title: Identification of bistable populations of Porphyromonas gingivalis that differ in epithelial cell invasion.

city: Sheffield

first: graham

last: stafford

address: School of Clinical Dentistry

country: United Kingdom

institute: University of Sheffield

summary: Bistable populations of bacteria give rise to two or more subtypes that exhibit different phenotypes. We have explored whether the periodontal pathogen, Porphyromonas gingivalis, exhibits bistable invasive phenotypes. Using a modified cell invasion assay, we show for the first time that there are two distinct sub-types within a population of P.ginigivalis strains NCTC 11834 and W50 that display differences in their ability to invade oral epithelial cells. The highly-invasive sub-types invade cells at 10-30 fold higher levels than the poorly-invasive subtype and remain highly invasive for approximately 12-16 generations. Analysis of the gingipain activity of these sub-types revealed that the highly invasive type had reduced cell-associated arginine specific protease activity. The role of arg-gingipain activity in invasion was verified by enhancement of invasion by rgpAB mutations and by inclusion of an arg-gingipain inhibitor in invasion assays using wild-type bacteria. In addition a population of DeltargpAB bacteria did not contain a hyperinvasive sub-type. Screening of the protease activity of wild-type populations of both strains identified high and low protease sub-types which also showed the corresponding reduction or enhancement of invasive capabilities. Microarray analysis of these bistable populations revealed a putative signature set of genes that include oxidative stress resistance and iron transport genes that might be key to invasion of or survival within epithelial cells.

overall_design:
Porphyromonas gingivalis comparison of Invasive V Non-invasive sub-types of NCTC11834 and W50 (samples 1-12 AND High V low protease subtypes (samples 13-24)
Samples 1-3 were compared top 4-6 and 7-9 V 10-12 for invasive experiments and similarly for protease strain experiments

first: S

last: Suwannakul

first: G

middle: P

last: Stafford

last: Whawell

first: C

middle: W

last: Douglas


title: Expression analyses of nanos(RNAi) and control(RNAi) Schmidtea mediterranea

status: Public on Sep 01 2010

city: Urbana

first: Phillip

last: Newmark

state: IL

address: C609 CLSL, 601 S. Goodwin Ave.

department: Cell and Developmental Biology

country: USA

institute: University of Illinois, Urbana-Champaign

summary:
Investigation of whole genome gene expression level changes in nanos(RNAi) Schmidtea mediterranea, compared to control animals. nanos(RNAi) animals are devoid of germ cells
The samples analyzed in this study are further described in Wang, Y., Stary, JM., Wilhelm, JE. and Newmark, PA. 2010.

overall_design: A eight chip study using total RNA recovered from asexual nanos(RNAi), asexual control, juvenile sexual nanos(RNAi), and juvenile sexual control animals.  Each chip measures the expression level of 16,797 ESTs from S. mediterranea with 10 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

first: Yuying

last: Wang

first: Joel

middle: M

last: Stary

middle: A


title: HSF1 regulates transcription of sex-chromosomal multicopy genes during post-meiotic repression

status: Public on Aug 31 2010

city: Turku

first: Lea

last: Sistonen

address: Tykistokatu 6 B

department: Biology

country: Finland

institute: Åbo Akademi University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Mapping of in vivo targets for HSF1 by using mammalian tissue material in a global ChIP-chip promoter screen. Chromatin was isolated from three wild-type (WT) mouse testes, crosslinked and sonicated into fragments of 100-500 bp, and the quality of the DNA was controlled before the immunoprecipitation, showing no signs of degradation.
The DNA amplified from the HSF1 immunoprecipitation samples was labeled and hybridized against the total input DNA samples, on a 1.5 kb promoter tiling array (NimbleGen Systems Inc.), covering ~26000 promoters of the mouse genome. After hybridization and scanning, HSF1 hybridization signals were Lowess normalized to produce log2 ratios  (HSF1 ChIP/Input DNA) for all  replicate arrays.
The promoter values were calculated as average log2 ratios over all probes for each promoter. To identify the HSF1 target population, we used a non-arbitrary analysis method called RankProd described in Breitling et al. 2004. RankProd has been published as an R/Bioconductor package.

overall_design: HSF1 ChIP sample vs. Input sample (reference),  biological replicates: 3, one replicate per array.

first: Malin

last: Åkerfelt

first: Anniina

last: Vihervaara

first: Asta

last: Laiho

first: Annie

last: Conter

first: Elisabeth

middle: S

last: Christians

first: Eva

last: Henriksson


title: Microarray profiling of expression patterns of fibroblasts from different skin types

city: Bethesda

first: Vincent

last: Hearing

state: MD

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

summary: Adult human fibroblasts derived from the dermis of 4 mm punch biopsies taken from the lower backs of 15 healthy subjects of 3 different phototypes (types I, III and VI). This study was approved by the Human Research Ethics Committee of Hamburg. Subjects with type I skin were #4, 12, 15, 19 and 26; subjects with type III skin were # 6, 9, 13, 14 and 23, and subjects with type VI skin were # 7, 8, 16, 17 and 28. The fibroblasts were cultured from the biopsies and were grown in monolayer culture in high glucose Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine plus 1% penicillin and streptomycin at 37°C in a humidified 5% CO2 atmosphere. Fibroblasts were subcultured using routine methods and were used at passages 3 to 6.

overall_design: Oligo-cDNA microarray hybridization was performed according to the National Cancer Institute in-house protocol, as detailed previously (Yamaguchi et al., 2008). Briefly, total RNAs were prepared from cultured fibroblasts using an RNeasy mini kit (Qiagen, Valencia, CA). The quality (purity and integrity) and quantity of each total RNA preparation was measured using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). A universal human reference RNA (Stratagene, La Jolla, CA) was used as a control. cDNA samples generated from RNA samples and purified before the coupling reaction were labeled with Cy3 (for fibroblast samples) or Cy5 (for reference RNA) mono-reactive dyes (GE Healthcare, Piscataway, NJ), and were hybridized simultaneously on an oligo-DNA chip (Hs-OperonV3.0-v1p24, p27, p31) overnight at 42°C. Two fluorescent intensities of the oligo-DNA chip were scanned using a microarray scanner (GenePix 4000B; Axon Instruments Inc., Molecular Devices Corp., Sunnyvale, CA). Differential gene expression was profiled using Genepix Pro 5.0 software and was analyzed by Miltenyi Biotec (Bergisch Gladbach, Germany).

middle: J

first: Wonseon

last: Choi


title: Study of keratinocyte differentiation in normal human epidermis

city: Toulouse

first: Nicolas

last: Mattiuzzo

address: CHU Purpan, place du Dr Baylac, TSA40031

department: UMR CNRS-UPS (Univ. Paul Sabatier) 5165

country: France

institute: Centre National de la Recherche Scientifique (CNRS, France)

summary:
In epidermis, granular keratinocytes are responsible for the synthesis of a great number of proteins of high tissue-specificity, and required for the epidermal barrier establishment and the regulation of the desquamation process. This project aims at characterizing the physiopathological function of genes implicated in these processes, and in the short term, defining their expression level in the course of keratinocyte differentiation. Pangenomic oligonucleotide microarrays are used to compare their expression between two cell populations enriched in basal or granular keratinocytes (T1 and T4 fractions resp.), obtained by successive incubations in trypsin solution of six independent normal human epidermis samples. Real-time quantitative PCR experiments were further performed to ensure the validity of the profiling for each candidate gene identified from microarrays data, and results of this multitechnique approach will be the object of a forthcoming publication. These results will be the basis for a better understanding of dermatological hyperkeratotic pathologies.
Within epidermis, keratinocytes achieve a differentiation program culminating in cornification, a programmed cell death required for the establishment of the barrier function. A complex genetic regulatory network underlies the numerous biochemical modifications taking place in the last living cells, the granular keratinocytes (GKs), but very few transcription factors specific from this process were identified. Here we describe a large-scale, multitechnique approach performed on cells purified from normal human epidermis, and mainly focused on identification of these regulators. We performed microarray experiments to compare gene expression in cell fractions enriched in granular or basal keratinocytes. These data, with in silico promoter analysis for 52 differentiation markers, and exploitation of an EST library from GKs, were filtered according to gene products’ known or putative function and ESTs number in UniGene database, and allowed identification of 298 candidates out of 3,662 genes potentially specific from the last differentiation steps. Half were detected for the first time in epidermis and quantified by quantitative real-time PCR. These genes are linked to various aspects of GKs function, including structural components, lipid metabolism and secretory apparatus, cell signaling, and regulation of transcription. Forty-nine new differentiation-associated genes were identified, and 38 transcription factors in 92 were positively or negatively regulated in the course of differentiation, therefore possibly involved in the final differentiation of GKs. These data give new leads to have a global view of the network involved in epidermal barrier function, and allow in the future a better understanding of several pathologies, including genodermatoses of unknown aetiology.

