title: ChIP-chip from dissected Drosophila egg chambers using antibody recognizing RNAPII

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Chromatin immunoprecipitation of RNAPII followed by hybridization to genome-wide tiling microarrays demonstrated that RNAPII localizes to all six Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified genomic loci

overall_design: Localization of RNAPII in stage 10 egg chambers with the nurse cells manually removed

first: Jane

last: Kim

first: Jared

last: Nordman

first: Fang

last: Xie

first: Helena

last: Kashevsky

first: Thomas

last: Eng

first: Sharon

last: Li

first: David

last: MacAlpine


title: Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity (Exiqon)

status: Public on May 31 2011

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

summary: Adipose tissue abundance relies partly on the factors that regulate adipogenesis, i.e. proliferation and differentiation of adipocytes. While the transcriptional program that initiates adipogenesis is well-known, the importance of microRNAs in adipogenesis is less well studied. We thus set out to investigate whether miRNAs would be actively modulated during adipogenesis and obesity. Several models exist to study adipogenesis in vitro, of which the cell line 3T3-L1 is probably the most well known, albeit not the most physiologically appropriate. We used a microarray strategy to provide a global profile of miRNAs in brown and white primary murine adipocytes (prior to and following differentiation) and evaluated the similarity of the responses to non-primary cell models, through literature data-mining. We found 65 miRNAs regulated during in vitro adipogenesis in primary adipocytes. When we compared our primary adipocyte profiles with those of cell lines reported in the literature, we found a high degree of difference in adipogenesis-regulated miRNAs. We evaluated the expression of 10 of our adipogenesis-regulated miRNAs using real-time qPCR and then selected 5 miRNAs that showed robust expression levels and profiled these by qPCR in subcutaneous adipose tissue of 20 humans with a range of body mass indices (BMI, range=21-48). Of the miRNAs tested, mir-21 was both highly expressed in human adipose tissue and positively correlated with BMI (R2=0.49, p<0.001). In conclusion, we provide the preliminary analysis of miRNAs important for primary cell in vitro adipogenesis and find that the inflammation-associated miRNA, mir-21, is up-regulated in subcutaneous adipose tissue in human obesity.

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

overall_design: 3 samples of pre adipocytes isolated from brown adipose tissue examined pre and post differentiation to brown adipocytes. 3 samples of pre-adipocytes isolated from white adipose tissue and examined pre and post differentiation to adipocytes.

middle: J

first: James

middle: A

last: Timmons


title: ROP16-dependent host transcriptional responses in chicken embryonic fibroblasts infected with T. gondii [RH, ROP16-KO]

status: Public on May 27 2011

city: Stanford

first: Yi-Ching

last: Ong

state: CA

address: 299 W. Campus Dr.

department: Microbiology & Immunology

country: USA

institute: Stanford University

summary:
Toxoplasma gondii is a ubiquitous protozoan pathogen able to infect both mammalian and avian hosts.  Surprisingly, just three strains appear to account for the majority of isolates from Europe and N. America.
To test the hypothesis that strain divergence might be driven by differences between mammalian and avian response to infection, we examine in vitro strain-dependent host responses in a representative avian host, the chicken.
To identify parasite drivers of strain-dependent host response, QTL mapping was used; analysis revealed a locus on Toxoplasma chromosome VIIb.  To determine whether this was the parasite gene ROP16, array analysis was performed on chicken embryonic fibroblasts infected with Type I parasites and ROP16-KO parasites (of a Type I background).

overall_design: Chicken embryonic fibroblasts were cultivated in vitro and infected with either Type I (RH) parasites or Type I ROP16-KO parasites; ROP16-dependent host transcriptional responses were then analyzed at 5 hours post-infection.


