title: Leaf gene expression profile of rice during sunrise

summary: A continuous gene expression profiling of leaves was performed at regular interval during the sunrise period to understand the changes of transcriptional program in the rice plant grown under natural field conditions in response to solar radiation.

overall_design: At 79 days after transplanting, leaf samples corresponding to the uppermost fully expanded leaves were collected at 10-min intervals in two replicates from 3:50 AM until 6:00 AM. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.


title: Diurnal and circadian gene expression profile of root throughout the entire growth of rice in the field

status: Public on Dec 03 2012

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: A continuous gene expression profiling of roots was performed at regular interval during a 48-hr period in 2 different growth stages to characterize the diurnal and circadian gene expression profile of rice growth under natural field conditions.

overall_design: Root was collected at 2-hr intervals during a 48-hr period at 2 different growth stages corresponding to early and late vegetative stages.  All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

first: Hinako

last: Takehisa

first: Baltazar

last: Antonio

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: Transcriptome of dehydrated vs hydrated Salmonella cells

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

summary: Transcriptional profiles of dehydrated Salmonella Typhimurium SL1344 cells post 22h air drying were compared to those of SL1344 cells incubated for 22 h in DDW

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Two-condition experiment, dehydrated versus hydrated (control) Salmonella cells. Biological replicates: 4 control, 4 dehydrated, independently grown and harvested. One replicate per array.

first: Steffen

last: Porwollik

first: Nadia

last: Gruzdev

first: Shlomo

last: Sela

first: Shany

last: Ofaim


title: Continuous gene expression profile of root at nighttime throughout the entire growth of rice in the field

summary: A continuous gene expression profiling of roots was performed during nighttime at regular interval from transplanting until harvesting to characterize the transcriptional and physiological changes in the root system of rice throughout the entire growth under natural field conditions.

overall_design: Roots were sampled at nighttime (24:00) at 7-day intervals encompassing 14 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.


title: Leukocyte gene expression in rhesus macaques reared under different conditions

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 4 mo old rhesus macaques subject to maternal rearing, peer rearing, or surrogate peer rearing.  The primary research question is whether gene expression differs as a function of early rearing conditions.


title: Airway Epithelial miRNA Expression in Asthma

status: Public on Dec 05 2012

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: We performed genome-wide profiling of miRNA expression in the airway epithelial compartment in asthma to identify miRNA pathways associated with epithelial abnormalities using miRNA microarrays and real-time PCR. We also sought to identify the effect of inhaled corticosteroids (ICS) on airway epithelial miRNA expression

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Samples were obtained from  airway epithelial cells by bronchoscopic brushing from three groups of subjects: Healthy Controls ( N=12), Steroid Naïve Asthma (N=16), Steroid-requiring Asthma (N=19).


title: Functional characterization of Arabidopsis WRKY15 overexpressor plants

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Transcriptional profiling of Col4WT and WRKY15 overexpressor (WRKY15OE) plants, grown under controlled and mild salt stress conditions in order to identify molecular mechanisms underlying the increased salt stress sensitivity of WRKY15OE plants.

overall_design: Two genotypes x two conditions experiment, including Arabidopsis Col4WT and WRKY15OE plants grown on half-strength MS plant medium supplemented with 0 or 50 mM NaCl. Three biological replicates. Each sample was hybridized to one Genechip® Arabidopsis Tiling 1.0R array.

first: Sandy

last: Vanderauwera

first: Frank

last: Van Breusegem


title: Pig adipose tissue: comparison between Basque and Large White breeds

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

summary: Transcriptional profiling of pig adipose tissue comparing two divergent breeds: Large white (LW, conventional) and Basque (B, local, indigeneous).

overall_design: Four-condition experiment, LW vs. B muscles at 35 kg and 145 kg live weight. Biological replicates: at 145 kg, 10 B and 10 LW; at 35 kg 5 B and 5 LW. One replicate per array.

first: Marie

last: Damon

first: Annie

last: Vincent

first: Isabelle

last: Louveau


title: Leaf gene expression profile of rice during sunset

first: Yutaka

last: Sato

summary: A continuous gene expression profiling of leaves was performed at regular interval during the sunset period to understand the changes of transcriptional program in the rice plant grown under natural field conditions in response to solar radiation.

overall_design: At 78 days after transplanting, leaf samples corresponding to the uppermost fully expanded leaves were collected at 10-min intervals from 5:00 PM until 8:00 PM. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

first: Baltazar

last: Antonio


title: Transcriptional profile of ΔcalA and ΔcrzA Aspergillus fumigatus mutants during  mammal infection

status: Public on Dec 02 2012

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

summary: Aspergillus fumigatus mutant strains were collected from bronchoalveolar lavage fluids (BALFs) during acute mouse infection (4 and 12 hours).

overall_design: Transcriptional analysis were conducted by comparison of each mutant with the wild type strain (CEA17) in a dye swap experiment. Besides, we performed the transcriptional profile of akuB(KU80) mutant compared to CEA17 wild type strain. All the strains were recovered from bronchoalveolar lavage fluid from CD1 mice infected with 10e8 spores for 4 and 12 hours.

first: Frederico

middle: M

last: Soriani

first: Charles

middle: T

last: Cairns

first: Omar

last: Loss

first: Elaine

last: Bignell

middle: H


title: Continuous gene expression profile of leaf at nighttime throughout the entire growth of rice in the field

summary: A continuous gene expression profiling of leaves was performed during nighttime at regular interval from transplanting until harvesting to understand the changes of transcriptional program and physiological state throughout entire growth of the rice plant under natural field conditions.

overall_design: The uppermost fully-expanded leaf in the main stem corresponding to the 1st leaf until 83 days after transplanting (DAT) and the flag leaf from them on were sampled in two replicates at 12:00 midnight at 7- day intervals encompassing 17 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy (DNA methylation)

status: Public on Dec 01 2012

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

country: Sweden

institute: Lund University

type: Methylation profiling by genome tiling array

summary:
To increase our understanding of epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient.
We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation.

overall_design: comparison of trisomy 8 cells with disomic as well as reference fibroblasts

first: Bertil

last: Johansson


title: Differential microRNA expression in the ovaries of high and low prolificacy pregnant sows from an Iberian x Meishan F2 intercross

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

summary: Prolificacy related traits are of great economical interest in the pig industry. microRNAs (miRNAs) are post-transcriptional regulators of gene expression important for reproductive processes. In pigs, the roles of ovarian miRNAs during gestation remain unknown although the ovaries are essential during gestation. It has been hypothesised that ovarian miRNAs could participate during the porcine gestation and, moreover, they could influence the prolificacy levels of sows. The miRNA expression profile was compared in the ovaries of pregnant Iberian x Meishan F2 sows displaying extreme phenotypes regarding prolificacy levels defined as the number of embryos (NE) attached to the uterus at 30-32 days of gestation. miR-146a-5p and miR-142-3p were differentially expressed between high (NE≥13) and low (NE≤11) prolificacy sows. In silico functional analyses of the predicted mRNA targets for these miRNAs revealed that miR-146a-5p targets were mainly involved in the immune system response important for the establishment of the maternal-foetal tolerance, implantation and maintenance of pregnancy. On the other hand, miR-142-3p targets participated in different biological processes that would contribute to the homeostasis maintenance to ensure a correct functional development of the ovaries. miRNAs associated with prolificacy levels could regulate negatively, by a novel post-transcriptional mechanism, their predicted mRNA targets, PPM1K, TLR1 and CPEB2 which have been reported as differentially expressed in the ovaries of pregnant sows regarding the prolificacy levels. Furthermore, among predicted mRNA targets for miRNAs associated with prolificacy, four genes, differentially expressed in the ovaries of pregnant sows regarding prolificacy levels, (LRRK1, BAT1, CPEB2, CCL8) are proposed to be good candidate genes for litter size due to their location within confidence intervals for prolificacy QTL described previously.  Overall, it is suggested that the up-regulation of miR-146a-5p and miR-142-3p in the ovaries of pregnant sows could help in the establishment of a uterine environment, which would favor the embryonic development.

overall_design: Total RNA was isolated from uterus of Iberian x Meishan F2 pregnant sows divided into two groups: High prolificacy sows (n=3) and Low prolificacy sows (n=3). RNA was labeled with the Cy3-like Hy3™ dye, mixed with a pool of RNA from the six samples labeled with the Cy5-like Hy5™ dye, and hybridized to two-color miRCURY™ arrays from Exiqon®.

first: Ingrid

last: Balcells

first: Oriol

last: Timoneda

first: Susanna

last: Cirera

first: Thomas

last: Litman

first: Amanda

last: Fernández-Rodríguez

first: José

middle: L

last: Noguera

first: Armand

last: Sánchez

first: Anna

last: Tomás


title: Expression Data from Acinetobacter baumannii strain ATCC 17978 and isogenic lpsB mutant cells

