and idiopathic pulmonary fibrosis (IPF) from non-specific interstitial pneumonitis (NSIP). Traditional pathway analysis revealed several disease-associated modules involving genes from the TGF-beta, Wnt, focal adhesion and smooth muscle actin pathways that may be involved in advancing fibrosis.
A comprehensively integrative approach was used to construct a global gene regulatory network based on the perturbation of key regulatory elements, transcriptional factors and miRNAs. The data also demonstrated that several subnetworks were significantly associated with key molecules involved in the diseases. We present a broad overview of the disease at a molecular level and discuss several possibly key regulatory molecular circuits that could play central roles in facilitating the progression of ILDs.

overall_design: Lung tissue samples from thirty patients with IPF or related disorders were obtained from the Lung Tissue Research Consortium (www.ltrcpublic.org). Ten samples came from patients who had been diagnosed with usual interstitial pneumonia/ idiopathic pulmonary fibrosis (UIP/IPF), nine samples came from patients with non-specific interstitial pneumonia (NSIP), four from patients with uncharacterized fibrosis, and the remaining samples came from patients with other ILD variants. Biopsies from uninvolved lung tissue from lung cancer patients (5 samples) and from one lung transplant patient were used as controls for comparison with the ILD samples.

first: Richard

last: Gelinas

first: Kai

last: Wang

first: Alton

last: Etheridge

first: Melissa

middle: G

last: Piper

first: Kara

last: Batte

first: Riscili

last: Brent

first: Jennifer

last: Price

first: Dan

last: Bornman

first: Shile

last: Zhang

first: Clay

last: Marsh

first: David

last: Galas


title: Temporal characterization of the organ-specific Rhipicephalus microplus transcriptional response to Anaplasma marginale infection

status: Public on Apr 13 2011

city: PULLMAN

first: Ricardo

middle: Francisco

last: Mercado-Curiel

address: BUSTAD 402

department: College Of Veterinary Medicine

institute: Washington State University

summary: In addressing R. microplus - A. marginale interactions, we propose and test three linked hypotheses.  The first is that the tick gene response is organ specific: the midgut gene regulation is unique during feeding and during acquisition of A. marginale as compared to the salivary gland.  This distinction is relevant as the two organs serve very different roles in the transmission biology of A. marginale with early survival and replication within the midgut epithelium, composed of highly phagocytic cells, required for initial colonization while a second round of replication in the salivary gland acini, composed of highly secretory cells, is required for transmission of an infectious dose in the saliva.  Importantly, both the midgut epithelium and salivary glands have been identified as separate and distinct barriers for transmission of A. marginale and thus represent two potential sites where transmission could be blocked.  The second hypothesis to be tested is that the salivary gland transcriptome is temporally dynamic.  Initiation of tick attachment and feeding involves secretion of a virtual pharmacopeia including lytic enzymes, anticoagulants, and inhibitors of the mammalian innate immune and nocioceptive systems.  Concomitantly, the acini provide an environment where A. marginale replicates >100 fold and are secreted into the saliva.  Prior studies show that duration of feeding is a critical component of transmission efficiency, with increased efficiency positively correlated with time of tick feeding.  The third hypothesis to be tested is that A. marginale colonization does not significantly modulate the tick midgut and salivary gland transcriptome.  This hypothesis is based on observations by ourselves and others that tick infection does not impart a significant fitness cost on the vector.  This is in contrast to other bacterial and protozoal pathogens that have dramatic effects on success of tick attachment, engorgement, and survival.  A. marginale, similar to other tick-borne pathogens in the Family Anaplasmataceeae, is believed to have evolved from an arthropod-specific bacterium with relatively late adaptation to specific niches in mammalian hosts.  Consequently, we predict that A. marginale is well adapted to its tick vector and utilizes the normal signaling pathways of the feeding tick with few, if any, effects on the midgut and salivary gland transcriptome.  In this manuscript, we report the testing of these three hypotheses and present the results in context of the vector-pathogen-mammalian host interaction at the time of transmission.

platform_organism:
Rhipicephalus microplus
Anaplasma marginale str. St. Maries

overall_design: A Roche NimbleGen high-density gene expression microarray was custom designed based on the expressed sequence tag (EST) database, B. microplus Gene Index Version 2 (BmiGI V2) for R. microplus. The expression level of 14,447 R. microplus genes was analyzed from total RNA extracted from 10 different tick tissue samples; 30 arrays were included since triplicates of each different sample were analyzed as follow: unfed (midgut and salivary glands), blood feeding (2 days midgut and 2, 6 and 9 days salivary glands), A. marginale-infected blood feeding (2 days midgut and 2, 6 and 9 days salivary glands).

first: Guy

middle: H

last: Palmer

first: Felix

last: Guerrero

first: Kelly

last: Brayton


title: Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (Affymetrix gene expression data)

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Enzymes catalyzing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression, genome stability, and maintaining cellular identity. Recently Tet1, which is highly expressed in embryonic stem (ES) cells, was found to oxidize the methyl group of mC converting it to 5-hydroxymethyl cytosine (hmC)3. Here, we present the genome-wide mapping of Tet1 and hmC in mouse ES cells. We show that Tet1 binds throughout the genome with the majority of binding sites located at transcription start sites (TSSs) and within genes. Similar to Tet1 and mC, also hmC is found throughout the genome and in particular in gene bodies. However, in contrast to mC, hmC is enriched at TSSs. Tet1 and hmC are associated with genes critical for the control of development and differentiation, which become methylated during differentiation. Surprisingly our results also suggest that Tet1 has a role in transcriptional repression. We show that Tet1 binds to a significant proportion of target genes that are positive for the Polycomb repressive histone mark H3K27me3, and that downregulation of Tet1 also leads to increased expression of a group of Tet1 target genes. In agreement with a potential repressive function, we show that Tet1 associates with the Sin3A co-repressor complex, which also co-localises with Tet1 throughout the genome. We propose that Tet1 fulfils dual functions in transcriptional regulation, where it fine-tunes DNA methylation and associates with the Sin3A co-repressor complex to prevent transcriptional activation.