Keywords: Cell type comparison

overall_design: Six independent samples of normal human epidermis were used for this study. For three samples, technical replicates (at the labelling step) were performed (ie AQQ003, AQQ005 and AQQ011 slides are dye-swaps of AQQ002, AQQ004 and AQQ010, respectively). Data from each pair of “swap arrays” were merged and considered as coming from three simple arrays (named AQQ002dw, AQQ004dw and AQQ010dw) for statistical analysis. For each slide, T4 is the test sample (total RNA from granular keratinocytes), and T1 the reference sample (total RNA from basal keratinocytes of the same subject), and both come from the same biological sample.

middle: R

first: Pascal

last: Barbry

first: Kevin

last: Le Brigand

first: Marina

last: Guerrin


title: Regulation of gene expression by ATF2 in mouse melanocytes

status: Public on Aug 30 2010

city: SAN DIEGO

first: Alexey

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

summary: primary melanocytes from WT and ATF2 mutant (transcriptionally inactive) mice expressing the mutant N-ras transgene were prepared and assessed for changes in gene expression when maintained under normoxia and hypoxia growth conditions.

overall_design: 12 mouse melanocyte samples were analyzed during normoxia and hypoxia, with different ATF2 genotypes. The pivotal samples are represented as duplicates. Treatment of tamoxifen was used to induce recombination and expression of the mutant ATF2 (inducible Cre). Doxycyclin was used to induce expression of mutant N-Ras transgene.

first: Ze'ev

last: Ronai

first: Vikas

last: Goel


title: Pellicle formation of MR-1

city: Norman

first: Yili

last: Liang

state: OK

address: 101 David L. Boren Blvd,

department: Botany and Microbiology

institute: Insitute Institute for Environmental Genomics, University of Oklahoma

summary: Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. In recent years, biofilm development of S. oneidensis has been extensively studied because it is essential to reduce solid metals. As a special form of biofilm, however, pellicles are largely overlooked. The goal of this work was to understand requirements of S. oneidensis pellicle formation and the molecular basis of pellicle formation. We demonstrated that successful pellicle formation and survival was likely to require the threshold level of cell density and higher concentration of oxygen. Proteinase K and EDTA were potent pellicle disrupter. DNA microarray experiments were used to study the gene expression profile of young air–liquid interface pellicle relative to planktonic cells, which indicated that the air–liquid interface pellicle was more metabolically active than the planktonic cells. Most notably, consistently up-regulation of iron or heme uptake and transportation proteins was observed in the S. oneidensis MR-1 pellicle. However, neither the hmuT nor hugA heme transport mutant was defective in pellicle formation. An examination of the influence of several metal cations on the anti-pellicle activity of EDTA showed that Ca (II), Mn(II), Cu(II), and Zn(II) fully protected S. oneidensis MR-1 pellicle against EDTA treatment while additional of iron enabled the initiation of pellicle formation but maturation was significantly impaired. Collectively, iron was less important than other metals with respect to pellicle formation in S. oneidensis.

overall_design: A fresh colony grown overnight on a LB plate was used to inoculate 50 ml LB and incubated in a shaker (200 rpm) to an OD600 of 0.8 at the room temperature. This culture was then diluted 500-fold with fresh LB, resulting in the starting cultures. Aliquots of 30ml starting cultures were transferred to 50-ml Pyrex beakers and allowed to develop pellicles at the room temperature. When a complete but thin (young pellicle) at the interface were formed (about 30h hours), planktonic culture and pellicle were separated and applied to centrifugation at 8000 rpm for 3 min at room temperature. 3 parallel starting cultures were used and 3 samlpes of pellicle cells or planktonic cells were collected at 30h. RNA from the pellicle cells was fluorescently labeled with Cy3, and that from the planktonic was labeled with Cy5.

first: Haichun

last: Gao

first: Xueduan

last: Liu

first: Jizhong

last: Zhou


title: Gene expression profiling of metastatic and non-metastatic osteosarcoma biopsies

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

country: Australia

institute: University of Queensland

summary:
Osteosarcoma (OS) is the most common primary bone tumour in children and young adults, and the second highest cause of cancer-related death in this age group. In spite of aggressive chemotherapy, disease-free survival has not improved significantly in the past 20 years, and 50% of patients subsequently develop fatal pulmonary metastasis. We have performed gene expression profiling of primary osteosarcoma biopsies (i) to identify prognostic markers, and (ii) to identify novel therapeutic targets.
Keywords: Comaprison between disease status (metastatic vs non-metastatic) and normal

overall_design: Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates).

middle: B

first: Andrew

last: Cumming

first: Danny

last: Rickwood

first: Charlotte

last: Ng

first: Geoff

last: Strutton

first: Ian

last: Cassady

first: Andreas

last: Evdokiou

first: Scott

last: Sommerville

last: Dickinson

first: Alexander

last: Guminski

first: Nicholas

last: Saunders


title: Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase

city: Boston

first: Amnon

last: Koren

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: In order to address the replication timing of the centromeres in yeast Candida albicans, we have determined at high temporal and spatial resolution its genome-wide DNA replication timing profile. This was done by sorting S- and G1-phase cells by FACS and hybridizing DNA from both fractions onto genomic tiling arrays. Data was normalized, organized by chromosomal positition, and smoothed. Replication timing is inferred from the DNA copy number along the chromosome with data peaks corresponding to predicted origins of DNA replication. We observe that the centromeric loci coincide with replication origins that are the first to replicate on each chromosome. We further analyzed replication timing in strain 9929s, in which the centromere of chromosome 5 was deleted and a neocentromere has formed at a distant location. A replication origin, again the first to replicate, appeared at the site of neocentromere formation. We conclude that centromeres cause their own early and distinct DNA replication timing.

overall_design:
Four repeats of the wild type strain (SC5314) and two repeats of strain YJB9929s, S phase- vs G1 phase-cell DNA with different Cy dyes for each.

The supplementary file 'GSE17963_final_data.txt' contains the fully processed replication timing data; its contents is described in 'GSE17963_readme.txt'.


title: DNA methylation data from human liver, frontal cortex, spleen and colon

status: Public on Aug 28 2010

city: Charlestown

first: Martin

last: Aryee

address: 149 13th Street

department: Pathology

institute: Massachusetts General Hospital

type: Methylation profiling by genome tiling array

summary: DNA methylation data from human tissues: 5 samples each of normal liver, frontal cortex, spleen and colon. 5 samples of colon tumor.

overall_design:
Genomic DNA was isolated and hybridized to custom-designed Nimblegen microarrays (CHARM human array v1).
4 normal tissues and 1 colon tumor

first: Christine

last: Ladd-Acosta

last: Feinberg


title: Recurrent disruption of HIP1 identified in patients with epilepsy, learning difficulties, intellectual disability, and neurobehavioral abnormalities

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

type: Genome variation profiling by genome tiling array

summary: We report 12 individuals from ten unrelated families with epilepsy, learning difficulties, intellectual disability, and neurobehavioral abnormalities, who segregated a microdeletion distally adjacent to the Williams-Beuren syndrome region. In six families, a recurrent ~ 1.1 Mb deletion likely resulted from nonallelic homologous recombination between flanking large complex low-copy repeats. Three smaller sized microdeletions (~ 180-500 kb) enabled us to narrow the critical region to one gene, HIP1, encoding Huntington interacting protein 1.

overall_design: genomic DNA from blood was used to analyse 12 samples  with control sample using custom made NimbleGen 12x135K microarrays for chr7 region.

first: Magdalena

last: Bartnik

first: Melissa

last: Ramocki

first: Przemyslaw

last: Szafranski

first: Katarzyna

middle: E

last: Kołodziejska

first: Zhilian

last: Xia

first: Jaclyn

last: Bravo

first: G

last: Miller

first: Diana

middle: L

last: Rodriguez

first: CA

last: Williams

first: Elżbieta

last: Szczepanik

first: Patricia

middle: I

last: Bader

first: James

middle: G

last: Coldwell

first: Cigdem

last: Akman

first: Karen

last: McAlmon

first: Susan

last: Reed

first: Melinda

last: Cohen

first: Jennifer

last: Mueller

last: McGrath

first: Elizabeth

last: Roeder

first: Gary

last: Clark

first: Sung-Hae

last: Kang

first: Carlos

last: Bacino

first: Ankita

last: Patel

first: Ewa

last: Bocian

first: Sau

last: Cheung

first: Tadeusz

last: Mazurczak


title: Comparative genomic profiling and gene expression of Escherichia coli O103:H25 Oslo 2006 outbreak strain

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

summary:
A food-borne outbreak of haemorrhagic colitis (HC) and HUS caused by E. coli O103:H25 occurred in Norway, 2006. The outbreak included 17 registered cases, of which 10 developed HUS. The aim of this study was to characterize two E. coli O103:H25 isolates from this outbreak. Only one of the isolates carry the stx2 gene (by PCR). Since they have the same typing profile by typing method MLVA, we expect the isolates to have identical gene content except from an Stx2-encoding phage. Therefore, we further investigate whether the Stx2-encoding phage has any impact on the gene expression.
Keywords: mixed, gene expression, comparative genomic hybridization

overall_design: Triplicate samples of mRNA from a test strain O157:H7 EDL933 and two outbreak strains - one Stx positive and one stx negative were co-hybridized with genomic DNA from the same strain. Triplicate samples of the Stx positive strain grown at acidic conditions was also co-hybridized with genomic DNA from the Stx positive strain. Genomic DNA for each strain is technical replicates only.

first: Camilla

last: Sekse

first: David

last: Ussery


title: Analysis of Notch signaling on Xenopus epidermis

city: La Jolla

first: Ian

middle: K

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary:
Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate and proton secreting cells or with dominant negative human Mastermind (HMM) to induce the formation of ectopic multi-ciliate and proton secreting cells.  Results show which genes are up or down-regulated when HMM is compared to ICD.
Specialized epithelial cells in the amphibian skin play important roles in ion transport, but how they arise developmentally is largely unknown.  Here we show that proton-secreting cells  (PSCs) differentiate in the X. laevis larval skin soon after gastrulation, based on the expression of “kidney” specific form of the H+v-ATPase that localizes to the plasma membrane, orthologs of the Cl-/HCO3- antiporters ae1 and pendrin, and two isoforms of carbonic anhydrase.  Like PSCs in other species, we show that the expression of these genes is likely to be driven by an ortholog of foxi1, which is also sufficient to promote the formation of PSC precursors.  Strikingly, the PSCs form in the skin as two distinct subtypes that resemble the alpha- and beta-intercalated cells of the kidney. The alpha-subtype expresses ae1 and localizes H+v-ATPases to the apical plasma membrane, whereas the beta-subtype expresses pendrin and localizes the H+v-ATPase cytosolically or basolaterally.  These two subtypes are specified during early differentiation, and can be distinguished based on the expression of ubp1, a transcription factor in the grainyhead family.  Finally, we show that ectopic expression ubp1 is sufficient to promote the differentiation of beta-subtypes while repressing alpha-subtypes. These results have implications for how PSCs are specified in vertebrates and become functionally heterogeneous.

overall_design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD or HMM.  At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip.  At stage 22 RNA was harvested from explants and used as the starting material for arrays.

last: Stubbs

first: Chris

last: Kintner


title: Campylobacter jejuni murine adaptation: unadapted v. adapted during growth in C57 BL/6 IL-10-/- germ-free mice.