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
lpsB encodes a glycosyltransferase involved in lipopolysaccharide (LPS) synthesis.  LPS is a major component of the Gram-negative bacterial outer membranes.
We used custom-made Affymetrix A. baumannii strain ATCC 17978 derived GeneChips to compare the gene expression properties of wild type and isogenic lpsB mutant cells.  Two mutants were evaluated; A. baumannii strain 5A7 is a ATCC 17978 derivative harboring a transposon (Tn5) within lpsB (A1S_0430 locus); A. baumannii strain containing a deletion of lpsB (A1S_0430).

overall_design: A. baumannii strain ATCC 17978, 5A7 (lpsB:Tn5) or IH1∆lpsB (∆lpsB) were grown to mid-exponential phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the transcription profile of lpsB mutated cells.

first: Eric

last: Skaar


title: mRNA profiling in HIV-1 latently infected cells

city: Hangzhou

first: Jin

last: Yang

address: Qingchun Road 79

country: China

institute: Zhejiang University

summary: Investigation of whole genome gene expression level changes in HIV-1 latented infected cells, compared to the replicated cells and control cells.

overall_design: In this study, the in vitro steady cell culture was used to explore the mRNA transcription signatures in HIV-1 infection. mRNA profiles were performed and compared among normal control,HIV-1 latency and HIV-1 replication .

first: Zongxing

first: Juan

last: Wang

first: Linfang

last: Cheng

first: Nanping

last: Wu


title: Diurnal and circadian gene expression profile of leaf throughout the entire growth of rice in the field

first: Yutaka

last: Sato

summary: A continuous gene expression profiling of leaves was performed at regular interval during a 48-hr period in 9 different growth stages from transplanting until harvesting to characterize the diurnal and circadian gene expression profile of rice and to understand the transcriptional program and physiological state throughout entire the growth under natural field conditions.

overall_design: The uppermost fully expanded leaf in the main stem was collected at 2-hr intervals during a 48-hr period at 9 different growth stages encompassing the vegetative, reproductive and ripening stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

first: Baltazar

last: Antonio

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: MicroRNA expression analysis of tumor tropic mesenchymal stem cells

city: New Orleans

first: Reza

last: Izadpanah

state: Louisiana

address: 1430 Tulane Avenue

department: Medicien

institute: Tulane University

summary: The subpopulations of mesenchymal stem cells isolated from breast adipose tissue which display migrated towards conditioned media from MDA-MB231 cell line were expanded for miRNA analysis. The tumor microenvironment (TM) is known to promote tumor growth and progression. Ubiquitously distributed tissue resident stem cells (MSCs) elicit regenerative properties. In addition, they are capable of homing to sites of inflammation, injury, and tumor. Considering the tumor tropic property of MSCs, the interaction between the breast cancer (BC) microenvironment and breast resident adipose tissue derived MSCs (ASCs) merits further investigations. Initial data indicate that a subset of ASCs derived from breast adipose tissue (B-ASCs) display a high affinity towards the conditioned media (CM) from two breast cancer cell lines, MDA-MB231 (MDA-CM) and MCF7 (MCF-CM). Profiling secreted cytokines of these CMs identified significant expression of angiogenin, GM-CSF, and IL-6. While the expression of GRO-α, MCP-1, RANTES, and IL-1α is more pronounced in MDA-CM, MCF-CM contains higher amounts of IGFBP2, TRAIL, and ErbB3. Gene expression profiling suggests that despite the distinct differences, both migratory subset of B-ASCs towards MDA-CM and MCF-CM display perturbed expression of genes like KISS1, TNSF1, IL18 and MMP2, which could be associated with a defensive role of B-ASCs. In addition, the BC microenvironment alters microRNA (miRNA) expressions in B-ASCs. in this study the migratory cells were evaluated for miRNA expression versus non-migratory counterparts. as controls unexposed parental cell lines (2) were used on the same hybridization chip in which one labeled Hy3 and other labeled Hy5. The ratio of the control parental cells was used as base nanalysis of miRNA expression in MSCs. we also include another control in this study, the migratory subpopulations of MSCs which display migratory potentials against protein gradient (M5) were analyzed for miRNA expression versus non-migratory counterparts (NM-5). using this control facilitate identification of those miRNA responsive to tumor CM. the data analysis confirm that altered gene and miRNA profiles resulted from exposure of MCF-CM and MDA-CM on B-ASCs are similar to those observed in B-ASCs isolated from breast adipose tissue of BC patients. Analysis the signaling between the B-ASCs and TM may help in understanding the possible role of B-ASCs in stasis, progression, or regression of the BC.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The microRNA expression of migratory subpopulations were compared to parental populations of MSCs.


title: Application of BiodegPhyloChip for expression profiling of functional genes from diverse contaminated habitats

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

type:
Genome variation profiling by array
Expression profiling by array

summary: Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.

overall_design: Agilent one-color CGH experiment and one-color Gene Expresssion expereiment,Organism: Genotypic designed Agilent-17159  Genotypic designed  Agilent  Multibacterial 8x15k Array , Labeling kits:  Agilent Genomic DNA labeling Kit (Part Number: 5190-0453) and Agilent Quick Amp Kit PLUS (Part number: 5190-0442).

first: Ashutosh

last: Pathak

first: Natesan

last: Manickam


title: Transcriptome analysis of rice infected with Rice gall dwarf virus

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary: Rice gall dwarf virus (RGDV) is the causal agent of rice gall dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection.

overall_design: Comparison between RGDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

first: Takumi

last: Shimizu

first: Takahide

last: Sasaya

first: Hiroaki

last: Kondoh

first: Hiromi

first: Setsuko

last: Kimura

first: Toshihiro

last: Omura

first: Shoshi

last: Kikuchi


title: Fusarium verticillioides wild type versus LAE1 deletion mutant at 6 days on fumonisin inducing medium

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

summary:
Investigation of whole genome gene expression level changes after 6 days growth of Fusarium verticillioides wild-type and LAE1 deletion mutant in liquid fumonisin inducing media (GYAM)
Fusarium verticillioides produces a polyketide derived mycotoxin, fumonsin, over time in liquid media, Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249.

overall_design: 6 arrays: Two samples (wild type, LAE1 deletion mutant), one time point (6 days), three biological replicates.

first: Daren

last: Brown


title: human Growth Hormone (GH) responsive genes in peripheral blood mononuclear cells (PBMC)

city: Worcester

first: Mahesh

last: Appari

state: MA

address: 381 Plantation St

department: Medicine, Diabetes division

institute: University of Massachusetts Medical School - Worcester

summary: Biomarkers of responsiveness to treatment with recombinant human GH (rhGH) have only poorly been described. We aimed at identifying biomarkes of rhGH treatment in children.  Our aim was to identify the genes in response to rhGH in human PBMC, that can be used as Biomarkes of growth prediction.

overall_design: Blood was obtained from pediatric patients before and 4 days after the growth hormone therapy. RNA was isolated from the PBMC and subsequently used to perform the whole genome cDNA microarrays. We used the type-1 microarray strategy (RNA isolated before the hormone treatment as a control, and RNA isolated after rhGH treatment). Microarrays represent PBMC RNA obtained from growth hormone treated patients (green channel = baseline, red channel = GH tretmanet for 4 days).   Stanford cDNA microarrays were used. Only genes corresponding to spots with fluorescence signals of 1.5-fold over array background in both, the experimental channel (Cy5) and the reference channel (Cy3) and only genes with at least 80% interpretable data in the 9 microarray experiments were considered. Of note, the Cy5/Cy3 ratios on the arrays correspond directly to the fold up-or down-regulation of gene transcription following rhGH treatment. Subsequently, the Cy5/Cy3 ratios on arrays were log2 transformed for further analyses and the dataset was further reduced by considering only those genes with at least a 2-fold up- or down- regulation of transcription in least 3 of the 9 microarray experiments. Microarray experiments and genes were then organized by unsupervised hierarchical clustering using the Pearson correlation metric and average linkage clustering.

first: Nuria

last: Bramswig

first: Maik

last: Welzel

first: Felix

middle: G

last: Riepe

first: Paul-Martin

last: Holterhu


title: Identification of differentially expressed miRNAs in PD vs. nonPD in cancer samples

city: Phoenix

first: Irene

last: Cherni

state: AZ

address: 445 N. fifth Street

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

summary: Lack of a standard method for stratifying advanced-stage NSCLC patients receiving platinum combination therapy often results in a number of patients that do not derive benefit yet are still exposed to treatment toxicity. We hypothesized that miRNAs in pre-treatment serum and/or plasma could be used to differentiate non-small cell lung cancer (NSCLC) patients who would have disease progression to first-line carboplatin and gemcitabine chemotherapy at first response assessment. miRNA profiling of mature and precursor miRNAs was performed on total RNA isolated from the pre-treatment serum and plasma of 24 NSCLC patients. Single validated candidates or combinations thereof were selected based on specificity and sensitivity to segregate patients with disease progression at first radiologic response (PD) vs. those without progressed disease (nonPD). Two precursor miRNA were significantly over-expressed in serum (but not plasma) of PD patients: pre-miR-518b and pre-miR-598. Serum miRNAs may serve as a screening tool in predicting chemoresistance to platinum-based combination chemotherapy.