overall_design:
[GSM611209-GSM611217] Control (shScr) or two different Tet1 knockdown (shTet1#4 or shTet1#5) mouse ES cells were used. Each experiment was performed in triplicates.
[GSM675884-GSM675889] Control (shScr) or Sin3A knockdown (shSin3A) mouse ES cells were used.Each experiment was performed in triplicates.


title: Experimental validation of HiSpOD probe design with complex background mRNA or 3 known antiense RNA and expression analysis on a contaminated groundwater sample

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

institute: CNRS - Blaise Pascal University

summary: HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 µg of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 µg of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed.

sample_organism:
synthetic construct
uncultured organism

overall_design: A 3 chip study was realized. The first one is a negative control performed with a complex background material (labelled antisense mRNA from sheep rumen content). The second one is a positive control realized with labelled antisense RNA derived from in vitro transcription of three synthetic genes mixed the same complex background material. The third consists in the hybridization of antisense mRNA retrieved from a contaminated groundwater. Each probe (3392) was synthetized in triplicate, and a total of 8,863 random probes was used to determine the background noise.

first: Eric

last: DUGAT-BONY

last: PEYRETAILLADE

first: Corinne

last: BIDERRE-PETIT

first: Pierre

last: PEYRET


title: Listeria monocytogenes transcriptional response to bile

status: Public on Apr 12 2011

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

institute: The University of Chicago

summary: These studies were designed to examine the acute Listeria monocytogenes transcriptional response to mammalian (porcine) bile.

platform_organism: Listeria monocytogenes serotype 4b str. F2365

platform_organism: Listeria monocytogenes serotype 1/2a str. F6854

platform_organism: Listeria monocytogenes serotype 4b str. H7858

overall_design: Triplicate WT Listeria monocytogenes (strain 10403S) were grown to mid-log in BHI at 37 °C.  Samples were divided, and either treated or not treated by addition of porcine bile (Sigma, to 1% final) for 30 minutes.


title: HapX positively and negatively regulates the transcriptional response to iron deprivation in Cryptococcus neoformans

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary: Analysis of the transcriptional response of C. neoformans WT, cir1 mutant, hap3 mutant and hapX mutant to different iron sources.

overall_design: The following experimental design was adopted for the study. Within each strain, each treatment pair (low-iron, +FeCl3, +Transferrin and +Hemin; 6 pairs) were hybridized to an array; and within each treatment, each strain (WT, hap3, hapX and cir1, 6 pairs) were hybridized to an array for a total of 48 microarrays. Each strain/treatment combination was labeled an equal number of times with Cy3 and Cy5 to ensure dye balance

first: W

first: S

last: Saikia

first: G

last: Hu

first: J

last: Wang

first: C

middle: K

last: Fung

last: D’Souza

first: R

last: White

middle: W

last: Kronstad


title: Performance of Immunochip 1.0 with hemolymph samples collected at 3 and 48 hours from Vibrio-challenged mussels

city: Padova

first: Laura

last: Varotto

address: via U. Bassi 58/3

department: Biology Department

country: Italy

institute: University of Padova

summary: We aimed to exemplify early and late transcriptional response of M. galloprovincialis to live Vibrio cells. Hemolymph was collected at 3 and 48 hours after the injection of 10 to 7 cells Vibrio splendidus LGP32 into the posterior adductor muscle. Hemolymph samples were similarly collected from paired control mussels injected with PBS-NaCl. The purified RNAs were successfully amplified, labelled and competitively hybridized to the new mussel oligoarray Immunochip 1.0.

overall_design: After acclimatization, groups of 40 farmed mussels from the Venice lagoon (Italy) were injected either with 10 to 7 cells of Vibrio splendidus LGP32 or with NaCl-enriched PBS. One ml of hemolymph was withdrawn at 3 h and 48 h post-injection from each control or treated mussel. Two RNA pools (N=10) per time point were composed from the treated mussels, processed and competitively hybridized in dye-swap combination (Cy3 / Cy5 aRNAs) on the same Immunochip slide against time-paired control RNA pools (N=40). Since each Immunochip array contains 4 replicates per probe, the dye-swap testing yielded a total of 16 expression values per probe per time-point.