title: ChIP-chip from Drosophila egg chambers using ORC2 antibody

type: Genome binding/occupancy profiling by genome tiling array

summary: Chromatin immunoprecipitation of the Origin Recognition Complex (ORC) followed by hybridization to genome-wide tiling microarrays demonstrated that ORC localizes to the six Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified loci

overall_design: Comparison of ORC2 ChIP sample compared to input DNA for two different Drosophila strains and two developmental stage samples

middle: C

middle: L


title: ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4

summary: Chromatin immunoprecipitation of tetra-acetylated histone H4 followed by hybridization to genome-wide tiling microarrays demonstrated that tetra-acetylated H4 is enriched at the two chorion Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified loci

overall_design: Comparison of tetra-acetylated H4 ChIP sample compared to input DNA for two different Drosophila strains


title: ChIP-chip of BMP2 or control treated human pulmonary artery endothelial cells with anti-beta-catenin or anti-ppar-gamma antibodies on promoter regions

status: Public on May 25 2011

city: Baltimore

first: Molong

state: MD

address: 733 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

summary:
Reduced bone morphogenetic protein receptor (BMPR)2 expression in patients with pulmonary arterial (PA) hypertension (PAH), can impair PA endothelial cell (EC) function. We now characterize, in human PAECs, a novel BMPR2-mediated transcriptionally active complex between peroxisome proliferator-activated receptor (PPAR) gamma and beta-catenin (BC), and show that disruption of this complex impairs BMP mediated HPAEC survival.
Using whole genome wide ChIP-Chip promoter analysis we delineate PPARG-BC dependent transcription of target genes that include apelin.

overall_design: Comparison of ppar-gamma and beta-catenin occupancy on promoter regions from human pulmonary artery endothelial cells after either treatment with BMP2 (10ng/ml) or control. A total of 8 samples were created using NimbleGen human HG18 promoter arrays.

first: Tero-Pekka

last: Alastalo

first: Marlene

last: Rabinovitch


title: 0.3M NaCl vs Control and 2M NaCl vs Control

status: Public on May 26 2011

city: Jeongeup

first: Im

last: Seong Hun

address: Jeongeup 580-185, Republic of KoreaInstitute

country: South Korea

institute: Korea Atomic Energy Research Institute

summary: Transcriptional profiling of Deinococcus radiodurans comparing control untreated wild type cells with wild type cells treated with 0.3M NaCl or 2M NaCl

sample_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

overall_design:
Two-condition experiment, wild type vs. 0.3 M NaCl. Biological replicates: 4 replicates (Two replicates per array, N=8), dye-swapped, independently grown and harvested.
Two-condition experiment, wild type vs. 2 M NaCl. Biological replicates: 4 replicates (Two replicates per array, N=8), dye-swapped, independently grown and harvested.

first: Min-ho

last: Joe

first: Seong-hun

last: Im


title: Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles [miRNA]

first: Matthew

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

institute: MRC Cancer Cell Unit

summary: Comparison of miRNA expression profiles in cervical carcinoma cell lines to study the effects of Drosha expression levels

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Analyzed global miRNA expression profiles from 18 samples  (7 samples in duplicate, 4 single sample) representing cervical carcinoma cell lines with either relative Drosha over-expression (Cluster 2) or Drosha under-expression (Cluster 1),  due to wild-type expression in those cell lines or manipulation with RNAi.

first: Balaji

last: Muralidhar


title: Candida albicans Microarray studies: CAP2 (Wild type) vs. cap2D (Homozygous null mutant)

city: New Delhi

first: Krishnamurthy

last: Natarajan

state: Delhi

address: 314/325, School of life sciences, JNU

department: School of life sciences

country: India

institute: Jawaharlal Nehru University

summary: Transcriptome profiling to identify Cap2/Hap43 regulons in the human fungal pathogen Candida albicans: Wild type vs. cap2D grown in iron-depleted medium

overall_design: Two-condition experiment, WT vs. cap2D cells. Biological replicates: Wild-type and cap2D, independently grown in iron-depleted medium and harvested. One replicate per array.  Hybridization was repeated (technical replicate) for each biological replicate.