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Expression arrays comparing Campylobacter jejuni 11168 before and after serial passage in C57 BL/6 IL-10 deficient mice.  Transcript abundance was compared between C. jejuni variants during growth in the ceca of C57 BL/6 IL-10 deficient germ-free mice.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: Unpassaged (p0) C. jejuni 11168 was compared to the same strain after three passages (p3) through the mice. Biological replicates: 4; 2 biological replicates were dye swaps.

first: John

last: Jerome

first: Anne

last: Plovanich-Jones

first: Julia

last: Bell


title: TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

address: 1450 3rd Street, MC 0520

institute: UCSF

summary: There is increasing evidence that microRNA and transcription factors interact in an instructive fashion in normal and malignant hematopoiesis.  We explored the impact of TEL-AML1 (ETV6-RUNX1), the most common fusion protein in childhood leukemia, on miRNA expression and the leukemic phenotype.  Using RNA interference, miRNA expression arrays, and quantitative PCR, we identified miRNA-494 and miRNA-320a to be upregulated upon TEL-AML1 silencing independently of TEL expression.  Chromatin immunoprecipitation analysis identified miRNA-494 as a direct miRNA target of the fusion protein TEL-AML1.    Using bioinformatic analysis as well as functional luciferase experiments we demonstrate that survivin is a target of the two miRNAs.   MiRNA-494 and -320a were introduced to the cells by transfection and survivin expression determined by western blot analysis.  These miRNAs blocked survivin expression and resulted in apoptosis in a similar manner as TEL-AML1 silencing by itself; this silencing was also shown to be DICER-dependent.  MiRNAs-494 and -320a are expressed at lower levels in TEL-AML1+ leukemias compared to immunophenotype-matched non-TEL-AML1 ALL subtypes, and within TEL-AML1+ leukemias their expression is correlated to survivin levels.  In summary our data suggest that TEL-AML1 might exert its anti-apoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression.

overall_design: DNAs from REH cells were pulled down using ChIP antibodies to TEL and hybridized to microRNA promoter tiling arrays.


title: DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells Using Custom Agilent CGH Arrays

status: Public on Aug 27 2010

city: Pittsburgh

first: Tianjiao

last: Chu

state: PA

address: 204 Craft Ave

institute: Magee Womens Research Institute

summary: We present a detailed structural and functional analysis of the placental epigenome at its maternal interface. Specifically, we analyzed the DNA methylation pattern of chromsomes 13, 18, and 21 in samples of chorionic villus (CVS) and maternal blood cells (MBC) using custom designed microarrays. We then compared these data with transcription data for the same tissues. In addition to the discovery that CVS genomes are significantly more hypomethylated than their MBC counterparts, we identified numerous tissue-specific differentially methylated regions (T-DMRs). We further discovered that these T-DMRs are clustered spatially along the genome and are enriched for genes with tissue-specific biological functions. We identified unique patterns of DNA methylation associated with distinct genomic structures such as gene bodies, promoters and CpG islands and identified both direct and inverse relationships between DNA methylation levels and gene expression levels in gene bodies and promoters respectively. Furthermore, we found that these relationships were significantly associated with CpG content. We conclude that the early gestational placental DNA methylome is highly organized and is significantly associated with transcription. These data provide a unique insight into the structural and regulatory characteristics of the placental epigenome at its maternal interface and will drive future analyses of the role of placental dysfunction in gestational disease.

overall_design: Two-condition experiment, CVS vs. MBC cells. Biological replicates: 2 pooled CVS samples, 2 pooled MBC samples, collected from different patients. Each sample is divided into two parts, one part treated with HpaII enzyme, one part without. The two parts then are hybridized to the two channels of the same array. Two arrays for each sample, with dye swap to remove dye bias.

last: Peters


title: Apoptotic bodies unleash functional CXCL12 expression through microRNA-126

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

summary: Apoptosis plays a pivotal role in embryogenesis and postnatal cell homeostasis, involving DNA or subcellular fragmentation, and shedding of small membranous microvesicles termed apoptotic bodies (AB). Following DNA damage, hypoxia, or vascular injury, the chemokine CXCL12 has been implicated in the recruitment of progenitor cells for tissue regeneration through its receptor CXCR4 and in mechanisms counteracting apoptosis. Whether AB deliver alarm signals for regenerative responses to neighbouring cells beyond recruitment or eat-me signals for phagocytes and relevance to diseases with abundant apoptosis, eg atherosclerosis, remains unknown. Here we show that endothelial cell-derived AB are generated during diet-induced atherosclerosis and can be transferred to recipient endothelial or smooth muscle cells to induce functional expression of CXCL12. This is mediated through miRNA-126 enriched in AB, which acts by silencing RGS16 translation and unlocking CXCR4 to unleash an auto-regulatory feedback loop inducing CXCL12. Injection of AB promoted mobilization and incorporation of progenitor cells, reducing diet-induced atherosclerosis in apolipoprotein E-deficient mice, and local transfer of microRNA-126 inhibited collar-induced arterial plaque formation. This was associated with increased smooth muscle content but decreased macrophage and apoptotic cell content, all features of plaque stability. Our data identify a new mechanism, by which AB confer microRNA-126 as a paracrine alarm messenger to enhance CXCR4 signals and CXCL12 expression, thereby limiting or repairing vascular damage. This adds to the important functions of microRNAs in health and disease and may extend to progenitor cell recruitment during other forms of tissue repair or homeostasis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: AB were isolated from supernatants of apoptotic, serum-starved human umbilical vein endothelial cells (HUVECs) by sequential centrifugation steps. Total RNA was isolated from AB or HUVECs and microRNA was purified using the mirVanaTM miRNA Isolation Kit (Ambion). microRNA obtained from 10 µg of total RNA was labeled using the mirVanaTM miRNA Labeling Kit (Ambion) and fluorescent Cy3 (Molecular Probes), and hybridized to the Ambion mirVanaTM miRNA Bioarray (1566 v.1). Hybridized mirVana miRNA Bioarrays were scanned and quantified by using ImaGene 5.5.4 (Bio Discovery). Resulted signal intensities were background corrected and then normalized using variance stabilization normalization. (Huber, 2002).

first: Alma

last: Zernecke

first: Kiril

last: Bidzhekov

first: Heidi

last: Noels

first: Bernd

last: Denecke

first: Erdenechimeg

last: Shagdarsuren

first: Mihail

last: Hristov

first: Christian

last: Weber


title: non-M1 covRS-intact and -mutant GAS vs  M1 controls

city: St Lucia

first: Peter

last: Maamary

address: Cooper Road

department: School of Chemistry and Molecular Biosciences

summary: Microarray was performed on RNA extracted from mid-logarithmic phase in vitro grown non-M1 Streptococcus pyogenes isolates, with either intact or mutant covRS operons. These isolates were compared with corresponding M1 covRS intact and mutant forms to link the expression prolfiles of these non-M1 isolates with invasive pathogenesis.

overall_design: A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=4 peplicates for each strain.

first: Ramy

last: Aziz

first: Andrew

last: Hollands

first: Rita

last: Kansal

first: William

last: Taylor

first: Malk

last: Kotb

first: Mark

last: Walker


title: Genome-wide analysis of time-dependent gene expression in MCF-10HER-2/E7 cells treated with the HER-2-specific inhibitor CP724,714 for 45 hours

status: Public on Aug 24 2010

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

summary: Results of blocking the activated HER-2 oncogene kinase activity in MCF-10HER-2/E7 cells by treatment with CP724,714 and measuring gene expression as a function of time provides information as to what genes are regulated by HER-2 in these transformed breast epithelial cells.

overall_design: MCF-10HER-2/E7 cells were treated with the HER-2-specific small molecule kinase inhibitor CP724,714 for 45 hours.  Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).

first: Stephen

last: Ethier


title: Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent

status: Public on Aug 26 2010

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary: Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes (‘paternal excess’) associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants.

overall_design: Six biological samples: 2xX2x, 2xX4x, 2xX6x, 6xX2x, 4xX2x and fis1X2x. Each non-2xX2x cross was co-hybridised with 2xX2x to a two-colour array (5 arrays). Dyes were then swapped and the hybridisations repeated using an additional 5 arrays.

first: Sushma

last: Tiwari

first: Roger

last: Pennel


title: Genome-wide analysis of time-dependent gene expression in MCF-10HER-2 cells treated with the EGFR-specific inhibitor gefitinib for 45 hours

summary: Results of blocking activated EGFR/HER-2 heterodimer signaling in MCF-10HER-2 cells by treatment with gefitinib and measuring gene expression as a function of time provides information as to what genes are regulated by EGFR/HER-2 signaling in these breast epithelial cells that are transduced to overexpress the HER-2 oncogene and express transformed phenotypes.

overall_design: MCF-10HER-2 cells were treated with the EGFR-specific small molecule kinase inhibitor gefitinib for 45 hours. Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).


title: Transcriptome analysis of the barley fast neutron mutants nec3

status: Public on Aug 25 2010

city: Riga

first: Nils

last: Rostoks

address: 4 Kronvalda Blvd.

country: Latvia

institute: University of Latvia

summary: Affymetrix Barley1 GeneChip microarray was used to study the transcriptome of two fast neutron barley mutants FN362 and FN363 allelic to characterized necrotic leaf spot 3 (nec3) mutants. PCR screening of the 21 genes at least two-fold down-regulated in mutants did not show any deletions in the genome of mutants and, thus, failed to identify a gene responsible for the nec3 mutant phenotype suggesting that either probe set for the NEC3 gene is not on the Barley1 GeneChip, or that the expression of wt NEC3 is confined to specific developmental stage or tissue type.