first: Umberto

last: Rosani

first: Filippo

last: Bernante

first: Stefano

last: Cagnin

first: Gerolamo

last: Lanfranchi

first: Alberto

last: Pallavicini

first: Paola

last: Venier


title: SigH, SigL, and SigC regulon in Listeria monocytogenes 10403S

city: Bangkok

first: Soraya

last: Chaturongakul

address: 272 Rama 6 Road

country: Thailand

institute: Mahidol University

summary: To characterize regulons of alternative sigma factor SigH, SigL, and SigC in Listeria monocytogenes, in-frame mutant strains were created in the 10403S background.  Regulons controlled by these 3 alternative sigma factors were characterized by whole-genome microarrays.  The L. monocytogenes 10403S wild type and sigma factor null mutation strains were grown at 37 °C to stationary phase (defined in this study as growth to OD600 = 1.0, followed by incubation for an additional 3 h) prior to RNA isolation.  Transcriptional profiles of 10403S wild type were compared to those of null mutation strain. In addition to stationary phase condition, SigC regulon was further characterized using heat stress (cultures grown to log phase at OD600 = 0.4, 37 °C and then exposed to heat at 55 °C for 10 min) and a condition with IPTG-inducible expression of sigC (sigC gene is placed under Pspac promoter using pLIV2 vector in wild type 10403S background). Under these conditions, expression profiles were compared between (i) wild type and sigC null mutant for heat stress and (ii) IPTG-inducible sigC strain and sigC null mutant, respectively. Using adjusted P < 0.05 and ≥ 1.5 fold change as cutoff values, microarray analyses identified 169 SigH-dependent, 51 SigL-dependent, and 3 SigC-dependent genes.  Keywords: Listeria monocytogenes, alternative sigma factor, SigH, SigL, SigC

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: Independent RNA isolations were performed for cultures grown to stationary phase (OD600 = 1 + additional incubation for 3 hours) at 37°C. In addition to RNA from stationary phase cultures, for SigC regulon characterization, cultures were also grown to log phase (OD600 = 0.4) then exposed to heat at 55 °C for 10 min) and grown in BHI with 0.5 mM IPTG to log phase prior to RNA isolations. Three biological replicates were used in competitive whole-genome microarray experiments. The LIMMA package from the R/BioConductor software project was used for data pre-processing and differential expression analyses.

first: Martin

last: Wiedmann

first: Kathryn

last: Boor


title: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with ferric citrate as an electron acceptor

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

institute: University of Massachusetts Amherst

summary: Geobacter sulfurreducens PCA was put under selective pressure for rapid Fe(III) oxide reduction. The resultant strain, V1, contained five confirmed mutations and reduced Fe(III) oxide 17 times faster. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 compared to PCA, both grown with ferric citrate as an electron acceptor.

overall_design: Three biological replicates were hybridized in duplicate. Experimental (V1) was labeled with cy5, control (wild type PCA) was labeled with cy3.

first: Richard

last: Glaven

first: Kelly

last: Nevin


title: microRNA expression profiling of lobular neoplasia

status: Public on Apr 11 2011

city: Bronx

first: olivier

last: Loudig

state: New York

address: 1300 Morris Park Avenue

department: Epidemiolkogy and Population Health

institute: Albert Einstein College of Medicine

summary: Invasive lobular carcinoma (ILC) of the breast accounts for 5-15% of breast cancers and is characterized by loss of E-cadherin and believed to arise via a linear histological progression. Genomic studies have identified a clonal relationship between ILC and concurrent lobular carcinoma in situ (LCIS) lesions, suggesting that LCIS may be a precursor lesion. It has been shown that an LCIS diagnosis confers a 15-20% risk of progression to ILC, over a lifetime. Currently no molecular test or markers can identify LCIS lesions likely to progress to ILC. Since microRNA (miRNA) expression changes have been detected in a number of other cancer types, we explored whether their dysregulation might be detected during progression from LCIS to ILC. Using the Illumina miRNA profiling platform, designed for simultaneous analysis of 470 mature miRNAs, we analyzed the profiles of archived normal breast epithelium, LCIS lesions found alone, LCIS lesions concurrent with ILC, and the concurrent ILCs, as a model of linear histological progression toward ILC. We identified two sets of differentially expressed miRNAs, the first set highly expressed in normal epithelium, including hsa-miR-224, -139, -10b, -450, 140 and -365 and the second set upregulated during lobular neoplasia, including hsa-miR-375, -203, -425-5p, -183, -565 and -182. Using quantitative RT-PCR, we validated a trend of increased expression for hsa-mir-375, hsa-mir-182, and hsa-mir-183 correlating with ILC progression. As we detected increased expression of hsa-miR-375 in LCIS lesions synchronous with ILC, we sought to determine whether hsa-mir-375 might induce phenotypes reminiscent of lobular neoplasia by expressing it in the MCF10A 3D culture model of mammary acinar morphogenesis. Increased expression of hsa-miR-375 resulted in loss of cellular organization and acquisition of a hyperplastic phenotype. These data suggest that dysregulated miRNA expression contributes to lobular neoplastic progression.

overall_design: 6 specimens were analyzed in duplicate. One frozen normal lobular epithelium and the matched FFPE (1 month old) normal lobular epithelium. One lobular carcinoma in situ (LCIS) found alone, one LCIS synchronous with an invasive lobular carcinoma (ILC), the synchronous ILC (from a different archived block), and one ILC found alone without presence of any other breast cancer.

first: Susan

last: Fineberg

first: Nella

last: Shapiro

first: Olivier

first: Christina

last: Liu


title: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with fumarate as an electron acceptor

summary: Geobacter sulfurreducens PCA was put under selective pressure for rapid Fe(III) oxide reduction. The resultant strain, V1, contained five confirmed mutations and reduced Fe(III) oxide 17 times faster. One of these five mutations inactivates dcuB, a fumarate/succinate antiporter necessary for growth with fumarate as an electron acceptor. V1 dcuB+ is a V1 strain containing a wild type copy of dcuB. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 dcuB+ compared to PCA, both grown with fumarate as an electron acceptor.