first: Rana

middle: P

last: Singh

first: Himanshu

middle: K

last: Prasad

first: Ishani

last: Sinha

first: Neha

last: Agarwal


title: Interaction of Aspergillus nidulans and Streptomyces rapamycinicus

city: Jena

first: Fabian

last: Horn

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI)

summary:
Gene expression analysis of four different treatments of Aspergillus nidulans.
reference line (A.nidulans), line A (A.nidulans + Streptomyces rapamycinicus), line B (A.nidulans + orsellinic acid), line C (A.nidulans + lecanoric acid)

overall_design: For each of these treatments 2 biological replicates were made.

first: Hans-Wilhelm

last: Nützmann

first: Volker

last: Schroeckh


city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
gnp06-03_microtrac - gene profiling of viral sirna in mutants at generation g1. Gene profiling of Turnip Crinkle Virus (TCV) siRNA in mutants at generation G1.
What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants?

overall_design: 4 dye-swap - gene knock out,treated vs untreated comparison

first: Virginia

last: Ruiz-Ferrer

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: transcriptomic effects of two Forafac® fluorosurfactants in turbot

status: Public on May 22 2011

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary: Fluorosurfactants are the key components in aqueous film forming foams (AFFF). They provide these fire fighting agents with the required low surface tension and they enable film formation on top of lighter fuels to prevent burn back. Development of effective and environmentally acceptable PFOS alternatives is one of the most important priorities in the fire fighting foam industry. DuPontTM offers the fluorosurfactant mixtures Forafac®1157 and Forafac®1157N for the formulation of AFFFs which are alternatives to the persistent and toxic perfluorooctane sulphonate (PFOS). Ecotoxicological testing of these inadequately documented mixtures is necessary to include them in AFFF hazard and risk assessment. Juvenile turbot (Scophthalmus maximus) was exposed for 14 days to 0.5 and 1.5 mg/l of the fluorosurfactant mixtures used in Forafac®1157 and Forafac®1157N. In a first transcriptomics experiment, microarray analysis revealed differentially expressed gene transcripts which were mainly involved in digestion and in the immune system. This discovery-driven screening approach offered the basis for new hypotheses that were tested in two subsequent experiments in which food intake, energy reserves, growth and a set of haematological parameters were examined. Additionally, effects of the two mixtures were compared to those of PFOS. Based on the results of this study, the mode of action of Forafac®1157N was the activation of the acute phase reaction resulting in increased leukocyte concentrations and the inhibition of growth due to the high energetic cost of toxicant exposure. For Forafac®1157, evidences of immunosuppression were found on the transcriptional level and the altered differential leukocyte profiles indicated that stress was induced in these fish. However, food intake, energy reserves and growth were not compromised, even at high exposure concentrations, which was in contrast to the effects seen after PFOS exposure. Taking into account that Forafac®1157 appeared to be less toxic than PFOS, this mixture could be considered as a more environmentally acceptable PFOS alternative for the use in AFFFs.

overall_design: Juvenile turbot with a mean weight of 7.21 ± 1.91 g and a mean length of 7.34 ± 0.33 cm were exposed to nominal concentrations of 0 mg/L; 0.5 mg/L and 1.5 mg/L for both Forafac®1157 and Forafac®1157N during 14 days. Three different 45 L aquaria per exposure condition were used resulting in 3 tank replicates. Each replicate aquarium contained six turbot.  After decapitation, the liver was dissected, homogenized in liquid nitrogen and stored at -80 °C until further analysis. The liver homogenates of the 6 fish per aquarium of exposure experiment 1 were pooled prior to RNA extraction. After RNA extraction, fluorescently labelled cRNA was constructed with each sample labelled with Cy3 as well as with Cy5.An Agilent custom 15k oligonucleotide microarray (Agilent Technologies) was used to measure gene transcription levels. The microarray platform, constructed by ACUIGEN (University de Santiago de compostela, Spain), contained 4 305 turbot-specific oligonucleotide fragments originating from an immune-related EST turbot database. Two probe volumes (Cy3 vs. Cy5) corresponding with 300 ng cRNA were mixed and applied onto every microarray. The hybridization design comprised one separate n+2 A-optimal design for each of the Forafac® mixtures.