overall_design: Transcriptome of the two barley fast neutron mutants was compared to the transcriptome of parental variety Steptoe

first: Robert

last: Brueggeman

first: Anete

last: Keisa

first: Andris

last: Kleinhofs


title: Genome-wide analysis of time-dependent gene expression in MCF-10A cells treated with the EGFR-specific inhibitor gefitinib for 45 hours

summary: Results of blocking EGFR kinase activity in MCF-10A cells by treatment with gefitinib and measuring gene expression as a function of time provides information as to what genes are regulated by EGFR in these nontransformed breast epithelial cells.

overall_design: MCF-10A cells were treated with the EGFR-specific small molecule kinase inhibitor gefitinib for 45 hours.  Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).


title: ucRNA profiling in human hepatocytes

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary: Genome-wide expression profiling has been performed in malignant HepG2 cells and compared to the expression in normal human hepatocytes. 56 ucRNAs, representing 11% of all ucRNAs analyzed, were aberrantly and significantly (p<0.05) expressed in malignant HepG2 cells compared to non-malignant human hepatocytes.

overall_design: RNA was extracted from three separate biological samples for each analysis using Trizol reagent (Invitrogen, Carlsbad, CA). Total RNA (5 μg) was reverse transcribed using biotin end-labeled random oligonucleotide primers and cDNA was hybridized to a custom microarray (OSU-CCC 4.0), which includes sense and antisense probes to all 481 human ultraconserved reported by Bejerano et al, each spotted in duplicate.  Biotin-containing transcripts were detected using streptavidin–Alexa647 conjugate, scanned and analyzed using an Axon 4000B scanner and the GenePix 6.0 software (Axon Instruments, Downingtown, PA). The mean fluorescence intensity of replicate spots were subtracted from background and normalized using the global median method. We selected ucRNAs measured as present in all the three replicates. Differentially expressed ucRNAs were identified using the Class Comparison Analysis of BRB tools version 3.6.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html).  The criterion for inclusion of a gene in the gene list was a p-value < 0.05.


title: MicroRNA profiling of Multiple Sclerosis

city: New Lambton

first: Mathew

last: Cox

state: NSW

address: HMRI, John Hunter Hospital, Lookout Road

institute: University Of Newcastle

summary: It is well established that Multiple Sclerosis (MS) is an immune mediated disease. Little is known about what drives the differential control of the immune system in MS patients compared to unaffected individuals. MicroRNAs (miRNAs) are small non-coding nucleic acids that are involved in the control of gene expression. Their potential role in T cell activation and neurodegenerative disease has recently been recognized and they are therefore excellent candidates for further studies in MS.   We investigated the transcriptome of currently known miRNAs using miRNA microarray analysis in peripheral blood samples of 59 treatment naïve MS patients and 37 controls. Of these 59, 18 had a primary progressive, 17 a secondary progressive and 24 a relapsing remitting disease course. In all MS subtypes miR-17 and miR-20a were significantly under-expressed in MS confirmed by RT-PCR. These miRNAs manipulate T cell activation genes in a knock-in and knock-down T cell model. The same T cell activation genes are also up-regulated in MS whole blood mRNA, suggesting these miRNAs or their analogues may provide useful targets for new therapeutic approaches.

overall_design: MicroRNA expression profiling in Multiple Sclerosis using 59 multiple sclerosis patients and 37 healthy controls

first: Murray

last: Cairns

first: Kaushal

last: Gandhi

first: Adam

last: Carroll

first: Sophia

last: Moscovis

first: Graeme

last: Stewart

first: Simon

last: Broadley

first: Rodney

last: Scott

first: David

last: Booth

first: Jeannette

last: Lechner-Scott


title: RNA expression for ethanologenic E coli strains LY180 and LY180 del yqhC in the absence and presence of furfural

city: Gainesville

first: Peter

middle: Christopher

last: Turner

address: Bldg 981, Museum Road

department: Micro and Cell Science

institute: University of Florida

summary:
The data explore the transcription of strain LY180 and the yqhC deletion mutant LY180 del yqhC without and with 0.5 g/L furfural.
LY180 and LY180 del yqhC are described in Turner, PC, EN Miller, LR Jarboe, P Pharkya, KT Shanmugam, and LO Ingram. 2009. Escherichia coli YqhC regulates transcription of the adjacent   yqhD and dkgA genes, and mutations in yqhC contribute to furfural resistance in ethanologenic strains (in preparation for submission to Appl Env Microbiol)

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

overall_design: Total RNA was prepared from cultures of LY180 and LY180 del yqhC immediately before and 15 min after addition of furfural to 0.5 g/L.  The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

middle: C

first: Elliot

middle: N

last: Miller

first: Laura

last: Jarboe

first: Lonnie

middle: O

last: Ingram


title: Genome-wide analysis of expression and DNA methylation at CpG-island-associated sense-antisense transcript loci in mouse

city: Tsukuba

first: Yutaka

last: Watanabe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center (BRC)

country: Japan

institute: RIKEN Tsukuba Institute

summary: Sense-antisense transcript (SAT) pairs are pairs of transcripts that fully or partially overlap but are transcribed in opposite directions. Although SAT expression occurs in various species, most SAT pairs have not been examined in detail. Because our previous studies revealed some tissue specificity in SAT expression, SAT pairs might be involved in cell differentiation and the maintenance of tissue-specific gene expression programs. To analyze such tissue-specific SAT pairs, we assessed the expression profiles of SATs from 12 tissues of normal mice at a genome-wide scale and found that a considerable number of SAT pairs showed expression patterns unique to testis. This finding prompted us to study the relationship between SAT expression pattern and another epigenetic gene regulatory mechanism, DNA methylation. We conducted a comparative global analysis of the DNA methylation status of CpG island (CGI)-associated SAT loci from various tissues and found that in 99 of the 4911 SAT pairs studied, DNA methylation could cooperatively suppress its downstream “sense” transcription together with the “antisense” transcriptional activity in a tissue-specific manner. The tissue-specific differentially methylated regions (T-DMRs) of these SAT pairs mainly occurred outside of the defined CGIs. In addition, some of these T-DMRs are situated at the 5′ region of the antisense transcripts. This positioning implies a novel mechanism for DNA methylation to regulate gene transcription, in which DNA methylation inhibits an opposing transcriptional activity and therefore maintains stable expression of a tissue-specific gene.

overall_design:
Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) of C57BL/6J Jc1 and a mouse fibroblast cell line (SL10) were used for the mouse expression oligo-microarray. The expression array data were obtained by both oligo-dT and random priming methods, except for SL10 (olio-dT only).

Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) were used for DIP chip experiments. Nine of twelve tissues were separately analyzed classified on the basis of sex.
A technical duplication of DIP chip analysis was performed by using the same genomic DNA of male kidney.

first: Koji

last: Numata

first: Shinya

last: Murata

first: Yuko

last: Osada

first: Rintaro

last: Saito

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazufumi

first: Hidemasa

last: Kato

first: Kuniya

last: Abe

first: Hidenori

last: Kiyosawa


title: Profiling of H3K9me3 levels predicts Transcription Factor Activity and Survival in Acute Myeloid Leukemia

status: Public on Aug 22 2010

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: Acute Myeloid Leukemia (AML) is commonly associated with alterations in transcription factors due to altered expression or gene mutations. These changes might induce leukemia specific patterns of histone modifications. We used ChIP-Chip to analyze histone H3 Lysine 9 trimethylation (H3K9me3) patterns in primary AML (n=108), ALL (n=28), CD34+ cells (n=21) and white blood cells (n=15) specimens. Hundreds of promoter regions in AML showed significant alterations in H3K9me3 levels. H3K9me3 deregulation in AML occurred preferentially as a decrease in H3K9me3 levels at core promoter regions. The altered genomic regions showed an overrepresentation of cis-binding sites for ets and c-AMP response elements (CREs) for transcription factors of the CREB/CREM/ATF1 family. The decrease in H3K9me3 levels at CREs was associated with increased CRE-driven promoter activity in AML blasts in vivo. AML specific H3K9me3 patterns were not associated with known cytogenetic abnormalities. But a signature derived from H3K9me3 patterns predicted event free survival in AML patients. Combination of the H3K9me3 signature with established clinical prognostic markers outperformed prognosis prediction based on clinical parameters alone. These findings demonstrate widespread changes of H3K9me3 levels at gene promoters in AML. Signatures of histone modification patterns are associated with patient prognosis in AML.

overall_design: Blasts from patients with AML and ALL were obtained at the time of diagnosis (in a few cases at first relapse). Two batches of experiments were performed and analyzed separately. One group of specimens contained ALL (n=28) and AML samples (n=38) and the other one contained AML samples (n=70) and CD34+ progenitor cells (n=21) and white blood cells (n=15) as controls. Immunoprecipitations were performed for anti-H3K9me3. Chromatin-IPs were amplified using ligation mediated PCR and labeled using Cy3 coupled to incorporated amino-allyl-UTP. Common reference DNA consisting of a mixture of genomic DNA from AML patients was prepared, amplified and labeled in a similar way with Cy5.

first: Carsten

last: Müller-Tidow

first: Antje

last: Hascher

first: Fabienne

last: Isken

first: Lara

last: Tickenbrock

first: Nils

last: Thoennissen

first: Christine

last: Disselhoff

first: Shuchi

last: Agrawal

first: Yipen

last: Wang

first: Anke

last: Becker

first: Christian

last: Thiede

first: Gerhard

last: Ehninger

first: Udo

last: zur Stadt

first: Steffen

last: Koschmieder

first: Matthias

last: Seidl

first: Frank

middle: U

last: Müller

first: Wilhelm

last: Schmitz

first: Michael

last: McClelland

first: Wolfgang

last: Berdel

first: Martin

last: Dugas

first: Hubert

last: Serve


title: Cerium_Oxide_Nanoparticles_e_coli

status: Public on Aug 20 2010

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

summary: The effects of cerium oxide nanoparticles on the gene expression of Gram-negative Escherichia coli is tested.

overall_design: 8 cultures of E. coli were treated with either cerium nanoparticles or cerium chloride solution at 50 mgs/ml. 4 cultures were untreated.

first: Steven

middle: D

last: Brown

first: Ting

middle: F

last: Yan

first: Stanton


title: Gene expression in canine uterine bacterial infection

city: Uppsala

first: Gunnar

last: Pejler

address: BMC, Box 575

department: Anatomy, Physiology and Biochemistry

country: Sweden

institute: SLU

summary:
The study was undertaken to analyze the effect of canine uterine bacterial infection (Pyometra) on local gene expression patterns in the uteri. The results show profound upregulation of various expected genes related to both the innate and innate immune system. In addition, there was a marked upregulation of many genes associated with proteolysis. Moreover, the bacterial disease resulted in downregulation of a large number of homeobox and zinc finger transcription factors.