overall_design: miRNA microarray was performed on RNA extracted from matched human serum or plasma obtained from NSCLC patients


title: Interior Spruce_Bark_PissodesStrobi _Herbivory

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary: We performed a transcriptome analysis of interior spruce (Picea glauca x engelmannii) bark response to weevil (Pissodes strobi) feeding using 21.8K spruce microarray (that contains 21.8 thousand unique transcripts). This microarray study revealed a large rearrangement of the interior spruce bark transcriptome in response to weevil feeding involving differential expression of close to 20% of the studied transcriptome.

overall_design: RNA was isolated from the bark of interior spruce exposed to weevil feeding and from the bark of untreated trees at three time points (6 hours, 2 days and 2 weeks). Four independent biological replicates were included for treatment and control at each time point. Four hybridizations were performed for treatment and control comparison within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for each comparison between time points for both treatment and control (total 18 hybridizations/slides).

first: Natalia

last: Kolosova

first: Rick

last: White

first: Steven

last: Ralph

first: Colette

last: Breuil


title: Effects of Disperse Yellow 7 in Silurana tropicalis Gene Network Analysis

status: Public on Nov 30 2012

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Dyes used in fabric and leather industry are being released and accumulated into Canadian ecosystems. Recent studies have demonstrated that dyes made of azo compounds significantly increase toxicity in biota, which is explained by their toxic metabolites (e.g., aromatic amines). The metabolites of azo compounds interact with hydrophobic surfaces of cell membranes causing expansion of the membrane which impede normal cellular functions. It has been suggested that this process leads to cell death due to improper ion balance. Currently, it is estimated that between 10 and 15% of azo dyes are released in the environment as effluent. The aim of this study was to evaluate toxicity and gene networks altered by azo compounds in amphibians using ecotoxicogenomic approaches. Larvae of the frog Silurana tropicalis (Western clawed frog) were exposed to sediment contaminated to 887 ppm Disperse Yellow 7 (DY7).  Larvae were exposed from Nieuwkoop-Faber developmental stage 12 to 46. Data suggest that the azo dye DY7 induced cellular stress and interfered with androgen biosynthesis in early tadpole development. At exposure completion, RNA was isolated from whole larvae and quality was ascertained using bioanalyzer analysis. A custom Agilent 4 X 44 K microarray for S. tropicalis was used to characterize gene regulatory networks underlying toxicity. This study presents the transcriptional regulatory pathways affected by DY7 in S. tropicalis early development.

overall_design: Embryos were exposed to the DY7 dye during development. There were 4 control groups exposed and 4 treatment groups exposed.

first: Valérie

middle: S

last: Langlois

first: Justine

last: Mathieu-Denoncourt

first: Shane

last: de Solla


title: Whole DNA methylome profiling in mice exposed to secondhand smoke

status: Public on Nov 29 2012

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: A large body of evidence has linked secondhand smoke (SHS) to lung cancer in nonsmokers. Yet, the underlying mechanisms of SHS carcinogenicity in nonsmokers' lung cancer remain elusive. Recently, we have demonstrated a genotoxic mode of action for SHS, based on the ability of this carcinogen to induce adduct-driven mutagenesis in transgenic Big Blue® mice. In the present study, we have expanded this investigation to determine whether SHS can also cause epigenetic effects through aberrations of DNA methylation. Here, we have globally profiled  DNA methylation in the lung of Big Blue® mice exposed to SHS for a duration of 4-months, both immediately after the termination of exposure and at several intervals post-exposure.

overall_design: We have used a genome-wide microarray-based approach to catalogue DNA methylation profile in the lung of mice exposed to SHS and at various recovery periods from the time of exposure. Mice exposed to clean air, for comparable amount of times, were used as controls. Mice that were injected intraperitoneally with chronic doses of B(a)P (a powerful carcinogen in SHS) or DMSO (sham) were used for comparison purposes .

first: Stella

last: Tommasi

first: Albert

last: Zheng

first: Jae-In

last: Yoon

first: Arthur

middle: X

last: Li

first: Ahmad

last: Besaratinia


title: methylation profile of dermal MSCs derived from psoriasis patients and normal control

city: Taiyuan

first: Ruixia

last: Hou

state: Shanxi

address: 1,Dong San Dao Xiang, Jiefang Road

department: Dermatology

institute: Taiyuan City Central Hospital

summary: Several studies have suggested that MSCs have pleiotropic immuno-modulatory effects,  including inhibition of T cell proliferation, suppression of NK cells proliferation, modulation of cytokine production, and inhibition of dendritic cell (DC) maturation etc. But the exactly mechanism are still largely unclear.We have found that the gene expression profile of psoriatic dermal MSCs was distinct different from normal MSCs. We proposed to investigate the DNA methylation profile of psoriatic MSCs.

overall_design: 6 patients and 6 normal control were inrolled in the study, the DNA methylation profile of dermal MSCs were studied using the microarry.

first: Kaiming

last: Zhang


title: Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72.

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

country: Germany

institute: University Bremen

summary: Endophytic colonization is a very complex process which is not yet completely understood. Molecules exuded by the plants may act as signals which influence the ability of the microbe to colonize the host or survive in the rhizosphere. Here we investigated whether root exudates of the host might play a role in initiating the endophyte-rice interaction. The whole genome microarray approach was used to investigate the response of the diazotrophic model endophyte, Azoarcus sp. strain BH72, to exudates of O. sativa cv. Nipponbare in order to identify differentially regulated genes. Azoarcus sp. strain BH72 was grown in the presence or absence of root exudates of Oryza sativa cv. Nipponbare for two different time points, and differences in the gene expression profile were monitored.

overall_design: RNA from cells grown on synthetic medium for 1 and 4 hours respectively in presence (experiment) and absence (control) of exudates  was used for two color whole genome microarray approach.

first: T

last: Shidore

first: B

first: A

last: Becker


title: Differentially regulated genes induced by in vitro generated Mycobacterium tuberculosis cell wall deficient forms

city: Amherst

first: Andrea

last: Cossu

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

summary: Transcriptional profile of chemically generated Mycobacterium tuberculosis cell wall deficient forms, comparing untreated control cells (bacillary forms) and cell wall deficient cells.

overall_design: Two-condition experiment, MTB-K vs. MTB-Sph cells. Biological replicates: 3 controls, 3 spheroplasts, independently grown and harvested. In controls and spheroplasts, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, five replicates per array.

first: Valentina

last: Rosu


title: Pleiotropic effects of the gene diacylglycerol-O-transferase 1 (DGAT1) polymorphism in the mammary gland tissue of dairy cows

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

institute: INRA

summary:
The objective of this study was to determine the effect of the DGAT1 K232A polymorphism on the global mRNA expression pattern of genes in the mammary gland tissue of grazing dairy cows in order to get more insight into the effects of this polymorphism on the physiology of the mammary glandgland of grazing dairy cows.
Microarray analysis was used to identify genes whose expression was affected by the DGAT1 polymorphism in the mammary gland biopsies of 9 A232A cows, 13 K232A cows, and 4 K232K cows. The Microarray Analysis of Variance (MAANOVA) and Factor Analysis for Multiple Testing method (FAMT) were used to associate the expression of the genes present on Affymettrix Bovine Genome Arrays with the DGAT1 polymorphism. The data was also analysed at the level of functional modules by gene set enrichment analysis. In this experimental setting, DGAT1 polymorphism did not modify milk yield and composition significantly, although changes occurred in the yields of C14:0, C16:1cis-9, and some long chain fatty acids in milk. The DGAT1 polymorphism resulted in 30 differentially expressed genes related to cell growth, proliferation and development, signalling, remodelling and immune system. At the functional level, the pathways most affected by DGAT1 polymorphism were related to lipid biosynthesis, which likely reflected counter mechanisms of mammary tissue to respond to changes in milk FA composition, signalling, as well as immune system responses.

overall_design: A total of 28 Holstein-Friesian dairy cows in mid-lactation (DIM; 153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%) were used in the study. Two consecutive milk samples (a.m. and p.m. milking) were obtained and pooled. One aliquot was stored at 4°C until analysis of fat, protein and lactose percentage, and another aliquot was frozen at -20°C until analysis for FA composition by gas chromatography. Specific details regarding the analysis of FA in milk are presented in Mach et al. (2011). Approximately 750 to 1,000 mg of mammary tissue from each cow was obtained by surgical biopsy. One part of the tissue was used for isolation of DNA and the other for extraction of the RNA. Genotyping of the DGAT1 polymorphism was performed using a TaqMan allelic discrimination method in an Applied Biosystems 7500 Real-Time PCR System (Applied Biosystems) as described by Schennink et al. (2007). The genotype at the DGAT1 locus was designated KK, KA, or AA for homozygous Lysine, heterozygous Lysine/Alanine, or homozygous Alanine, respectively. Microarray analysis was used to identify genes whose expression was affected by the DGAT1 polymorphism in the mammary gland biopsies of 11 A232A cows, 13 K232A cows, and 4 K232K cows. Total RNA from mammary gland tissue (50-100 mg) was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands), following the manufacturer’s instructions. The RNA purity and concentrations were determined using a NanoDrop ND-1000 spectrophotometer (Isogen, Maarssen, the Netherlands), and the RNA quality was assessed using the BioAnalyzer 2100 (Agilent Technologies, Amsterdam, the Netherlands). The RNA of each biopsy was amplified, biotin-labeled, and hybridized to single-dye Affymetrix GeneChip® Bovine Genome Array (#900493) by ServiceXS (Leiden, the Netherlands)

first: Yuna

last: Blum

first: André

last: Bannink

first: Roselinde

last: Goselink

first: David

last: Causeur

first: Magalie

last: Houee-Bigot

first: Sandrine

last: Lagarrigue

first: Mari

last: Smits


title: Differentially regulated genes induced by in vitro generated Mycobacterium smegmatis cell wall deficient form

summary: Transcriptional profile of chemically generated Mycobacterium smegmatis cell wall deficient forms, comparing untreated control cells (bacillary forms) and cell wall deficient cells.