title: Expression data from primary hepatocytes isolated from miR-143DOX mice

status: Public on Apr 08 2011

city: Cologne

first: Jens

middle: Claus

last: Bruening

address: Zuelpicher Str.47

department: Mouse Genetics and Metabolism

country: Germany

institute: Institute for Genetics, University of Cologne

summary: The contribution of altered posttranscriptional gene silencing (PTGS) to the development of insulin resistance and type 2 diabetes mellitus so far remains elusive. We have described that expression of microRNAs (miR)-143 and -145 is dysregulated in genetic and dietary mouse models of obesity. Induced transgenic overexpression of miR-143, but not miR-145, causes insulin resistance and impaired insulin-stimulated AKT activation. We used microarrays to analyze the underlying molecular mechanisms of miR-143-mediated development of insulin resistance.

overall_design: miR-143DOX mice (n=3) and wildtype littermate controls (n=3) were treated with doxycycline via the drinking water to induce miR-143 overexpression in the transgenic animals. Primary hepatocytes were isolated for RNA extraction and hybridization on Affymetrix microarrays.

middle: C

last: Brüning

first: Sabine

last: Jordan


title: Gene expression analysis of Staphylococcus aureus strain 1422 vs. Staphyloccus aureus strain 2798 to find a novel mechanism of methicillin resistance

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary: The study aims to characterize a new isolate that lacks mecA but is nevertheless resistant to methicillin in order to find a novel mechanism of methicillin resistance.

overall_design: Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

middle: B

last: Jones

first: Rosslyn

last: Maybank

first: Bryan

last: Frank

last: Boyle-Vavra

first: Lakshmi

last: Appalla

first: Scott

last: Scott


title: Gene expression analysis of Linezolid resistance in various clinical Stapyloccoccus aureus strains.

first: Wei

last: Liang

address: 9704 Medical Center Drive

institute: JCVI

summary:
The study aims to identify genes associated with Linezolid resistance.
Linezolid resistant strains were compared to a Linezolid sensitive reference strain in the presence of linezolid and absence of linezolid (mock).

overall_design:
 Samples were hybridized on aminosilane coated slides with 70-mer oligos.
63 samples were submitted (31 dye swap pairs and 1 unpaired hyb result).
Reference sample for all hybridizations was Staphylococcus aureus strain 378 (a Linezolid sensitive strain) . Query strains were clinical isolates (Linezolid resistant strains) 3577, 5612, 6939, and 7210.  In some hybs both query and reference samples were exposed to Linezolid and in others both query and reference samples were exposed to a mock (control) treatment.  Samples were assayed 30, 60, 90, or 120 minutes after inoculation to observe time dependent responses.  The query and reference samples were time matched, e.g. a 30 minute query sample was paired with a 30 minute reference sample.

last: Boyle-Varra

last: Peterson


title: Gene expression analysis of Staphyloccoccus aureus USA300 vs USA300 agr knockout.

summary: The study aims to compare gene expression patterns of Staphyloccoccus aureus USA300 wild type (reference) vs USA300 agr knockout(query). The agr quorum sensing system is an important regulator of density dependent gene expression. To determine the role of agr in USA300 virulence a agr mutant was constructed and differential gene expression compared to the parental wildtype.

overall_design: Wild type and an agr mutant USA300 strain were grown in TSA broth over a time course. RNA samples were harvested at early, mid-log, late log and early station ary phase. Samples were hybridized on aminosilane coated slides with 70-mer oligos.  Gene expression patterns of the WT and mutant strains were compared.


title: Gene expression analysis of Daptomycin resistance in Stapyloccoccus aureus strains: 2818 and 2819.

first: Brian

last: Bishop

state: Maryland

institute: Bishop, Brian

summary: The study aims to identify genes associated with daptomycin resistance.


title: Gene expression analysis of Oxacilin resistance in Stapyloccoccus aureus strains: 923 and V3

first: Vasily

middle: A

last: Sharov

department: PFGRC

summary: The study aims to identify genes associated with oxacilin resistance. Staphylococcus aureus USA300 (also referred as 923) is used as reference strain through the whole study.

overall_design: 10 arrays total.


title: Gene expression analysis of Staphyloccoccus aureus USA300 vs USA300 sae knockout

summary: The study aims to compare gene expression patterns of Staphyloccoccus aureus USA300 vs USA300 sae knockout. Samples were hybridized on aminosilane coated slides with 70-mer oligos.

overall_design: 12 arrays total.


title: Gene expression analysis of Vancomycin resistance in Stapyloccoccus aureus strains: 2275, 2279, 2276, 2277, 2278, and 2283.

first: PFGRC

last: JCVI

institute: J. Craig Venter Institute

summary: Understanding novel mechanism bacteria ustilize in the clinics to become resistant to antibiotics is critical. The study aims to identify genes associated with Vancomycin resistance. Clinical isolates from a single patient with increasing resistance to vancomycin were grown in the presence and absence of vancomycin.Staphylococcus aureus strain 2275 is the reference for this series.

overall_design: S. aureus isolates from a single patient were grown in the presence and absence of vancomycin over a 2 hour time course.  RNA samples were extracted at 30, 60 90 and 120 minutes post exposure to antibiotic.  Samples were hybridized on aminosilane coated slides with 70-mer oligos comparing mock treated and treated cells to the first strain isolated in the lineage. Differnetial gene expression patterns were determined.


title: Histone H3 lysine 9 dimethylation of miRNA genes in HMEC and HMF

status: Public on Apr 05 2011

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

summary: Normal cell type specific histone H3 lysine 9 dimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 9 dimethylation affect miRNA expression.

overall_design: Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 dimethylated at lysine 9 (CS200587, Millipore).

first: James

last: Garbe

first: Martha

middle: R

last: Stampfer

first: Bernard

last: Futscher


title: Histone H3 lysine 4 trimethylation of miRNA genes in HMEC and HMF

summary: Normal cell type specific histone H3 lysine 4 trimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 4 trimethylation affect miRNA expression.

overall_design: Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 trimethylated at lysine 4 (05-745, Upstate).


title: Gene expression analysis of Vancomycin resistance in Stapyloccoccus aureus strains: PA, C1 and T8.