Keywords: Expression profiling by array

overall_design: Gene expression patterns in the uterus from dogs with pyometra disease compared to healthy dogs. 4 replicates each.


title: DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

city: Research Triangle Park

first: Deepak

last: Mav

address: 2 Davis Drive

institute: Sciome LLC

summary:
Elevated DNA methylation in the first intronic region of the BCL6 locus in B cell lymphomas enforces transcription of the BCL6 gene
Promoter tiling arrays were used to investigate the distribution of DNA methylation near the promoter region of BCL6 locus

overall_design: Comparison of DNA methylation at promoter regions of lymphoma (Raji) and myeloma (H929) cell lines by methylated CpG island recovery assay (MIRA-chip)

first: Anne

middle: Y

last: Lai

first: Mehrnaz

last: Fatemi

first: Archana

last: Dhasarathy

first: Christine

last: Malone

first: Steve

last: Sobol

first: Cissy

last: Geigerman

first: David

last: Jaye

first: Ruchir

last: Shah

first: Leping

last: Li

first: Paul

middle: A

last: Wade


title: Comparison of transcriptome between free-living and symbiotic cells of Frankia alni ACN14a

status: Public on Sep 12 2010

city: Kagohima

first: Ken-ichi

last: Kucho

address: Korimoto 1-21-35

institute: Kagoshima University

summary: The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living cells and on Alnus glutinosa nodule bacteria, using whole genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to symbiosis were highly induced: nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster) and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signalling processes, protein drug export, protein secretion, lipopolysaccharide and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We showed that this nodule transcriptome of Frankia was highly similar among phylogenetically distant plant families.

overall_design: To address gene expression changes of Frankia alni ACN in the symbiotic state, we compared transcript levels between young nodules formed on 4 species of trees (Alnus glutinosa, Alnus nepalensis, Myrica gale and Myrica rubra) and free-living cells grown in nitrogen-replete minimal medium. For A. glutinosa nodule and free-living cells, two sets of experiments (A and B) were performed in two different laboratories. Three biological replicates were preformed for each condition.

first: Nicole

last: Alloisio

first: Clothilde

last: Queiroux

first: Pascale

last: Fournier

first: Petar

last: Pujic

first: Claudine

last: Médigue

first: Masatoshi

last: Yamaura

first: Kentaro

last: Kakoi

first: Philippe

last: Normand


title: mRNA expression in wild-type of Thermus thermophilus HB8 strain grown on a rich (TT) medium at 45˚C and 70˚C

status: Public on Aug 23 2010

city: Toyonaka

first: Ryosuke

last: Mega

state: Osaka

address: 1-1 Machikaneyama-cho

department: Biological Sciences

institute: Osaka University

summary:
We observed the expression profile of the total mRNA of wild-type of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 45˚C compared with that of 70˚C.

Keywords: Growth temperature

overall_design: Wild-type T. thermophilus HB8 strain was pre-cultured at 70˚C for 5 h in 5 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 7.5 with NaOH.  The cells (5 ml) were inoculated into 0.30 liter of the same medium and then cultivated at 70˚C. At the Abs600 =0.8 (0min), this culture was divided into two flasks.  Then, equal volume of cold medium (4˚C) was added and the temperature were shifted down to 45˚C.  Hot medium (70˚C) was added to the other flask.  Cells were collected at 0.5 min and 10 min after temperature shift in the equal volume of 100% ice-cold ethanol, and then crude RNA was extracted. In order to compare mRNA expression in the wild-type strain between 45˚C and 70˚C, the expression of each mRNA at each time point was analyzed on a GeneChip as described for each sample in this website.

first: R

first: A

last: Shinkai

first: N

last: Nakagawa

last: Masui

first: S

last: Kuramitsu


title: Heterologous acyl-homoserine lactone synthase expression in Pseudomonas putida

city: College Station

first: Yunho

last: Lee

address: 1501 Harvey Road

department: Chemical engineering

institute: Texas A&M

summary: Many bacteria harbor an incomplete quorum sensing system, wherein they possess LuxR homologues without the quorum sensing acyl-homoserine lactone (AHL) synthase, which is encoded by a luxI homolog. An artificial AHL-producing plasmid was constructed using a cviI gene encoding for C6-AHL (HHL) synthase from Chromobacterium violaceum and was introduced successfully into both wild-type and the ppoR (a luxR homolog) mutant. Our data provides evidence to suggest that the PpoR-HHL complex, but neither PpoR nor HHL alone, could attenuate growth, antibiotic resistance, and biofilm formation ability. In contrast, swimming motility, siderophore production, and indole degradation were enhanced by PpoR-HHL. The addition of exogenous indole increased biofilm formation and reduce swimming motility. Interestingly, indole proved ineffective in the presence of PpoR-HHL, thereby suggesting that the PpoR-HHL complex masks the effects of indole. Our data was supported by transcriptome analyses showing that the presence of the plasmid-encoded AHL synthase altered the expression of many genes on the chromosome in strain KT2440. Our results showed that heterologous luxI expression occurring via horizontal gene transfer can regulate a broad range of specific target genes, resulting in alterations of the phenotype and physiology of host cells.

overall_design:
Strains: wild-type (pRK415), wild-type (pHHL), luxR mutant (pRK415), luxR mutant (pHHL)
Medium: M9 minimal medium supplemented with 10 mM glucose and 10 mM succinate
Temperature: 28 °C

first: Jinki

last: Yeom

first: Jisun

last: Kim

first: Jaejoon

last: Jung

first: CheOk

last: Jeon

first: Woojun

last: Park


title: microRNA expression profile in mouse lung development

status: Public on Aug 17 2010

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

type:
Non-coding RNA profiling by array
Other

summary: We performed miRNA and mRNA profiling over a 7-point time course, encompassing all recognized stages of lung development and explore dynamically regulated miRNAs and potential miRNA-mRNA interaction networks specific to mouse lung development

overall_design: replicated time course of mouse lung development in 7 time points

first: Dennis

last: Wigle


title: NCI-H460-LNM35 vs NCI-H460-N15

status: Public on Aug 21 2010

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary:
Comparing genome-wide gene expression profiles of highly metastatic lung cancer cell line NCI-H460-LNM35 vs low metastatic parental clone NCI-H460-N15

Keywords: Expression profiling with cDNA microarray

overall_design: Two-condition experiment, LNM35 vs. N15 cells.

first: Kiyoshi

last: Yanagisawa

first: Hiroyuki

last: Konishi

first: Chinatsu

last: Arima

first: Shuta

last: Tomida

first: Toshiyuki

last: Takeuchi

first: Yukako

last: Shimada

first: Yasushi

last: Yatabe

first: Tetsuya

last: Mitsudomi

first: Hirotaka

last: Osada


title: Drosophila Pph13 mutant vs. wildtype and Orthodenticle, Pph13 double mutant vs. wildtype

status: Public on Aug 19 2010

city: Bloomington

first: Andrew

last: Zelhof

state: IN

address: 1001 E Third Street

department: Department of Biology

institute: Indiana University

summary: Transcriptional profiling of Drosophila eye mutants Pph13 and orthodenticle

overall_design: Total head RNA cn bw vs. Pph13 cn bw and cn bw vs. otd; Pph13 cn bw at various developmental time points

first: Ashwini

last: Oke


title: Oxidant-NO-dependent gene regulation in dogs with type I diabetes

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

summary: The global changes in cardiac gene expression in dogs with alloxan-induced diabetes were studied using Affymetrix Canine Array. Cardiac RNA was extracted from the control and DM (n=4). The array data revealed that 797 genes were differentially expressed (P<0.01; fold change of at least ±2). 150 genes were expressed at significantly greater levels in diabetic dogs and 647 were significantly reduced.

overall_design: Mongrel dogs (weighing 22-29 kg, n = 13) were chronically instrumented for measurements of systemic hemodynamics. The control hemodynamics were recorded 10-14 days after the surgery. After the control recording, the dogs were divided into two groups: one normal (n = 7) and the other diabetic (n = 6). In the diabetic group, the dogs were injected with alloxan monohydrate (40-60 mg/kg iv) over 1 min. Alloxan was prepared as a 5% solution in citrate buffer (pH 4-4.5). Only dogs with blood glucose >200 mg/dl (fasted for at least 16 h) on day 7 were included in the diabetic group. Before and after the development of diabetes, the dogs had free access to water. Systemic hemodynamics were measured again after 4-5 wk. All the microarray analysis were perormed after 4 weeks of alloxan injection.