overall_design: Two-condition experiment, MSMEG-K vs. MSMEG-Sph cells. Biological replicates: 3 controls, 3 spheroplasts, independently grown and harvested. In controls and spheroplasts, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, Three replicates per array.


title: Differentially regulated genes induced by in vitro generated Mycobacterium avium subspecies paratuberculosis cell wall deficient forms

summary: Transcriptional profile of chemically generated Mycobacterium avium subspecies paratuberculosis cell wall deficient forms, comparing untreated control cells (bacillary forms) and cell wall deficient cells.

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Two-condition experiment, MAP-K vs. MAP-Sph cells. Biological replicates: 3 controls, 3 spheroplasts, independently grown and harvested. In controls and spheroplasts, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, four replicates per array.


title: Transcriptional profile of pathogenic and non-pathogenic in vitro generated mycobacterial cell wall deficient forms

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism: Mycobacterium avium subsp. paratuberculosis

overall_design: Refer to individual Series


title: Ralstonia solanacearum effector-specific effect on Medicago truncatula trancriptome

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_ralstonia_peeters_medicago - We have identified two essential virulence determinants (GALA7, a type III secretion effector and HpaP, a chaperone-like protein) of Ralstonia solanacearum for the infection and colonisation of the host plant Medicago truncatula. The scope of this project is to identify the GALA7 and HpaP-specific transcriptome alteration. For this purpose wild type and mutant infected root material (13h and 72h postinfection) will be analysed on M. truncatula affymetrix chips. Medicago truncatula (A17 line) are grown in vitro on Farheus medium (with Nitrogen source) plantlets are inoculated with water R. solanacearum wt, gala7 and hpap mutants, and root tips are collected at 13h and 72h postinoculation. Experiment was performed 3 times independently. 4 bacteria conditions x 2 harvest times x 3 biological repeats = 24 samples

Keywords: gene knock out,normal vs disease comparison,time course,treated vs untreated comparison

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 24 arrays - Medicago

first: Stephanie

last: Huguet

first: Fabienne

last: Vailleau

first: Nemo

last: Peeters

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Maize source leaf metabolism under high (15mM) or low (0.15mM) nitrogen supply

status: Public on Nov 01 2012

city: Erlangen

first: Urte

last: Schluter

address: Staudtstr. 5

department: Biology

institute: FA University Erlangen

summary: The metabolic response of maize source leaves to low nitrogen supply was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under controlled growth chamber conditions and supplied with either sufficient (15mM) or limiting (0.15mM) nitrate supply. Leaf lamina material was harvested at day 20 and day 30 after germination with the fifth and sixth leaf representing the main source leaf respectively. Four replicates were collecetd from individual plants for each combination of genotype, growth stage and nitrogen treatment. The leaf material was frozen, homogenised and aliquoted for transcriptome and metabolome analysis. The molecular data was further supplemented by phenotypic characterisation of the maize seedlings under investigation.  Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions.

overall_design: Maize inbred lines A188 and B73 were cultivated in pots containing nutrient poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions containing either 15mM (high N) or 0.15mM nitrate (low N). Source leaf lamina were harvested at day 20 and day 30 after start of germination for parallel analysis of transcriptome and metabolome profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.

first: U

last: Schlüter

last: Bräutigam

last: Sonnewald


title: Interior spruce_Bark_Leptographium abietinum_inoculation

first: Joerg

last: Bohlmann

summary: Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of interior spruce (Picea glauca x engelmannii) inoculated with the spruce beetle (Dendroctonus rufipennis) vectored blue stain fungal pathogen Leptographium abietinum or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 5% of the interior spruce transcriptome.

overall_design: RNA was isolated from the bark of interior spruce inoculated with Leptographium abietinum, treated with wounding, or untreated control for three time points (6h, 2days and 2 weeks). Three independent biological replicates were included for each treatment and each time point. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points (total 36 hybridizations/slides).

first: Natalia

last: Kolosova

first: Rick

last: White

first: Steven

last: Ralph

first: Colette

last: Breuil


title: Lodgepole pine_Bark_Grosmannia clavigera_inoculation

summary: Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of lodgepole pine (Pinus contorta) inoculated with the mountain pine beetle (Dendroctonus ponderosae) vectored fungal pathogen Grosmannia clavigera or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 2% of the lodgepole pine transcriptome.

overall_design: RNA was isolated from the bark of lodgepole pine inoculated with Grosmannia clavigera, treated with wounding, or untreated control for three time points (6h, 2days and 2 weeks). Three independent biological replicates were included for each treatment and each time point. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points (total 36 hybridizations/slides).


title: Comparative transcriptome analysis of Saccharomyces cerevisiae wild type and Δasc1 strain

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Asc1p and its essential orthologues in higher eukaryotes, as e.g. RACK1 in mammals, are involved in several distinct cellular signaling processes, but the implications of a total deletion have never been assessed in a comprehensive genome-wide manner. This study reveals the major cellular processes affected in a Saccharomyces cerevisiae Δasc1 deletion background via de novo proteome and transcriptome analysis, as well as subsequent phenotypical characterizations. The deletion of ASC1 reduces iron-uptake and causes nitrosative stress, both known indicators for hypoxia, which manifests in a shift of energy metabolism from respiration to fermentation in the Δasc1 strain. The impact of Asc1p in cellular metabolism is further expressed by its regulative role in the MAP kinase signal transduction pathways of invasive/filamentous growth, pheromone response and cell wall integrity. In the Δasc1 mutant strain aberrations from the expected cellular response, mediated by these pathways, can be observed and are linked to changes in protein abundances of pathway-targeted transcription factors. Evidence for the translational regulation of such transcription factors suggests that ribosomal Asc1p is involved in signal transduction pathways by controlling the biosynthesis of the respective final transcriptional regulators.

overall_design: The transcriptional data results from from 3 biological replicates for each strain, whereas for each biological replicate 2 technical replications and dye-swaps were analyzed.

first: Nicole

last: Rachfall

first: Susanne

last: Bandau

first: Kerstin

last: Schmitt

first: Armin

last: Ehrenreich

first: Oliver

last: Valerius

first: Gerhard

last: Braus


title: Transcriptional profiling and ChIP-chip analyses of S. pombe strains exhibiting flocculation phenotype by overexpression and deletion

status: Public on Nov 02 2012

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

type: Genome binding/occupancy profiling by genome tiling array

summary: In the fission yeast Schizosaccharomyces pombe, the transcriptional-regulatory network that governs flocculation remains poorly understood. Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP-chip analysis to identify the flocculin target genes. We identified five transcription factors that displayed novel roles in the activation or inhibition of flocculation (Rfl1, Adn2, Adn3, Sre2, and Yox1), in addition to the previously-known Mbx2, Cbf11 and Cbf12 regulators. Overexpression of mbx2+ and deletion of rfl1+ resulted in strong flocculation and transcriptional upregulation of gsf2+/pfl1+ and several other putative flocculin genes (pfl2+-pfl9+). Overexpression of the pfl+ genes singly was sufficient to trigger flocculation, and enhanced flocculation was observed in several combinations of double pfl+ overexpression. Among the pfl1+ genes, only loss of gsf2+ abrogated the flocculent phenotype of all the transcription factor mutants and prevented flocculation when cells were grown in inducing medium containing glycerol and ethanol as the carbon source, thereby indicating that Gsf2 is the dominant flocculin. In contrast, the mild flocculation of adn2+ or adn3+ overexpression was likely mediated by the transcriptional activation of cell wall-remodeling genes including gas2+, psu1+, and SPAC4H3.03c. We also discovered that Rfl1, Mbx2, and Cbf12 displayed transcriptional autoregulation, and Rfl1 repressed gsf2+ expression in an inhibitory feed-forward loop involving mbx2+. These results reveal that flocculation in S. pombe is regulated by a complex network of multiple transcription factors and target genes encoding flocculins and cell wall-remodeling enzymes. Moreover, comparisons between the flocculation transcriptional regulatory networks of Saccharomyces cerevisiae and S. pombe indicate substantial rewiring of transcription factors and cis-regulatory sequences.