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

summary: The study aims to identify genes associated with Vancomycin resistance. Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples  extracted over a two hour time course.Staphylococcus aureus strain PA is the reference for this series.

overall_design: Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples  extracted over a two hour time course. Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Susan

first: Lakshimi

last: Apalla


title: [E-MTAB-366] Transcription profiling by array of chicken embryos at 15 different stages

city: Kobe

first: Naoki

last: Irie

state: Hyogo

address: 2-2-3 Minatojima-minami Chuo-ku

country: Japan

institute: RIKEN Center for Developmental Biology

summary:
Transcription profiling of chicken development
The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

overall_design: Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to the Affymetrix Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.


title: Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3

status: Public on Apr 07 2011

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

institute: IRD

summary:
Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in C. glauca.
Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen  which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis:  -  an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time)  - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d).  Three biological replicates were used for each condition.

overall_design: Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.

last: Hocher

first: Florence

last: Auguy


title: Expression analysis of mouse retinas after treatment with VEGF-A or Dll4-Fc.

city: Tarrytown

first: Ivan

last: Lobov

address: 777 Old Saw Mill River Road,

department: Regeneron Pharmaceuticals

institute: Regeneron Pharmaceuticals

summary: Transcriptional profiling of retinas extracted from mouse pups 24 hours after IVT injection (at P8) of 1 microgram VEGFA, 4 micrograms Dll4-Fc, or 4 microgram hFc alone.  Goal was to determine the mechanism by which inhibiting Dll4/Notch pathway is vasoprotective during retinal development.

overall_design: Three-condition experiment: VEGF-A treated vs hFc, Dll4-Fc vs hFc.  Four replicates each for Dll4-Fc and hFc, five for VEGF-A.

first: Yi

last: Wei

first: Gabor

last: Halasz

first: Stanley

middle: J

last: Wiegand


title: Gene expression analysis of Staphyloccoccus aureus USA300 vs USA400.

summary: In the community and clinical settings MRSA infections are more commonly caused by a USA300 strain vs a USA400 strain. The study aims to compare gene expression patterns of Staphyloccoccus aureus USA300(reference) vs USA400(query) and to determine why USA400 is being replaced by a USA300 strain.

overall_design: The USA300 and USA400 isolates were grown in TSA media to early log, mid log, late log and stationary phase. RNA samples were extracted and samples were hybridized on aminosilane coated slides with 70-mer oligos. Differential gene expression patterns were compared between the two strains.

first: Marcus

last: Jones

first: Rosslyn

last: Maybank

first: Bryan

last: Frank

last: Boyle-Vavra

first: Lakshmi

last: Appalla

first: Scott

last: Peterson


title: Comparative genome hybridization of meningococcal isolates I

status: Public on Apr 09 2011

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

summary: Meningococcal strains from different serogroups and different clonal complexes were compared using cGH analyses

overall_design: DNA isolated from the various strains were compared using a common reference design where the common reference comprised of a pool of all individual DNA´s.

first: Roland

last: Schwarz

first: Biju

last: Joseph

first: Gabriele

last: Gerlach

first: Kathrin

last: Engelhard

first: Mathias

last: Frosch

first: Tobias

last: Müller

first: Christoph

last: Schoen


title: Aire regulates transfer of antigen from mTEC to dendritic cells for induction of thymic tolerance

status: Public on Apr 06 2011

city: Melbourne

first: Francois-Xavier

last: Hubert

state: Victoria

address: 1G Royal Parade

department: Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: To investigate the role of Aire in thymic selection, we examined the cellular requirements  for generation of ovalbumin (OVA)-specific CD4 and CD8 T cells in mice expressing  OVA under the control of the rat insulin promoter (RIP). Aire-deficiency reduced the  number of mature single positive (SP) OVA-specific CD4+ or CD8+ T cells in the  thymus, independent of OVA expression. Importantly, it also contributed in two way to  OVA-dependent negative selection depending on the T cell type. Aire-dependent  negative selection of OVA-specific CD8 T cells correlated with Aire-regulated  expression of OVA. By contrast, for OVA-specific CD4 T cells, Aire affected tolerance  induction by a mechanism that operated independent of the level of OVA expression,  controlling access of antigen presenting cells to mTEC-expressed OVA. This study  supports the view that one mechanism by which Aire controls thymic negative selection  is by regulating the indirect presentation of mTEC-derived antigens by thymic dendritic  cells. It also indicates that mTEC can mediate tolerance by direct presentation of Aireregulated  antigens to both CD4 and CD8 T cells.

overall_design: Total RNA was extracted from medullary thymic epithelial cells isolated from wildtype and Aire-deficient C57BL/6 mice for comparison of gene expression profiles.