first: Shintaro

last: Kinugawa

first: Fabio

last: Recchia

first: Thomas

middle: H

last: Hintze


title: Mapping of the GDI1 duplication at Xq28 in four unrelated XLMR patients

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: In a study to elucidate the genetic defects in patients with X-linked mental retardation (XLMR) we performed X chromosome-specific BAC-array-CGH and identified a 0.33 Mb inherited recurrent copy number gain at Xq28 in affected males of four unrelated XLMR families. All aberrations segregate with the disease in the families and the carrier mothers show a nonrandom X-inactivation. Tiling Xq28 region-specific oligo-array revealed that all aberrations start at the same position (153.218 Mb) and end between 153.530 and 154.542 Mb. The copy number gain is complex in nature but always included 18 genes of which three, RPL10, ATP6AP1 and GDI1, are highly expressed in brain. From these, the copy number of GDI1 correlated with the severity of clinical features since it was duplicated in one family with nonsyndromic moderate MR, triplicated in males from two families with mild MR and additional features, while in a fourth family with a severe syndromic form of MR, it was present in four copies. Moreover, expression analysis revealed copy number-dependent increased mRNA levels in affected patients compared to control individuals. Interestingly, the breakpoint junction regions suggested a yet unknown recombination mechanism between two adjacent but different sets of low copy repeats.

overall_design: For duplication mapping and exact copy number analysis in all four families, differentially-labeled patient versus male control DNA samples were hybridized onto a custom designed 4x44k oligo-array (Agilent Technologies) that covers the repeat-masked region 152.70 Mb to 153.65 Mb at tiling resolution.

first: Hilde

last: Van Esch

first: Joke

last: Vandewalle

first: Karen

last: Govaerts

first: Jelle

last: Verbeeck

first: Christiane

last: Zweier

first: Irene

last: Madrigal

first: Montserrat

last: Mila

first: Elly

last: Pijkels

first: Isabel

last: Fernandez

first: Detlef

last: Böhm

last: Spaich

first: Jürgen

last: Kohlhase

first: Anita

last: Rauch

first: Peter

last: Marynen

first: Jean-Pierre

last: Fryns

first: Guy

last: Froyen


title: Role of zyxin in the tension-induced expression change in endothelial cells

status: Public on Aug 16 2010

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary:
One of the hallmarks in hypertension is a pressure-induced change in endothelial cell phenotype. A cytoskeletal protein zyxin, which was seen to translocate from focal adhesion contacts to the nucleus in response to the increased wall tensionis, mediates the tension-induced endothelial signaling.
Microarrays were used to detail the role of zyxin in the tension-induced expression changes in endothelial cells.

overall_design: Primary endothelial cells (Huvec) from four treatment groups were used for RNA extraction and hybridization on Affymetrix microarrays: wild type under normal condition, wild type under tension, Zyxin-SiRNA-treated under normal condition and Zyxin-SiRNA-treated under tension.

first: Marco

last: Cattaruzza


title: Copper exposures on the endangered delta smelt

status: Public on Aug 18 2010

city: Davis

first: Richard

middle: Edward

last: Connon

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

summary: The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively).  Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system.

overall_design:
We utilized 3 replicates for exposed samples and 3 replicates for controls, both of which were hybridized to a reference pool.  Each replicate contained 4 pooled larval delta smelt.  The Reference pool consisted of delta smelt samples from this experiment and a number of prior tests. No dye swaps were performed due to limited material.

Supplementary file linked below reports candidate differentially expressed cDNAs. Data represented as filtered, normalized, Log-2 Alexa (547/555) ratios.

middle: E

first: Sebastian

last: Beggel

first: Leandro

middle: S

last: D'Abronzo

first: Juergen

middle: P

last: Geist

first: Janice

last: Pfeiff

first: Alexander

middle: V

last: Loguinov

first: Christopher

last: Vulpe

first: Inge

last: Werner


title: Clear cell and chromophobe renal cell carcinoma samples

city: Stanford

first: Hongjuan

last: Zhao

address: 300 Pasteur Drive

department: Urology, Edwards Building R116

institute: Stanford University

summary:
Background: Clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) can usually be distinguished by histologic characteristics. Occasionally, diagnosis proves challenging and diagnostic difficulty will likely increase as needle biopsies of renal lesions become more common.
Method: To identify markers that aid in differentiating ccRCC from chRCC, we used gene expression profiles to identify candidate markers that correlate with histology.  39 antisera and antibodies, including 35 for transcripts identified from gene expression profiling, were evaluated. Promising markers were tested on a tissue microarray (TMA) containing 428 renal neoplasms. Strength of staining of each core on the TMA was formally scored and the distribution of staining across different types of renal neoplasms was analyzed.
Results: Based on results from initial immunohistochemical staining of multitissue titer arrays, 23 of the antisera and antibodies were selected for staining of the TMA. For 7 of these markers, strength of staining of each core on the TMA was formally scored. Vimentin (positive in ccRCC) and CD9 (positive in chRCC) best distinguished ccRCC from chRCC. The combination of vimentin negativity and CD9 positivity was found to distinguish chRCC from ccRCC with a sensitivity of 100.0% and a specificity of 95.2%.
Conclusions: Based on gene expression analysis, we identify CD9 and vimentin as candidate markers for distinguishing between ccRCC and chRCC. In difficult cases and particularly when the amount of diagnostic tissue is limited, vimentin and CD9 staining could serve as a useful adjunct in the differential diagnosis of ccRCC and chRCC.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Disease State: Stage of Clear Cell renal cell carcinoma (I - V))


title: microRNA expression in murine hematopoietic stem cells

status: Public on Aug 14 2010

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

summary: MicroRNAs influence hematopoietic differentiation, but little is known about their effects on the stem cell state. Here, we report that the microRNA processing enzyme Dicer is essential for stem cell persistence in vivo and a specific microRNA, miR-125a controls the size of the stem cell population by regulating stem/progenitor cell (HSPC) apoptosis. Conditional deletion of Dicer revealed an absolute dependence for the multipotent HSPC population in a cell autonomous manner, with increased HSPC apoptosis in mutant animals. An evolutionarily conserved microRNA cluster containing miR-99b, let-7e and miR-125a was preferentially expressed in long term HSCs. miR-125a alone was capable of increasing the number of hematopoietic stem cells in vivo by more than eight fold. This was accomplished through a differentiation stage-specific reduction of apoptosis in immature hematopoietic progenitors, possibly through targeting multiple pro-apoptotic genes. Bak1 was directly down-regulated by miR-125a and expression of a 3’UTR-less Bak1 blocked miR-125a-induced hematopoietic expansion in vivo. These data demonstrate cell-state-specific regulation by microRNA and identify a unique microRNA functioning to regulate the stem cell pool size.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bone marrow populations were FACS-sorted and profiled using a bead-based profiling platform. Long-term HSCs, short-term HSCs, multipotent progenitors, Lin-Kit+Sca+ cells, Lin-Kit+Sca- cells, Lin-Kit-Sca+ cells, Lin- cells and unfractionated whole bone marrow cells were prepared for total RNA using TriZol (Invitrogen) in replicates. For rare populations, cells from multiple mice were pooled. To perform microRNA profiling, 60 ng of total RNA were used for each sample.

first: Shangqin

last: Guo

first: Todd

middle: R

last: Golub

first: David

middle: T

last: Scadden


title: DNA methylation data from mouse hematopoietic progenitors

status: Public on Aug 15 2010

city: Baltimore

first: Hong

last: Ji

state: MD

address: 855 N Wolfe Street, Rangos 580

department: Medicine

institute: Johns hopkins school of Medicine

summary:
Genome-wide DNA methylation was studied to determine the methylome map of lymphoid and myeoloid commitment from hematopoietic progenitors
We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in FACs purified mouse hematopoietic progeniors

overall_design: We isolated genomic DNA from mouse MPPFL-, MPPFL+, CLP, DN1, DN2, DN3, CMP and GMP cells and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: Lauren

middle: I

last: Ehrlich

last: Seita

first: Irving

middle: L

last: Weissman

first: Andrew

last: Feinberg


title: FixK, a universal regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

summary: Facultative phototrophic bacteria are excellent models for analyzing the coordination of major metabolic traits including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In Rhodobacter sphaeroides and R. capsulatus, a two-component system called RegBA (PrrBA) controls these functions and it has been thought that this redox sensing regulatory system was essential for coordinating electron flow and could not be easily replaced in facultative phototrophs. Here we show that this is not the case and that the oxygen-sensing FixlJ-K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and several other metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth and has very little bacteriochlorophyll. Transcriptome analyses indicated that FixK positively regulates heme and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for hydrogen uptake, iron oxidation, and aromatic compound degradation. Electrophoretic mobility shift assays showed that FixK binds directly to the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome-histidine kinase gene and the fnr-type regulatory gene, aadR. AadR is likely responsible for mediating some indirect effects of FixK on expression of anaerobic genes. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms.

overall_design: Comparison of transcription profiles of Rhodopseudomonas palustris wild type and fixK mutant grown microaerobically.

first: Federico

last: Rey

first: Caroline

last: Harwood


title: Influence of the early stress of maternal separation on the prefrontal cortex transcriptome

city: Mumbai

first: Madhurima

last: Benekareddy

state: Maharashtra

address: 1, Homibhabha Road, Colaba

department: Department of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: Exposure to early stress (ES) is known to enhance adult vulnerability for anxiety and depressive behaviors. The molecular and cellular pathways altered in response to ES that contribute to the establishment of a substrate for susceptibility to adult psychopathology are not well understood. Focusing on the prefrontal cortex (PFC), a brain region implicated in the modulation of emotional responses, we examined the consequences of the early stress experience of maternal separation (MS) on the adult PFC transcriptome. Microarray analysis identified alterations in genes associated with signal transduction, neuronal excitability, G-protein signaling and stress responses in the PFC of adult animals previously exposed to ES. Our results also indicated that the pattern of gene expression changes observed in ES animals contains a component in common with that induced by 5-HT2A/C receptor stimulation in control animals, suggesting enhanced 5-HT2A/C receptor-mediated signaling in ES animals. Further, our microarray results reveal that a history of ES alters the DOI-induced transcriptome in the PFC.

overall_design:
We used the early stress (ES) paradigm of maternal separation (MS), which was performed as described below. In brief, post birth the litters were assigned to either the control or the MS group. Pups from the MS litters were separated from their mother every day for a period of 3 hours from postnatal day 2 (p2) to postnatal day 14 (p14), while the control litters were left undisturbed. After p14, the MS pups were left undisturbed and all litters were weaned at postnatal day 30. Experiments on adult control and MS rats were performed at postnatal day 60. To determine transcriptome alterations that arise in the PFC following a history of ES, a microarray analysis was performed. Further, to address gene expression changes that arise following 5-HT2 stimulation, we used the 5-HT2 partial agonist, DOI. We further compared to the DOI-induced transcriptome in the PFC of control animals with the ES induced transcriptome.