overall_design: We generated 2 overexpression microarrays and 1 deletion microarray with dye swaps, 2 overexpression single replicate microarray experiments, 3 deletion single replicate microarray experiments, and 3 single replicate ChIP-chip experiments. The effect of the mutant strains were all compared to wild type or empty vector strains.

first: Eun

last: Kwon

first: Amy

last: Laderoute

first: Kate

last: Chatfield-Reed

first: Lianne

last: Vachon

first: Jim

last: Karagiannis


title: Gene expression profiles using microarrays in diaphragm of normal Beagle dogs and Beagle-based canine muscular dystrophy (CXMDJ) before and 1 hour after initial respiration.

status: Public on Oct 31 2012

city: Matsumoto

first: Akinori

last: Nakamura

state: Nagano

address: Asahi 3-1-1

department: Department of Neurology and Rheumatology

institute: Shinshu University School of Medicine

summary: Canine muscular dystrophy (CXMDJ) is a dog model of the lethal X-linked muscle disorder Duchenne muscular dystrophy (DMD), which is caused by loss of dystrophin. Gene expression profile was analyzed in the diaphragm muscles of normal Beagle dogs and CXMDJ before and 1 hour after initial respiration.

overall_design: Diaphragm were isolated from four groups (normal Beagle dogs and  CXMDJ before and 1 hour after initial respiration). Total RNA was purified and prepared to Agilent-021193 Canine (V2) Gene Expression Microarray (Feature Number version) (Agilent Technologies) using Agilkent reagents and protocols. The mRNA levels of differential expressed genes from gene chip analysis were confirmed by quantitative real-time PCR assay.

first: Masanori

last: Kobayashi

first: Katsutoshi

last: Yuasa

first: Naoko

last: Yugeta

first: Takashi

last: Okada

first: Shin’ichi

last: Takeda


title: Chromosomal abnormalities in colorectal cancer

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

type: Genome variation profiling by genome tiling array

summary: Microarray-based comparative genomic hybridization of CRC DNA samples from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma.

overall_design: Microarray-based comparative genomic hybridization of CRC DNA samples against a common reference.

first: Claudia

last: Gebhard


title: Transcriptomic signature in bovine blastocysts resulting from oxidative stress exposure at the time of embryonic genome activation

status: Public on Nov 14 2012

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine


title: Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity.

status: Public on Nov 20 2012

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary:
To better understand how innate immune responses to vaccination can lead to lasting protective immunity, we used a systems approach to define immune signatures in humans over 1 wk following MRKAd5/HIV vaccination that predicted subsequent HIV-specific T-cell responses. Within 24 h, striking increases in peripheral blood mononuclear cell gene expression associated with inflammation, IFN response, and myeloid cell trafficking occurred, and lymphocyte-specific transcripts decreased. These alterations were corroborated by marked serum inflammatory cytokine elevations and egress of circulating lymphocytes. Responses of vaccinees with preexisting adenovirus serotype 5 (Ad5) neutralizing antibodies were strongly attenuated, suggesting that enhanced HIV acquisition in Ad5-seropositive subgroups in the Step Study may relate to the lack of appropriate innate activation rather than to increased systemic immune activation. Importantly, patterns of chemoattractant cytokine responses at 24 h and alterations in 209 peripheral blood mononuclear cell transcripts at 72 h were predictive of subsequent induction and magnitude of HIV-specific CD8(+) T-cell responses. This systems approach provides a framework to compare innate responses induced by vectors, as shown here by contrasting the more rapid, robust response to MRKAd5/HIV with that to yellow fever vaccine. When applied iteratively, the findings may permit selection of HIV vaccine candidates eliciting innate immune response profiles more likely to drive HIV protective immunity.

This SuperSeries is composed of the SubSeries listed below.

middle: E

first: Alan

last: Aderem

first: Erica

last: Andersen-Nissen

first: Margaret

last: McElrath


title: Global gene expression changes during the estrous cycle in equine endometrium

status: Public on Oct 23 2012

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from 5 time points of the estrous cycle (D0, D3, D8, D12, and D16) was performed to study the dynamics of endometrial gene expression. Endometrial biopsies were collected from five mares (Bavarian Warmblood) at the respective time points. Samples were divided and subjected to isolation of RNA for microarray analysis and analysis of tissue composition. Blood samples were collected to determine serum progesterone levels for every sample. Statistical analysis of microarray data revealed almost 10,000 differential probes corresponding to 4,996 differentially expressed genes. A cluster analysis based on gene expression profiles during the estrous cycle revealed 8 major gene expression profiles: mRNAs with highest levels 1) at D0, 2) from D0 to D3, 3) at D3, 4) from D3 to D8, 5) at D8, 6) from D8 to D12, 7) from D12 to D16, and 8) at D16. DAVID Functional Annotation Clustering revealed overrepresentation of distinct functional terms in different phases of the cycle, e.g. ‘extracellular matrix’ and ‘protein transport’ during estrus, ‘DNA replication and ‘cell cycle’ during early luteal phase, ‘endoplasmic reticulum’ and ‘protein transport’ in the luteal phase, and ‘inflammatory response’ in the late luteal and follicular phase. Expression of selected genes of the expression clusters was validated by quantitative Real-time PCR (qPCR). This study provides new insights into global changes of equine endometrial gene expression during the estrous cycle.

overall_design: Equine endometrial tissue samples were collected at 5 time points during the sexual (estrous) cycle from 5 mares (5 biological replicates per time point) and analyzed with Agilent microarrays.

first: Simone

last: Gebhardt

first: Maximiliane

last: Merkl

first: Johannes

last: Handler


title: Effect of zonisamide co-administration with levodopa on global gene expression in the striata of rats with Parkinson’s disease

status: Public on Oct 30 2012

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: The anti-epileptic drug zonisamide is reported to exert beneficial effects in patients with Parkinson's disease. To elucidate the pathophysiological mechanisms underlying the anti-parkinsonism effects of zonisamide, we examined the effect of zonisamide co-administered with levodopa in the striata of rats with 6-hydoroxydopamine hemiparkinsonism by using a DNA microarray for genome-wide gene expression profiling. We found that the expression of some genes related to metabolism and nervous system development and function were upregulated by zonisamide; expression of these genes was downregulated by levodopa. Furthermore, many genes related to the immune system and inflammation were downregulated by zonisamide, and their expression was upregulated by levodopa. These results indicate that zonisamide has a protective effect when co-administered with levodopa.

overall_design: Rats were anesthetized with pentobarbital 240 mg/kg, i.p. and unilateral lesions of the left medial forebrain bundle were made via injection of 8 mg 6-OHDA hydrobromide in 4 ml of sterile saline containing 0.01% ascorbic acid. Motor disturbance was assessed by counting the number of full rotations per min in a cylindrical container of φ30 cm diameter at 10-min intervals for the first 60 min after METH (3 mg/kg, i.p.) administration [3]. Behavioral screening was carried out after 2-3 weeks of recovery and animals that performed at least 7 turns/min during METH challenge were certified as hemiparkinsonism rats and included in the study. Seven days after METH challenge, hemiparkinsonism rats were treated with saline, L-DOPA (100 mg/kg, i.p.), or L-DOPA (100 mg/kg, i.p.) and ZNS (50 mg/kg, i.p.) once per day for 7 days. L-DOPA was injected 30 min after benserazide hydrochloride (a peripheral decarboxylase inhibitor). ZNS was injected 30 min after L-DOPA injection. The 4 experimental groups were classified as follows: the non-lesioned side of saline-treated 6-OHDA-injected rats (NL), the lesioned side of saline-treated 6-OHDA-injected rats (SL), the lesioned side of L-DOPA-treated 6-OHDA-injected rats (DL), and the lesioned side of L-DOPA and ZNS-treated 6-OHDA-injected rats (ZDL). Three animals were assigned to each group.

first: Yuto

last: Ueda

first: Shoko

last: Tokashiki

first: Ai

last: Kanemaru


title: Comparative transcriptome analysis of two olive (Olea europaea L.) cultivars in response to NaCl stress

city: Chania

first: Maria

middle: E.

last: Manioudaki

address: Makedonias 1

department: Horticultural Genetics and Biotechnology

country: Greece

institute: MAICH

first: Christos

last: Bazakos

first: Ioannis

last: Therios

first: Demetrios

last: Voyiatzis

first: Dimitris

last: Kafetzopoulos

first: Tala

last: Awada

first: Panagiotis

last: Kalaitzis


title: Genetics of gene expression responses to temperature stress in a sea urchin gene network (DASL)

city: Durham

first: Daniel

last: Runcie

state: NC

department: Biology Department

institute: Duke University

summary: Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.