first: Sarah

last: Kinkel

first: Gayle

middle: M

last: Davey

first: Belinda

last: Phipson

last: Mueller

first: Adrian

last: Liston

first: Anna

middle: I

last: Proietto

first: Ping

middle: Z

last: Cannon

first: Simon

last: Forehan

first: Gordon

last: Smyth

first: Li

last: Wu

first: Christopher

last: Goodnow

first: Francis

last: Carbone

first: Hamish

last: Scott

first: William

last: Heath


title: Mechansisms of resistance to decitabine in myelodysplastic syndrome

city: Houston

first: Taichun

last: Qin

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

type: Methylation profiling by genome tiling array

summary: Investiage global methylation changes between patients at diagnosis and after relapse by CpG island methylation microarray analysis and determine the role of gene-specific methylation associated with relapse of cancer patients.

overall_design: Two-condition experiment, Biological replicates: 2 biological replicates and 2 samples from the same methylated CpG island amplification (MCA).

first: Jean-Pierre

last: Issa


title: Histone H3 acetylation of miRNA genes in HMEC and HMF

first: Lukas

last: Vrba

summary: Normal cell type specific histone H3 acetylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 acetylation affect miRNA expression.

overall_design: Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-acetylated histone H3 antibody (06-599, Millipore).

first: James

last: Garbe

first: Martha

last: Stampfer

first: Bernard

last: Futscher


title: WT_SK1 meiotic time course on expression/splicing microarrays

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary:
synchronized WT_SK1 meiotic time course
The SK1 strain background undergoes meiosis with high efficiency and synchronicity (ATCC:MYA-2089)

overall_design: Two independent time courses; Dye swap of each time point; Reference pool WT RNA comprised of 50% time zero RNA plus 10% each of time 2 hours, 5, hours, 7 hours, 9 hours and 11 hours

first: Lisa

last: Trevino

first: Elizabeth

last: Munding


title: ume6D_BY4741 on expression/splicing microarrays

summary:
ume6D_BY4741 vegetative RNA compared to WT_BY4741 vegetative RNA.
ume6D haploid was generated in the BY4741 strain background (ATCC: 201388) by PCR-mediated cassette-based gene replacement where the UME6 ORF was replaced with KANMX6, the deletion was verified by PCR.

overall_design: Vegetatively grown; Dye swap; Reference vegetative WT_BY4741

first: Manuel

last: Ares Jr.


title: mer1D_SK1, mer2D_SK1, mer3D_SK1, spo22D_SK1, and spo70D_SK1 on expression/splicing microarrays

summary:
mer1D_SK1, mer2D_SK1, mer3D_SK1, spo22D_SK1, spo70D_SK1 late 9h meiotic time point.
mer1D, mer2D, mer3D, spo22D diploid, and spo70D diploid was generated in the SK1 strain background (ATCC: MYA-2089) by PCR-mediated cassette-based gene replacement where the MER1, MER2, MER3, SPO22, or SPO70 ORF respectively was replaced with HIS3 from S. kluyveri then the transformants were sporulated and the homozygous deletion was verified by PCR.

overall_design: Meiotic time point =9h; Dye swap; Reference WT_SK1 9h

first: Haller

last: Igel


title: CpG Island methylation variation in placentae of Intra-Uterine Growth Restricted (IUGR) fetuses versus controls

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Methylation profiling of CpG Island Methylation of genomic DNA samples extracted from placentae of Intra-Uterine Growth Restricted newborns and gestational age matched controls. These data can be used for methylation comparisons between these two types of samples. The results of such comparisons can be used to generate hypotheses on the involvement of DNA methylation variation in placenta development and fetal growth.

overall_design: Two-condition Methyl DNA Immunoprecipitation (MeDIP) experiment, IUGR vs. Control placenta samples. Biological replicates: 8 control, 8 IUGR cases.

first: Jose

last: Ferreira

first: Sanaa

last: Choufani

first: Daria

last: Grafodatskaya

first: David

last: Chitayat

first: Cheryl

last: Shuman

first: John

last: Kingdom

first: Sarah

last: Keating


title: mer1D_SK1 meiotic time course on expression/splicing microarrays

summary:
Synchronized mer1D_SK1 meiotic time course.
mer1D diploid was generated in the SK1 strain background (ATCC: MYA-2089) by PCR-mediated cassette-based gene replacement where the MER1 ORF was replaced with HIS3 from S. kluyveri then the transformants were sporulated and the homozygous deletion was verified by PCR.


title: Escherichia coli O157:H7 : Control vs. PEG8000 treated

status: Public on Apr 02 2011

city: Seoul

first: Jinki

last: Yeom

address: Anam-Dong, Sungbuk-Gu

department: Life Science

institute: Korea University

summary: Transcriptional profiling of E.coli O157:H7 cells comparing control untreated cells with PEG8000treated cells

overall_design: Two-condition experiment, Control vs. PEG8000. Biological replicates: 1 control, 1 treated.

first: Yunho

last: Lee


title: MicroRNA expression during Hematopoiesis

status: Public on Apr 03 2011

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

summary: Murine ES cells were grown on confluent OP-9 and differentiated along the hematopoitic lineage. To assess the effects of Notch in hematopoiesis, activated Notch was overexpressed from Day 5 to Day 8.

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

overall_design: Samples included Day 5 (control) and Day 8 Notch On and Day 8 Notch Off, the samples were done in triplicates.

first: Hamidi

last: Habib

first: Gasson

last: Judith


title: Glioblastoma Cell lines vs. Normal Glial Cells

city: San Antonio

first: Jonathan

middle: Adam

last: Gelfond

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

summary:
Examination of alternative splicing in 4 glioblastoma cell lines (U118, t98g, a172, U87) vs. FGG cells grown in culture.