Control and MS animals (3 - Control and 4 - Maternally Separated) were examined in adulthood. In addition, control animals were injected with with 8 mg/kg DOI, a 5Ht2a agonist. The groups included Control (Control rats injected with saline; n=3), DOI (control rats injected with 8 mg/kg DOI; n=4), MS (MS rats injected with saline, n=4). Rats were sacrificed 2 hours after the injection by decapitation. The prefrontal cortex was quickly dissected out and stored at -70 till further use. Total RNA from each rat was extracted, labeled with Cy3 and hybridized onto Agilent Custom Rat Array 8X15K (AMADID: G2509F_16352). Each biological replicate was hybridized onto one array, making the total number of arrays 11.

first: Vidita

last: Vaidya


title: Steroid Pretreatment of Organ Donors to Prevent Postischemic Renal Allograft Failure: A Randomized, Controlled Trial

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

summary: Comparison between pretreated donor grafts corticosteroid vs. placebo

overall_design: Prospective, randomised, double-blind, placebo-control trial, xls files contain normalized data (Default Total Intensity Normalization, see Stanford Microarray Database website), gpr files the raw data

first: Alexander

last: Kainz

first: Rainer

last: Oberbauer

first: Christa

last: Mitterbauer

first: Maria

last: Haller

last: Burghuber

first: Paul

last: Perco

first: Robert

middle: M

last: Langer

first: Georg

last: Heinze


title: Protein Microarrays Discover Angiotensinogen and PRKRIP1 as Novel Targets for Autoantibodies in Chronic Renal Disease

status: Public on Aug 13 2010

first: Persis

last: Wadia

address: 269 W Campus Drive, CCSR 2210

summary: Biomarkers for early detection of chronic kidney disease are needed, as millions of patients suffer from chronic diseases predisposing them to kidney failure. Protein microarrays may hold utility in the discovery of auto-antibodies in other conditions not commonly considered auto-immune diseases. We hypothesized that proteins are released as a consequence of damage at a cellular level during end-organ damage from renal injury, not otherwise recognized as self-antigens, and an adaptive humoral immune response to these proteins might be detected in the blood, as a non-invasive tracker of this injury. The resultant antibodies (Ab) detected in the blood would serve as effective biomarkers for occult renal injury, enabling earlier clinical detection of chronic kidney disease than currently possible, due to the redundancy of the serum creatinine as a biomarker for early kidney injury. To screen for novel autoantibodies in chronic kidney disease, 24 protein microarrays were used to compare serum Ab from patients with chronic kidney disease against matched controls.  From a panel of 38 antigens with increased Ab binding, 4 were validated in 71 individuals, with (n=50) and without (n=21) renal insufficiency.  Significant elevations in the titer of novel auto-Ab were noted against Angiotensinogen (AGT) and PRKRIP1 in renal insufficiency.  Current validation is underway to evaluate if these auto-Ab can provide means to follow the evolution of chronic kidney disease in patients with early stages of renal insufficiency, and if these rising titers of these auto-Ab correlate with the rate of progression of chronic kidney disease.

overall_design: Serum antibodies were profiled for 7 healthy individuals and 17 patients with chronic kidney disease, using the Invitrogen ProtoArray® Human Protein Microarray v3.0 platform (Invitrogen, Carlsbad, CA). This platform contains 5,056 non-redundant human proteins expressed in a baculovirus system, purified from insect cells and printed in duplicate onto a nitrocellulose-coated glass slide. Each protein is spotted twice on each array, to measure the quality of the signal intensity. Details for experiment processing and analysis follow the previous publication from our group (Li et al Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4148-53). Prospector software was used to retrieve the expression based on immune response profiling of the .gal files.

first: Atul

middle: J

last: Butte

first: Tara

last: Sigdel

first: David

middle: B

last: Miklos

first: Minnie

last: Sarwal


title: Gene expression-based global role of CovR in GBS A909 using stk1 deletion mutant

first: Lakshmi

last: Rajagopal

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

summary:
Global regulatory roles of the TCS response regulator CovR  in GBS serotype 1a A909
Keywords: Strain comparison; global regulation

overall_design: Deletion mutant was examined for alterations in gene expression

first: Wan-Jung

last: Lin

first: Kelsea

last: Jewell


city: Chapel Hill

first: Tom

last: Kawula

address: 119 Manning Drive

department: Microbiology and Immunology

institute: University of North Carolina-Chapel Hill

summary: These microarray studies are part of a larger study characterizing a deletion mutant of the putative transcriptional regulator IclR in Francisella tularensis LVS and SchuS4 strains. The microarrays were performed using RNA isolated from wild-type LVS and a LVS iclR deletion mutant after growing in Chamberlain?s defined media pH 6.3 to early mid-log phase. Results suggest that IclR affects expression of several genes after determining statistically significant differences by SAM.

overall_design: Comparison of gene expression between LVS iclR deletion mutant vs. wild-type LVS.


title: Staphylococcus aureus small colony variant (JKD6229) vs. parent strain (JKD6210)

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

institute: Austin Health

summary: Transcriptional profiling of the small colony variant (SCV) S. aureus isolate (JKD6229) compared to the parent isolate with a normal phenotype (JKD6210). Both isolates were from a patient with persistent S. aureus infection, and the SCV strain arose during failed antibiotic therapy.

overall_design: Two condition experiment JKD6229 vs JKD6210. 4 biological replicates, one replicate per slide.

first: Wei

last: Gao


title: Identification and expression analysis of differentially expressed genes in a hepatocyte model of cold-induced glycerol production in rainbow smelt (Osmerus mordax)

status: Public on Aug 11 2010

city: Logy Bay

first: Jennifer

middle: Rejeanne

last: Hall

state: NL

address: 1 Marine Lab Rd.

department: Ocean Sciences Centre

country: Canada

institute: Memorial University of Newfoundland

summary: The rainbow smelt (Osmerus mordax, Mitchill, 1814) is an anadromous teleost that overwinters in the estuaries and inshore waters along the North American Atlantic coastline. In the winter months, smelt avoid freezing in subzero temperatures by the production of antifreeze proteins and high levels of glycerol. Glycerol production (glyceroneogenesis) occurs in the liver via a branch point in glycolysis and gluconeogenesis and is directly activated by low temperature. In these studies, hepatocytes were isolated from the liver of individual warm fish and incubated at either a warm (8ºC; non-glycerol accumulating) or cold (0.4ºC; glycerol accumulating) temperature over a 72 h time course. Functional genomic techniques were used to identify and validate hepatic transcripts that were differentially expressed between the warm and cold cells. Reciprocal suppression subtractive hybridization (SSH) cDNA libraries enriched for cold-responsive liver transcripts were constructed at the 72 h incubation time. Microarray analyses using the consortium for Genomic Research on All Salmonids Project (cGRASP) 16K (salmonid) cDNA array were performed at the 24, 48 and 72 h incubation times. For quantitative reverse transcription – polymerase chain reaction (QPCR) studies, we focused specifically on the non-colligative [type II antifreeze protein (AFPII)] and colligative (glycerol accumulation) freeze prevention strategies. AFPII (SSH identified) and 21 transcripts (SSH and/or microarray identified or selected by the authors based on a conceptual link to glycerol production) involved in the metabolism of glycolytic (glycogen, glucose) and gluconeogenic (amino acids) sources of glycerol and of lipids with a glycerol backbone (triglyceride, phosphoplipid) were analyzed using QPCR.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design:
Rainbow smelt were collected by seine netting from Mount Arlington Heights, Placentia Bay, Newfoundland in late October 2007 and transported to the Ocean Sciences Centre, Memorial University of Newfoundland. The fish were held in a 3000 L indoor free-flowing seawater tank maintained at 8°C to 10°C and followed a natural photoperiod with fluorescent lights set by an outdoor photocell.    Hepatocyte isolations were performed for individual male fish (i.e. no pooling of cells from different fish) from Nov. 27th to Dec.17th, 2007. Hepatocytes were not pooled as individual smelt produce different amounts of glycerol in response to cold temperature challenge. Each liver was perfused with medium containing collagenase and yielded approximately 300 million cells per individual. Initial or “pre-incubation” samples were collected and the remaining cell suspension was divided into 20 ml glass scintillation vials (6 x106 cells per vial) containing 2 ml of incubation medium and incubated at either a warm (8ºC; non-glycerol accumulating) or cold (0.4ºC; glycerol accumulating) temperature. Duplicate vials from each temperature were sampled at 24, 48 and 72 h incubation times for RNA isolation.    RNA isolated from the hepatocytes of the 9 fish with the highest levels of glycerol production at 0.4°C were used to generate 2 mRNA pools (a “cold” pool and a “warm” pool) for each incubation time (24, 48 and 72 h). To summarize, the “cold” pools contained cells from 9 individual fish incubated at 0.4°C for either 24, 48 or 72 h and which exhibited the highest increase in glycerol levels at 72 h relative to pre-incubation levels, and the “warm” pools contained cells from these same 9 individual fish but incubated at 8°C for either 24, 48 or 72 h and therefore exhibited no increase in glycerol levels at 72 h relative to pre-incubation levels.    Comparisons were made for the cold compared to warm pools at the 24, 48 and 72 h time points. For each time point, technical quadruplicate slides including two dye swaps were run per comparison.
Incubation time: 24 h: Cold_24h_1, Cold_24h_2, Cold_24h_3, Cold_24h_4
Incubation time: 48 h: Cold_48h_1, Cold_48h_2, Cold_48h_3, Cold_48h_4
Incubation time: 72 h: Cold_72h_1, Cold_72h_2, Cold_72h_3, Cold_72h_4
Technical replicate: Cold_24h_1, Cold_24h_2, Cold_24h_3, Cold_24h_4
Technical replicate: Cold_48h_1, Cold_48h_2, Cold_48h_3, Cold_48h_4
Technical replicate: Cold_72h_1, Cold_72h_2, Cold_72h_3, Cold_72h_4

first: Kathy

last: Clow

first: K

last: Ewart

first: Matthew

last: Rise

first: William

last: Driedzic


title: Gene expression profiling of endocycling cells vs mitotic cells

status: Public on Aug 12 2010

first: Brian

middle: R.