overall_design: 191 samples representing 32 cultures from 8 male and 8 female parents, grown in replicate at 3 temperatures

first: David

middle: A

last: Garfield

first: Courtney

middle: C

last: Babbitt

first: Jennifer

last: Wygoda

first: Sayan

last: Mukherjee

first: Gregory

last: Wray


title: Gamma irradiation does not induce detectable changes in DNA methylation in exposed human cells

city: Duarte

first: Xiwei

last: Wu

state: CA

institute: City of Hope National Medical Center

summary: Ionizing radiation, released during accidents at nuclear power plants or after atomic bomb explosions, is a potentially serious health threat for the exposed human population. This type of high-energy radiation causes DNA damage including single- and double-strand breaks and induces chromosomal rearrangements and mutations, but it is not known if ionizing radiation directly induces changes in the epigenome of irradiated cells. We treated normal human fibroblasts and normal human bronchial epithelial cells with different doses of gamma-radiation emitted from a cesium 137 (137Cs) radiation source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a small number of potential methylation changes with low fold-difference ratios in the irradiated cells. These minor methylation differences seen on the microarrays could not be verified by COBRA (combined bisulfite restriction analysis) or bisulfite sequencing of selected target loci. Our study shows that acute gamma-radiation treatment of two types of human cells had no appreciable effect on DNA cytosine methylation patterns in exposed cells.

overall_design: DNA methylation patterns in gamma-irradiated cells and non- treated cells analyzed by microarrays

first: Christoph

last: Lahtz

first: Steven

last: Bates

first: Yong

last: Jiang

first: Arthur

last: Li

first: Gerd

middle: P

last: Pfeifer


title: human placenta-derived cell line (JEG-3): Control vs. valproic acid(VPA)-treated

status: Public on Oct 11 2012

city: Seongnam

first: Youn-Jung

last: Kim

address: 212 Yangi-dong Sujeong-gu

department: Department of Food and nutrition

country: South Korea

institute: Eulji University

summary: Transcriptional profiling of human placenta-derived JEG-3 cell line comparing vehicle control with 7.38 mM of valproic acid(VPA)-treated JEG-3 cells for 48 hr. 7.38 mM valproic acid(VPA) induced the 30% inhibiotion of JEG-3 cell proliferation, G1 phase cell cycle arrest and the reduction of cell size. The Goal was to analyze the mechanism of valproic acid-induced adverse effects in placental cells.

overall_design: Two-condition experiment, JEG-3 cells vs. valproic acid(VPA)-treated JEG-3 cells. Biological replicates: 3 control replicates, 3 VPA-treated replicates.

first: Jae-Chun

last: Ryu

first: Jina

last: Lee


title: Developing rice endosperm at seven days after flowering: Aleurone layers vs central starchy endosperm

status: Public on Nov 27 2012

city: Tsukuba

first: Tsutomu

last: Ishimaru

state: Ibaraki

address: 1-1 Ohwashi

institute: JIRCAS

summary: Transcriptional profiling of developing rice endosperm at seven days after flowering comparing aleurone layers with central starchy endosperm. Cereal productivity is dependent on the accumulation of storage compounds in the endosperm, a nutritive tissue that is composed of aleurone cells in the outermost regions and starchy endosperm in the inner region. The transcriptional analyses provides clues to the molecular basis for different metabolic pathways in response to the spatial and nutritional differences between rice aleurone cells and starchy endosperm.

overall_design: Two-condition experiment, Aleurone layers vs. central starchy endosperm. 3 biological replicates with color swap for each biological replicate

first: Yoshiaki

last: Nagamura


title: Colorectal tumor DNA vs. normal control DNA

status: Public on Oct 25 2012

city: Sheffield

first: Ian

middle: Wallace

last: Brock

state: South Yorkshire

address: Beachhill Road

department: Cancer Studies

country: United Kingdom

institute: University of Sheffield Medical School

summary: Genomic DNA samples were extracted from microdissected colorectal tumour tissue and then compared against normal DNA extracted from the peripheral blood from the same patients.

overall_design: 53 Normal/Tumor matched samples.

first: George

last: Burghel


title: Expression data in response to pepper leaf curl virus (PepLCV) infection in Chili pepper at three leaf stage

city: Varanasi

first: Ved

middle: Prakash

last: Rai

state: Uttar Pradesh

address: Lanka

department: Genetics and Plant Breeding

institute: Banaras Hindu University, Varanasi

summary:
A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage.
To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage.

sample_organism:
Capsicum annuum
Capsicum chinense x Capsicum frutescens

overall_design: Tomato microarrays consisting of 43,803 probes were used for whole genome expression analysis of chilli peppers for resistance against PepLCV. Transcripts from the leaves of resistant (BS-35) and susceptible plants (IVPBC-535) were compared in response to PepLCV inoculation at three leaf stage.

first: Ashutosh

first: Rajesh

last: Kumar

first: S

last: Singh

first: Sanjeet

first: Major

first: Mathura


title: Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock

status: Public on Oct 05 2012

city: Seville

first: Jose

middle: M.

last: Colmenero-Flores

address: Av. Reina Mercedes 10

department: Plant Biotechnology

country: Spain

institute: IRNAS (CSIC)

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Thierry

last: Allario

first: Javier

last: Brumos

middle: M

first: Domingo

middle: J

last: Iglesias

last: Pina

first: Luis

last: Navarro

first: Manuel

last: Talon

first: Patrick

last: Ollitrault

first: Raphaël

last: Morillon


title: Expression profile of wild-type Thermus thermophilus HB8 strain cultured in TT medium for 6 h, reproduced in 2011

status: Public on Oct 02 2012

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary: We observed the expression profile of the total mRNA of the wild-type strain grown in a rich medium at 70 deg-C for 360 min.

overall_design: Four wild-type T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells were inoculated into 1 liter of the same medium to a final OD600nm of 0.0005 and then cultivated at 70°C. Cells were collected after 360 min (OD600nm =~ 1.4), and then, the expression of each mRNA was analyzed.

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto

first: Seiki

last: Kuramitsu


title: Expression profile of wild-type Thermus thermophilus HB8 strain cultured in TT medium for 6 h, reproduced in 2010

overall_design: Three wild-type T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360 min, and then, the expression of each mRNA was analyzed.


title: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

status: Public on Oct 03 2012

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre


title: Genomic transcriptional profiling identifies candidates genes for successful aging

status: Public on Oct 01 2012

city: Marseille

first: PABAN

last: Veronique

address: 3 place V. Hugo

institute: Aix-Marseille Universite

summary: The inbred LOU/C/Jall rat is currently described as a model of successful aging. These rats have a longer healthy median lifespan than other strains, do not develop obesity, diabetes, or tumor and more importantly they do not show cognitive decline with aging. This is the first study to examine gene expression changes in the inbred LOU/C/Jall rat hippocampus and frontal cortex. Microarray data from LOU/C/Jall rats aged of 5 months were compared to the one measured in rats aged of 26 month. We have identified a set of 15 genes in the hippocampus and 70 genes in the frontal cortex that could be grouped into several clusters of similar expression profiles and that are involved in biological functions, namely regulation of plasticity, inflammatory response, metabolic, catabolic and homeostatic processes, and transcription. Genes were mainly up-regulated in aged brain.

overall_design: Gene expression profil in hippocampus and cortex frontal of LOU/C/Jall rats strain. Rats were 3 and 26 months old.

first: Veronique

last: Paban

first: Beatrice

last: Loriod


title: Comparative genomic analysis of Aggregatibacter actinomycetemcomitans of JP2 and non-JP2 genotypes using a pan-genome microarray

status: Public on Sep 28 2012

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

summary: To assess the performance of our custom-designed pan-genome microarray and characterize the differences in gene content between JP2 and non-JP2 genotypes of A. actinomycetemcomitans.

overall_design: Comparative genomic hybridization reactions were carried out to assess the performance of our pan-genome microarray by using genomic DNA of 11 previously sequenced Aggregatibacter actinomycetemcomitans strains (I23C, SCC1398, ANH9381, HK1651, D7S-1, D11S-1, I63B, SCC393, D18P-1, SCC2302, and D17P-2). The microarray was subsequently used for comparative genomic hybridization of 6 strains  of JP2 (S067, A26, G111-1, G121-2, D41S-1, and HK1651) and 6 strains non-JP2 (I23C, SCC1398, ANH9381, ATCC29524, 194, and G104-2) genotypes of Aggregatibacter actinomycetemcomitans. Two biological duplicates were carried out for each strain.

first: Yanyan

last: Huang

first: Marcia

last: Alves Mayer

first: Roger

last: Bumgarner

first: Casey

last: Chen


title: OsDDM1 regulated genes in rice: Control (wt: cultivar "Nipponbare") vs. Transgenic (antisense OsDDM1)

first: Naoki

last: Kishimoto

address: 2-1-2 Kannondai

department: Agrogenomics Research Center

institute: National Institute of Agrobiological Sciences

summary: Transcriptional profiling of young leaves of rice (Oryza sativa) comparing control wild-type plants with transgenic plants transformed with a pBI-nptII-OsDDM1 gene. The latter makes the methylation level of the genomic DNA decreased. Goal was to determine the effects of decreased level of genomic DNA on global rice gene expression.

overall_design: Two-condition experiment, Control vs. Transgenic plants. Biological replicates: 2 control replicates, 2 transfected replicates.

first: Yoshiki

last: Habu


title: Expression profile of PfmR (TTHB023)-deficient Thermus thermophilus HB8 strain

summary: In order to find function of PfmR protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the PfmR-deficient strain grown in a rich medium at 70°C for 360 min.