SUBMITTER_CITATION: Jonathan Gelfond, Lee Ann Zarzabal, Tarea Burton, Suzanne Burns, Mari Sogayar, Luiz O. F. Penalva. Latent rank change detection for analysis of splice-junction microarrays with nonlinear effects. Annals of Applied Statistics 2011, Vol. 5, No. 1, 364-380

overall_design: 4 Cancer Cell lines vs. Normal Cells in a dye-swap design with 2 replicates in each dye orientation (4 tumor lines x 2 reps x 2 dye-orientations = 16 arrays)

first: Luiz

last: Penalva


title: Microarray analysis of differential utilization of plant based diets by rainbow trout

status: Public on Apr 01 2011

city: Hagerman

first: Ken

last: Overturf

state: Idaho

address: 3059-F National Fish Hatchery Road

institute: USDA-ARS

summary: Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes.

overall_design: Genotyped samples linked to families that had 4 or more members sampled on each diet were identified and ranked according to average family weight on each diet. Size rankings corresponded to large (>750 g), medium (600-640 g), and small (<500 g). From these identified groups 2 families were chosen for microarray expression analysis that demonstrated individuals with growth differences between the two diets. Data for the two families used for analysis and slide arrangements are listed in table 3. The families compared for growth differences between diets used for this study only differed by one growth range, large fish on fish meal compared to medium fish on plant-based diet and medium sized fish on fishmeal diet compared to small fish on plant-based diet. This strategy to use size separation within family was an attempt to identify gene changes more specific to diet utilization than specific for growth differences.

first: Yniv

last: Palti

first: Rick

last: Barrows

first: James

last: Parson

first: Roger

last: Vallejo


title: Histone H3 lysine 27 trimethylation of miRNA genes in HMEC and HMF

first: Lukas

last: Vrba

summary: Normal cell type specific histone H3 lysine 27 trimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 27 trimethylation affect miRNA expression.

overall_design: Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 trimethylated at lysine 27 (07-449, Millipore).

last: Garbe

first: Martha

last: Stampfer

first: Bernard

last: Futscher


title: Campylobacter jejuni Utilization of Mucin

city: Ottawa

first: Alain

last: Stintzi

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

institute: University of Ottawa

summary: While growing in the human intestine, C. jejuni grows within the mucus layer.  The largest constituents of this layer are the large mucin glycoproteins.  A transcriptomic profile of C. jejuni NCTC11168 growing in a mucin-containing minimal medium seeks to describe the effect of the presence of mucin proteins on the transcriptome of C. jejuni.

overall_design: Microarray data was collected from three independent biological replicates and 9 technical replicates for each biological replicate.

first: Martin

last: Stahl


title: Campylobacter jejuni Utilization of Fucose

summary: Transcriptional profile of C. jejuni NCTC11168 while growing in MEM medium containing L-fucose.  We hypothesize that certain C. jejuni strains, containing A certain genomic island, have acquired the ability to metabolize fucose.  This study demonstrates the transcriptional profile C. jejuni growth while utilizing fucose.

overall_design: Microarray data was collected from three independent biological replicates and 6-9 technical replicates for each biological replicate.


title: DNA methylation of miRNA genes in HMEC and HMF

summary: Normal cell type specific DNA methylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including DNA methylation effect miRNA expression.

overall_design: Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-Methylcytosine (5MeC) antibody.


city: Guangzhou

first: chen

last: wen

address: 74 Zhongshan Road 2

department: Department of Toxicology

institute: Sun Yat-sen University

summary: To identify miRNAs involved in ST-induced cell transformation, we used microarray chips containing 856 miRNA probes to define miRNA expression profiles in 16HBE,16HBER and 16HBERST cells.

overall_design: we created HBE cells at different stages of the cell transformation process (Pang et al., 2008). In brief, primary human bronchial epithelial cells were immortalized by expressing SV40 LT and hTERT (named as HBELH cells). HBER cells were created by introduction of an oncogenic version of H-Ras into HBELH cells. In agreement with previous studies, the expression of the oncogene H-Ras led to an increase in cell proliferation; however these cells (HBER) were unable to grow in soft agar or form tumors in immunodeficient mice. Subsequently, HBERST cells generated by the additional introduction of SV40 ST into HBER cells grew in an anchorage independent fashion and formed tumors in immunodeficient mice. Therefore, these cell lines represent distinct stages of immortalized cells (HBELH), pre-transformed cells (HBER) and transformed cells (HBERST). And then, the different miRNA expression profiles of HBE cells at different stages were assayed by miRNA microarray.

first: Wen

last: Chen

first: Qing

last: Wang

first: Daochuan

last: Li


title: Transcriptome analysis of genes regulated by CUP-SHAPED COTYLEDON1 (CUC1) transcription factor in Arabidopsis thaliana

status: Public on Mar 31 2011

city: Kumamoto

first: Mitsuhiro

last: Aida

address: 2-39-1 Kurokami, Chuo-ku

institute: Kumamoto University

summary:
Samples 1 & 2: Comparison of gene expression between wild type (ecotype Ler) and 35S:CUC1, in which CUP-SHAPED COTYLEDON1, a master regulator of the shoot meristem and boundary establishment, is constitutively expressed under the cauliflower mosaic virus 35S promoter.
Samples 3 & 4: Comparison of gene expression between stm-1 (ecotype Ler) and stm-1 35S:CUC1

overall_design: RNA was isolated from cotyledons of 5-day-old  (for Ler vs 35S:CUC1) or 10-day-old (for stm vs 35S:CUC1stm) seedlings.  Two independent biological replicates were analyzed for each comparison.