last: Calvi

department: Biology

summary: In this study we used expression microarrays as an entry point to gain further insights into the differences between endocycling cells and mitotic cycling in tissues of the Drosophila larva.

overall_design: Gene expression analyses were performed on tissues hand dissected from yw67c2 early 3rd instar larval tissues collected 70-75hr after egg laying. Total RNA was isolated using RNeasy Micro Kit (QIAGEN Valencia, CA 91355), and reverse transcribed and fluorescently labeled with Cy3 or Cy5 (Amersham) using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX 78744), according to the manufacturer's instructions. This was used to probe the DGRC-2 array, a Drosophila oligonucleotide array created by the Drosophila Genomics Resource Center (DGRC) which represents ~93% of annotated Drosophila genes from genome release 4.1 (Bogart et al., 2006). Two color microarray hybridizations were repeated with material from independent dissections representing two (fat body versus brain) and three (salivary gland versus brain) independent biological replicates. Slides were scanned by GenePix 4100A (Axon Instruments, Union City, CA) and the data was extracted with Axon GenePix Pro 5 image analysis software.

first: Shahina

last: Maqbool

first: Sonam

last: Mehrotra

first: Alexis

last: Kolpakas

first: Chris

last: Durden

first: Bingqing

last: Zhang

first: Hua

last: Zhong


title: Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes

city: Nashville

first: Britney

last: Grayson

state: TN

address: MCN T-3219, 1161 21st Ave South

institute: Vanderbilt University School of Medicine

summary: Gene expression in peripheral blood is shown sufficient to differentiate patients with metabolic disorders from control. The signatures of metabolic syndrome, coronary artery disease and type 2 diabetes also have significant overlap.

overall_design: Microarrays were performed on 35 subjects in the following groups: control (n=9), rheumatoid arthritis (n=6), metabolic syndrome (n= 6), coronary artery disease (n=6) and type 2 diabetes (n=8). Intensity values for each array were normalized to a sum of 10,000.

first: Thomas

last: Aune


title: Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

status: Public on Aug 10 2010

city: Ann Arbor

first: YU

last: CHEN

state: MI

address: 2300 Hayward

department: Chemical Engineering

institute: University of Michigan

summary: BACKGROUND:Isobutanol is a promising next generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titers.  Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches.  We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases on adaptation to exogenous isobutanol stress. RESULTS:The adaptations acquired in our evolved lineages exhibit antagonistic pleiotropy between minimal and rich medium, and appear to be specific to the effects of longer chain alcohols. By examining genotypic adaptation in multiple independent lineages, we find evidence of parallel evolution in hfq, mdh, acrAB, gatYZABCD, and rph genes. Many isobutanol tolerant lineages show reduced rpoS activity, perhaps related to mutations in hfq or acrAB. Consistent with the complex, multigenic nature of solvent tolerance, we observe adaptations in a diversity of cellular processes. Many adaptations appear to involve epistasis between different mutations, implying a rugged fitness landscape for isobutanol tolerance. We observe a trend of evolution targeting post-transcriptional regulation and high centrality nodes of biochemical networks. Collectively, the genotypic adaptations we observe suggest mechanisms of adaptation to isobutanol stress based on remodelling the cell envelope and surprisingly, stress response attenuation. CONCLUSIONS:We have discovered a set of genotypic adaptations that confer increased tolerance to exogenous isobutanol stress.  Our results are immediately useful to efforts to engineer more isobutanol tolerant host strains of E. coli for isobutanol production. We suggest that rpoS and post-transcriptional regulators, such as hfq, RNA helicases, and sRNAs may be interesting mutagenesis targets for futurue global phenotype engineering.

overall_design: Two strains (WT strain and G3.2 mutant strain), each with two culture conditions (with and without isobutanol in medium). Three biological replicates for each strain/culture condition. Twelve samples in total.

first: Jeremy

last: Minty

first: Ann

middle: A

last: Lesnefsky

first: Fengming

last: Lin

first: Yu

last: Chen

first: Ted

last: Zaroff III

first: Artur

last: Veloso

first: Bin

last: Xie

first: Catie

last: McConnell

first: Rebecca

last: Ward

first: Donald

last: Schwartz

first: Jean-Marie

last: Rouillard

first: Yuan

first: Erdogan

last: Gulari

first: Xiaoxia

middle: N


title: MicroRNA miR-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: This is the first report to document circadian rhythmicity of specific microRNAs in rat jejunum. Our data provide a link between the anti-proliferative microRNA miR-16 and the intestinal proliferation rhythm and point to miR-16 as an important regulator of proliferation in jejunal crypts. This function may be essential to match proliferation and absorptive capacity with nutrient availability.

overall_design: Time course data with 7 time points and 3 replicates per time point. Each 2-color array is hybridized against a reference from time point 0, and dye swaps are included.


title: Phenothiazine Neuroleptics Signal To The Human Insulin Promoter As Revealed By A Novel Human b-Cell Line Based Screen

status: Public on Aug 07 2010

city: La Jolla

first: Roy

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary:
(original Title) Phenothiazine Neuroleptics Signal To The Human Insulin Promoter As Revealed By A Novel Human b-Cell Line Based High-Throughput Screen.

To address the current deficiency in human beta-cell models, we have developed a cell line from human islets in which the expression of insulin and other beta-cell restricted genes are modulated by an inducible form of the bHLH transcription factor E47. In an effort to probe the global pattern of gene expression in T6PNE in an unbiased fashion, oligonucleotide microarray analysis was performed on T6PNE in the presence and absence of E47 induction and compared against human islets. Our analysis reveals that T6PNE express a substantial percentage of the b-cell specific geneset, and that this is further enhanced by the induction of E47. This cell line, T6PNE, was then screened against a library of known drugs for those that increase insulin promoter activity. Interestingly, members of the phenothiazine class of neuroleptics increased insulin gene expression upon short term exposure. Chronic treatment, however, resulted in suppression of insulin promoter activity, consistent with the effect of phenothiazines observed clinically to induce diabetes in chronically treated patients. In addition to providing insights into previously unrecognized targets and mechanisms of action of phenothiazines, the novel cell line described here provides a broadly applicable platform for mining new molecular drug targets and central regulators of beta-cell differentiated function.

overall_design: Gene expression studies in: Three human islet samples; Five T6PNE samples; Seven T6PNE induced with E47.

first: Alice

last: Kiselyuk

first: Fred

last: Levine


title: 5-aza-2-deoxycytidine treatment of Swarm rat chondrosarcoma cells

status: Public on Aug 06 2010

city: Chicago

first: Christopher

last: Hamm

state: IL

address: 2430 N. Halsted Street

department: Cancer Biology and Epigenomics

institute: Children’s Memorial Research Center

summary: The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells.  The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM).

overall_design: Five chip study.  For these experiments, microarray was carried out on untreated (control) Swarm rat chondrosarcoma cells (3 biological replicates), and microarray was also carried out on Swarm rat chondrosarcoma cells  treated with 5-aza-2-deoxycytidine (2 biological replicates).


title: Array CGH analysis of 56 primary gastric cancers for elucidating prognostic biomarkers

city: Sapporo

first: Nobumoto

last: Tomioka

state: Hokkaido

address: Nishi 7 chome, Kita 15 jo, Kita-ku

department: General Surgery

institute: Hokkaido University

summary: Array CGH analysis was done with 56 primary gastric cancers to elucidate prognostic biomarkers on the BAC basis.

overall_design: Using the extracted genomic DNA from 56 primary gastric cancers, array CGH was done to elucidate the prognostic biomarkers.

first: Keiko

last: Morita

first: Soichiro

last: Saitoh

first: Takashi

last: Hirano


title: Human lung squamous cell carcinoma expression profiling

first: Matthew

middle: D

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Lung squamous cell carcinoma gene expression (LSCC) is highly variable.  This study discovered and validated LSCC gene expression subtypes.

overall_design: RNA from tumors and a common reference were hybridized to Agilent two color microarrays

first: D

last: Hayes


title: Expression analysis of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp and B. fragilis NCTC 9343 delta-lfg

first: Michael

last: Coyne

address: 181 Longwood Avenue

institute: Brigham & Women's Hospital

summary: Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.

overall_design: A nine chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343, three separate cultures of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp, in which gmd (BF1888) and fcl (BF1887) and fkp (BF2607) are deleted, and three separate cultures of Bacteroides fragilis NCTC 9343 delta-lfg, in which nine genes (BF4298 through BF4306) of the lfg locus are truncated or deleted entirely.  Each chip measures the expression level of 4,231 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with eighteen 60-mer probes per gene, with five-fold technical redundancy.

first: Laurie

middle: E

last: Comstock

first: Maria

last: Chatzidaki-Livanis