overall_design: Three PfmR-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1.6 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360 min, and then, the expression of each mRNA was analyzed.


title: Expression analysis of purified intestinal phagocytes in Schmidtea mediterranea

city: Urbana

first: Noelle

last: James

state: IL

address: 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: U of IL / HHMI

summary: Identification of differentially expressed genes in intestinal phagocytes, compared to non-intestinal cells in Schmidtea mediterranea.

overall_design: Total RNA was isolated from either intestinal phagocytes or non-intestinal cells (control). Four independent biological replicates were conducted with two dye swaps. Labeled targets were hybridized to two oligonucleotide arrays on which 11,521 planarian transcripts were represented.

first: David

last: Forsthoefel

last: Escobar

first: Joel

last: Stary

first: Ana

last: Vieira

first: Forrest

last: Waters

first: Phillip

last: Newmark


title: Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

summary: To characterize the differences in pattern of gene expression between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Transcriptome analysis of 3 strains of JP2 and 2 strains of non-JP2 genotypes of A. actinomycetemcomitans was performed

overall_design: Transcripome of three strains of JP2 genotype (HK1651, D28S-1 and D41S-1) and two strains of non-JP2 genotype (SCC1398 and ANH9381) were examined where two biological duplicates were carried out for each strain.

last: Mayer


title: Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides

status: Public on Sep 20 2012

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Background. Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumes in the semi-arid tropics. While most cowpea accessions are susceptible to the root parasitic weed Striga gesnerioides, several cultivars have been identified that show race-specific resistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S. gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots of cultivar B301 develop a strong resistance response characterized by a hypersensitive reaction and cell death at the site of parasite attachment. In contrast, no visible response occurs in B301 roots parasitized by SG4z.  Results. Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, were investigated at 6 and 13 days post-inoculation (dpi), in the early and late stages of the resistance response using a Nimblegen custom design cowpea microarray. A total of 111 genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102 genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed during compatible (susceptible) interactions of B301 with SG4z . Genes and pathways involved in signal transduction, programmed cell death and apoptosis, and defense response to biotic and abiotic stress were differentially expressed in the early resistance response; at the later time point, enrichment was primarily for defense-related gene expression, and genes encoding components of lignifications and secondary wall formation. In compatible interactions (B301 – SG4z), multiple defense pathways were repressed, including those involved in lignin biosynthesis and secondary cell wall modifications, while cellular transport processes for nitrogen and sulfur were increased.   Conclusion. Distinct changes in global gene expression profiles occur in host roots following successful and unsuccessful attempted parasitism by Striga. Induction of specific defense related genes and pathways defines components of a unique resistance mechanism. Some genes and pathways up-regulated in the host resistance response to SG3 are repressed in the susceptible interactions, suggesting that the parasite is targeting specific components of the host’s defense. These results add to our understanding of plant-parasite interactions and the evolution of resistance to parasitic weeds.

overall_design: A Nimblegen custom design cowpea microarray investigating gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, at 6 and 13 days post-inoculation (dpi), in the early and late stages of the resistance response.

first: K

first: M

last: Timko


title: Arabidopsis thaliana wild type mechanical damage (MD) vs Myzus persicae wounding (Myz)

status: Public on Sep 18 2012

city: Turin

first: Cinzia

middle: Margherita

last: Bertea

state: To

address: via Quarello 11/A

department: Department of Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: Transcriptional profiling of Arabidopsis thaliana wild type (WT) comparing mechanical damage (MD) and Myzus persicae feeding (Myz). The differences in the biochemical responses to insect feeding seen when compared to the control sample prompted us to search for less obvious differences between the treatments using gene expression profiling. Biological replicates: 4 biological replicates

overall_design: Two-condition experiment, MD vs. Myz Arabidopsis leaves of WT plants. Biological replicates:  4 biological replicates.

first: Massimo

last: Maffei

first: Ivan

last: Paponov


title: Arabidopsis thaliana wild type mechanical damage (MD) vs herbivore wounding (HW)

summary: Transcriptional profiling of Arabidopsis thaliana wild type (WT) comparing MD (mechanical damage) and HW (herbivore wounding). The differences in the biochemical responses to herbivory seen prompted us to search for less obvious differences between treatments using gene expression profiling. Biological replicates: 4

overall_design: Two-condition experiment, MD vs. HW Arabidopsis leaves of WT plants. Biological replicates:  4 biological replicates.


title: Slug overexpression

status: Public on Sep 21 2012

city: Tianjin

first: baocun

last: sun

address: Qixiangtai Road No.22, Heping District

institute: Tianjin Medical University

type: Genome binding/occupancy profiling by array


title: Agilent 44K Rice Oligo DNA Microarray RAP-DB (G2519F#15241); genome-wide transcriptional analysis of Aluminum-responsive genes in rice (Oryza sativa).

status: Public on Sep 19 2012

city: Bunkyo-ku

first: Tomokazu

last: Tsutsui

state: Tokyo

address: Room 02 (BF), Faculty of Science Building 2, 7-3-1 Hongo

department: Biological Sciences

institute: The university of tokyo

summary: By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice.

overall_design: The transcriptional profiling between the wild-type rice and an Al-sensitive mutant, star1. +Al vs. -Al in the roots of wild-type rice and star1 mutant. Biological replicates: +Al/-Al WT root tip 4 replicates, +Al/-Al WT basal tip 4 replicates, +Al/-Al star1 root tip 4 replicates, +Al/-Al star1 basal tip 4 replicates

last: Yamaji

first: Chaofeng

last: Huang

first: Ritsuko

last: Motoyama

first: Yoshiaki

last: Nagamura

first: Jian

middle: F

last: Ma


title: Arabidopsis thaliana wild type control (C) vs Pseudomonas syringae infected (Pseu)

summary: Transcriptional profiling of Arabidopsis thaliana wild type (WT) comparing Mg chloride infiltration (C) and Pseu infection (Pseu). The differences in the biochemical responses to bacterial infection seen when compared to the control sample prompted us to search for less obvious differences between the treatments using gene expression profiling.

overall_design: Two-condition experiment, MgCl2 vs. Pseu Arabidopsis leaves of WT plants. Biological replicates:  4 biological replicates.


title: Dynamics of membrane potential variation and gene expression induced by Spodoptera littoralis, Myzus persicae, and Pseudomonas syringae in Arabidopsis


title: High-resolution, genome-wide analysis of human metastatic neuroblastoma samples by array-Comparative Genomic Hybridization (aCGH)

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

institute: "San Martino" Hospital

summary: Less than 30% of children with high-risk (HR) metastatic neuroblastoma (NB) show a long survival (Pearson 2000). In order to identify novel molecular prognostic markers useful to better predict patients’ relapse risk estimation, we performed genome- and/or transcriptome-wide analyses of 129 stage 4 HR-NBs. This is the largest study for this NB subtype. Children older than 1 year of age at diagnosis were categorized as “short-survivors” (dead of disease within 5 years from diagnosis) and “long-survivors” (alive with an overall survival time > 5 years). A significant correlation of patient survival with the presence of small number of segmental copy number aberrations (CNA < 3) was observed. Thus, within the group of stage 4 HR-NBs, we identified a specific subgroup of patients (those with highest number of CNA) that have a higher risk of progression/recurrence. The complex genomic pattern is an independent prognostic marker, since MYCN oncogene amplification only affects the predictive value of single CNA (i.e., 1p loss, 17q gain). Integrative analysis of genomic and expression signatures demonstrated that fatal outcome is associated with loss of cell cycle control and with progression of tumor due to deregulation of Rho GTPase signaling and genes related to cell motility. Tumors with MYCN amplification showed a lower chromosome instability compared to MYCN-single copy NBs (P=0.0008), dominated by 17q gain and 1p loss. Moreover, our results suggest that the MYCN amplification mainly drives the disruption of neuronal differentiation and the reduction of cell adhesion process involved in tumor invasion and metastasis.

overall_design: For array-CGH profiling, we analyzed 91 samples of metastatic neuroblastomas. All patients were classified  as stage 4 and they were older than 1 year of age at time of diagnosis. Regarding the clinical course, 46 were short-survivors (dead of disease within 60 months from diagnosis. Deaths due to toxicity were censored) and 45 were long-survivors (alive with an overall survival time > 60 months). This submission consists of 22 new samples and 69 other cases previously deposited in GEO under Series accessions GSE14109 and GSE25771.