first: Ayano

last: Kariya


title: Identification of changes in gene expression in seedlings of the ashh2/sdg8 Arabidopsis mutant

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: Mutation of the ASHH2 gene has pleiotropic developmental effects. The aim of the study was to identify changes in gene expression in seedlings of the ashh2-1/sdg8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) and look for  correlation wth changes in  methylation marks on histone tails. Wild type Arabidopsis thaliana (ecotype Colombia) seedlings were used as reference. For low-expresssed tissue-specific genes there was a correlation between reduced H3K36me3 levels and reduction in expression. Although some highly expressed genes with low tissue-specificity show reduced H3K36me3 levels in the mutant, expression levels were, however, not affeccted.

overall_design: Six biological replicates with 12 plants each both of Arabidopsis thaliana wild type (ecotype Colombia-0) and ashh2-1/sgd8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) were sown out on soil and grown under the following conditions; 22oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity. The inflorescences of each biological replikate were harvested in bulk from 30-36 days old plants at same time of the day (between 12:45 and 13:45) and at the same developmental stage in bulk.

first: Vibeke

last: Alm

first: Tage

last: Thorstensen

first: Tommy

middle: S

last: Jørstad

first: Per

last: Winge


title: Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Analysis of cross talk of epigenetic marks in HBEC by using tilling arrays chr19. In Human Bronchial epithelia cells (HBEC), H3K9me3, H4K20me3, H3K4me3, H3K27me3, H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA and UnmethylCollector (UMC).
Study of epigenetic changes in HCT116 DNMT1-/- and DNMT3b -/- (HCT116-DKO) in comparison to intact HCT116. In HCT116 and HCT116-DKO, H3K9me3,  H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA.
Analysis of epigenetic changes caused by siRNA for SED2 transcript in HBEC. In HBEC and SETD2 siRNA HBEC, H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA.

overall_design: Comapre DNA methylation and other histone modification marks

first: Maria

last: Hahn

first: Arthur

middle: X

first: Torsten

first: Gerd

middle: P

last: Pfeifer


title: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Populus]

city: Oak Ridge

first: David

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

summary: The heat shock response continues to be layered with additional complexity as interactions and cross-talk among heat shock proteins, the reactive oxygen network and hormonal signaling are discovered. However, comparative analyses exploring variation in each of these processes among species remains relatively unexplored. In controlled environment experiments, photosynthetic response curves were conducted from 22 °C to 42 °C and indicated that temperature optimum of light saturated photosynthesis was greater for Glycine max relative to Arabidopsis thaliana or Populus trichocarpa. Transcript profiles were taken at defined states along the temperature response curves and inferred pathway analysis revealed species-specific variation in the abiotic stress and the minor carbohydrate raffinose/galactinol pathways. A weighted gene co-expression network approach was used to group individual genes into network modules linking biochemical measures of the antioxidant system to leaf-level photosynthesis among P. trichocarpa, G. max and A. thaliana. Network enabled results revealed an expansion in the G. max HSP17 protein family and divergence in the regulation of the antioxidant and heat shock module relative to P. trichocarpa and A. thaliana. These results indicate that although the heat shock response is highly conserved, there is considerable species-specific variation in its regulation.

overall_design: fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum).This resulted in 16 separate samples hybridized to independent microarrays totaling 4 – replicates x 4 physiological states).

first: Sara

last: Jawdy


title: Defining the serotype M3 RopB regulon

first: Samuel

last: Shelburne

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: Recent whole-genome sequencing of large populations of the same bacterial species has revealed significant disparity among genes in the frequency of single nucleotide polymorphisms (SNPs).  For example, a previous analysis of invasive serotype M3 group A streptococci (GAS) found the highest frequency of SNPs in the gene (ropB) encoding the regulator of proteinase B (RopB).  This finding led us to hypothesize that RopB polymorphisms contribute to altered GAS host-pathogen interactions.  Sequencing of ropB in 171 invasive serotype M3 GAS strains from a surveillance study identified 19 distinct ropB alleles.  Inactivation of the ropB gene in strains producing distinct RopB variants had dramatically different effects on GAS global gene expression.  Further, analysis of laboratory-generated isoallelic GAS strains differing only by a single amino acid replacement in RopB confirmed that the variant protein affected the transcript level of the gene encoding streptococcal proteinase B, a major RopB-regulated virulence factor.  Comparison of parental, RopB-inactivated, and RopB isoallelic strains in mouse infection models demonstrated that RopB polymorphisms significantly influence GAS virulence and disease manifestations.  These studies detail a paradigm in which unbiased, whole-genome sequence analysis of populations of clinical bacterial isolates creates new avenues of productive investigation into the pathogenesis of common human infections.

overall_design: This study examined the effects of RopB inactivaiton on two distinct serotype M3 group A streptococcal strains with distinct forms of the RopB protein.  RopB was inactivated in a strain with a wild-type RopB allele (strain MGAS10870) and in a strain with a RopB allele containing a C85Y polymorphism (strain MGAS9937). The wild-type and RopB inactivated strains were grown in duplicate to the early stationary growth phase in standard laboratory medium (THY).  Total RNA was isolated, converted to cDNA, and hybridized to a custom-made Affymetrix GeneChip.

first: Ronan

last: Carroll

first: James

last: Musser