first: Paola

last: Scaruffi

first: Jessica

last: Theissen

first: Simona

last: Coco

first: Sara

last: Stigliani


title: Genomic Binding of Human Linker Histone H1.5 during differentiation (ChIP-chip)

city: Los Angeles

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles

summary: In humans, there are eleven subtypes of linker histones that exhibit cell- and tissue-specific expression. Linker histone H1 proteins bind to both the core histones and linker DNA of chromatin fibers; and not only participate in control of gene activity but also serve to stabilize higher order chromatin structure. To determine the potential roles of linker histones in differentiation, we examined the global distribution of linker histone subtype H1.5 in human IMR90 fibroblasts and H1 embryonic stem cells (hESCs). Surprisingly, H1.5 binds to and represses a large fraction of gene family clusters in fully differentiated cell types representing all three embryonic germ layers. Little or no H1.5 enrichment at gene family clusters was detected in undifferentiated hESCs or partially differentiated somatic cells. We also found that SIRT1 histone deacetylase and H3K9me2, a repressive histone modification, are also enriched at gene family cluster in IMR90 cells, likely generating a stably repressive chromatin domain. To find out the mechanism of H1.5 targeting, H1.5 or SIRT1 was depleted in IMR90 cells by siRNA, and the binding patterns of SIRT1 and H1.5 were examined. In H1.5 knockdown cells, SIRT1 binding pattern was changed dramatically, and this changed pattern highly correlates to SIRT1 distribution in hESC. However, depletion of SIRT1 could not change the global binding pattern of H1.5. Depletion of H1.5 or SIRT1 leads to up-regulation of ~50% gene family clusters. However, the sets of gene family clusters that are affected by these two factors are different, suggesting H1.5 and SIRT1 may regulate gene transcription via different pathways.

overall_design: ChIP-chip against H1.5 in human H1 ES cells, HSF1 ES cells, IMR90 cells, human keratinocytes, calcium induced keratinocytes, in vitro differentiated neural progenitor cells, in vitro differentiated neurons, primary human hepatocytes, H1.5 knockdown IMR90 cells, SIRT1 knockdown IMR90 cells. ChIP-chip against SIRT1 in IMR90 cells, H1.5 knockdown IMR90 cells. ChIP-chip against di-methyl histone H3 lysine 9 in IMR90 cells. ChIP-chip against RNA polymerase II in IMR90 cells.

first: Michaela

last: Patterson

first: Hanna

middle: K

last: Mikkola

first: William

last: Lowry

first: Siavash

last: Kurdistani


title: Gene responses in mouse brain to long-term exposure to microgravity

status: Public on Sep 13 2012

city: Toyonaka

first: Yoshinobu

last: Ohira

state: Osaka

address: 1-17 Machikaneyama-cho

department: Applied Physiology

institute: Osaka University

summary: The spaceflight experiment was carried out using male C57BL/10J mice (8 weeks old at launch).  Wild type mice (n=3) were launched by Space Shuttle Discovery and housed on the International Space Station (ISS) for 91 days.  They returned to the Earth by Space Shuttle Atlantis.  But only one mouse returned to the Earth alive.  Whole brain was sampled from the mouse killed by inhalation of carbon dioxide at the Life Sciences Support Facility of Kennedy Space Center within 3-4 hours after landing.  After the spaceflight experiment, the on-ground experiment was also carried out at the Advanced Biotechnology Center in Genova, Italy.  A mouse with the same species, sex, and age was housed in mice drawer system (MDS), which was utilized for the spaceflight (SF) mice, for 3 months as the ground control (GC).  Another mouse was housed in normal vivarium cage as the laboratory control (LC).  Amount of food and water supplementation and environmental conditions were simulated as the flight group.  After 3 months, brain was sampled from one mouse in group GC and LC, respectively.  Comprehensive analyses of gene expression were performed in the right brain.  Total of 4,000 genes were analyzed.  The expression levels of 60 genes significantly changed in response to SF compared with LC and/or GC.  The 15 and 16 genes were up- (> 2 folds) and down-regulated (< 0.5 folds), respectively, following SF vs. GC.  The levels of 58 genes were significantly altered by housing in MDS in space and/or on the ground.  Forty seven and 11 genes were significantly up- and down-regulated vs. LC.  Twenty seven out of these genes responded to caging in MDS both in space and on the ground.  Further, 31 genes were influenced by housing in MDS on the Earth.

overall_design: Responses of the characteristics of brain to long-term gravitational unloading were investigated in mice.

first: Takashi


title: DNA methylation data from newly emerged queens, newly emerged workers, adult nurses, adult foragers and adult reverted nurses Honeybees (Apis mellifera)

status: Public on Sep 16 2012

city: Baltimore

first: Brian

middle: R

last: Herb

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: JHU

summary:
We investigated genome-wide DNA methylation of newly emerged queens, newly emerged workers, adult nurses, adult foragers and adult reverted nurses using comprehensive high throughput arrays for relative methylation (CHARM)
We used custom Nimblegen microarrays

overall_design: We isolated genomic DNA from newly emerged queens, newly emerged workers, adult continuous nurses, adult continuous foragers and adult reverted nurses hybridized to custom-designed Nimblegen microarrays (CHARM arrays). Multiple brains were pooled for each sample and used for the genome-wide DNA methylation analysis.

first: Andrew

last: Feinberg


title: Changes in gene expression analysis of alphaCD3alpha/CD28 activated human naive and memory regulatory T cells (Treg) upon IL-7 treatment as measured by quantitative PCR array

status: Public on Sep 12 2012

city: Dresden

first: Anke

last: Theil

address: Fetscherstr. 105

institute: CRTD

summary: This study evaluated changes in gene expression upon IL-7 treatment in human naive and memory Treg. CD4+CD25+CD127low naïve and memory Treg were isolated from fresh PBMC and separately stimulated with αCD3α/CD28 coupled beads (Invitrogen-Dynal) at a 1:10 bead/T cell ratio, treated with or without 10 ng/ml of rhIL-7 (R&D Systems) for 16 hours.

overall_design: qPCR gene expression profiling of CD4+CD25+CD127low naïve and memory Treg obtained from 2 separate donors. Cell lysates were prepared separately from the 2 donors and pooled prior to RNA extraction.

first: Paolo

last: Monti

first: Anne

last: Heninger


title: Expression data from primary bovine mammary epithelial cells (pbMEC) challenged with heat inactivated E. coli and S. aureus particles

status: Public on Sep 07 2012

city: Dummerstorf

first: Juliane

last: Guenther

address: Wilhelm-Stahl-Allee 2

institute: Leibniz-Institute for Farm Animal Biology (FBN)

summary: Infections of the udder by Escherichia coli very often elicit acute inflammation, while Staphylococcus aureus infections tend to cause mild, subclinical inflammation and persistent infections. The molecular causes undercovering the different disease patterns are poorly understood. We therefore profiled kinetics and extent of global changes in the transcriptome of primary bovine mammary epithelia cells (MEC) subsequent to challenging them with heat inactivated preparations of E. coli or S. aureus pathogens. E. coli swiftly and strongly induced expression of cytokines and bactericidal factors. S. aureus elicited a retarded response and failed to quickly induce expression of bactericidal factors. Both pathogens induced a similar pattern of chemokines for cell recruitment into the udder, but E. coli stimulated their synthesis much faster and stronger. The genes which are exclusively and most strongly up-regulated by E. coli may be clustered into a regulatory network with Tumor necrosis factor alpha (TNF-a) and Interleukin 1 (IL-1) in a central position. In contrast, the expression of these master cytokines is barely regulated by S. aureus. Both pathogens quickly trigger enhanced expression of IL-6. This is still possible after completely abrogating MyD88 dependent TLR-signalling in MEC. The E. coli specific strong induction of TNF-a and IL-1 expression may be causative for the severe inflammatory symptoms of animals suffering from E. coli mastitis while avoidance to quickly induce synthesis of bactericidal factors may support persistent survival of S. aureus within the udder. We suggest that S. aureus subverts MyD88-dependent activation of immune gene expression in MEC.

overall_design:
We challenged pbMEC cultures with 1E+07 particles per ml of heat inactivated E. coli strain 1303 for 1, 3, 6, and 24 h and compared their transcriptomes to that of untreated control cells. The experiment included three biological replicas (rep1, rep2, rep3), each from a different cow
We challenged pbMEC cultures with 1E+07 particles per ml of heat inactivated S. aureus strain 1027 for 1, 3, 6, and 24 h and compared their transcriptomes to that of untreated control cells. The experiment included three biological replicas (rep1, rep2, rep3), each from a different cow

last: Günther

first: Kathrin

last: Esch

first: Norbert

last: Poschadel

first: Wolfram

last: Petzl

first: Holm

last: Zerbe

first: Simone

last: Mitterhuemer

first: Helmut

last: Blum

first: Hans-Martin

last: Seyfert


title: Noise in rpoS expression determines cellular permissiveness for horizontal transfer of an Integrative and Conjugative Element

status: Public on Sep 01 2012

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

institute: University of Lausanne

summary: To support our molecular hypothesis of the effect of rpoS and inrR genes over the activation of the ICEclc genome in Pseudomonas knackmussii B13, we have employed Agilent DNA custom microarray in the 8X15K format.

overall_design: ICEclc-specific gene expression in Pseudomonas knackmussii strain B13 was measured after 48 hours of stationary phase following a growth on 10mM 3-chlorobenzoate (3CBA) as sole carbon and energy source. Various genotypes were tested: wild type (strain n°78, in 5 replicates), inrR-/- (strain 2201, in triplicates), delta::rpoS (strain 2671, in triplicates).

first: Nicolas

last: Pradervand