first: Izak

last: Meyer

first: Dorte

last: Herzke

first: Belén

middle: G

last: Pardo

first: Paulino

last: Martinez

first: Martial

last: Pabon

first: Wim

last: De Coen

first: Dries

last: Knapen


title: Modulation of growth and angiogenesis of OSCC cells with Sal B

status: Public on May 21 2011

city: Shanghai

first: Ya

last: Yang

address: 639 Zhi Zao Ju Road

department: General Dentistry

country: China

institute: Ninth People's Hospital, School of Stomatology

summary: In this study we used in vitro approaches to investigate whether it has any inhibitory properties on OSCC cells. We also tried to understand the possible mechanisms of Sal B on this type of malignancy with respect to angiogenesis.

overall_design: 2 OSCC cell lines were treated with 100ug/ml Sal B for 48hours. cDNAmicroarray was used to evaluated the expressions of 96 genes known to be involving in modulating the biological process of angiogenesis.

first: Jian-ping

last: Ge

first: Long

last: Jiang

first: Li-li

last: Feng

first: Ya-qin

last: Zhu


title: Cell cycle promoter tiling

first: Tiffany

last: Hung

address: 371 SERRA MALL

type: Non-coding RNA profiling by genome tiling array

summary:
Discover novel transcriptional units upstream of cell cycle genes
Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such noncoding transcription are not known.  Here we use an ultra-high density array that tiles the promoters of 56 cell cycle genes to interrogate 108 samples representing diverse perturbations.  We identify 216 transcribed regions that encode putative lncRNAs--many of which have RT-PCR-validated periodic expression during the cell cycle, show altered expression in human cancers, and are regulated in expression by specific oncogenic stimuli, stem cell differentiation, or DNA damage.

overall_design: 53 samples tiled against respective controls

first: Howard

last: Chang

first: David

last: Wong


title: DEVELOPMENT OF A XENOGRAFT MODEL FOR CLINICAL OLIGO- AND POLY-METASTATIC PROGRESSION

city: Chicago

first: Xinan

middle: Holly

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

summary: We previously proposed a clinically meaningful intermediate metastatic state defined by a limited number of new metastases (≤5) after 3 months of follow-up, termed oligometastasis that has the curative potential by local cancer treatments as in contrast to the incurable widespread polymetastatic dissemination. While animal models of polymetastasis exist and this phenotype can be further enhanced upon serial in vivo passage, animal models of oligometastasis are not available. Here, we report the creation of an oligometastasis model of MDA-MB-435 human tumor in nude mice in which the oligometastatic phenotype exhibits stability during successive in vivo testing, and satisfies the criteria of ≤ 5 total body macroscopic metastases definition of the human cancer oligometastatic state. In parallel, we also developed an MDA-MB-435 polymetastatic model in which the polymetastatic dissemination pattern was either poly-foci at lung, or involved multiple anatomic sites including lung, heart, muscle, ovaries, kidney, brain and pleura. We have conducted microRNA expression profiling of cell lines derived from distinct lungs of oligo- and poly-metastatic animals. Animal model-derived microRNA expression features that discriminate oligometastatic cell lines from those of polymetastases accurately identify oligometastatic patients who failed to develop widespread metastases (P=0.005). These results demonstrate the clinical relevance of the oligo- and polymetastatic animal models we have developed and their potential in elucidating the molecular underpinnings of oligometastasis progression.

overall_design: We developed a stable human tumor (MDA-MB-435-GFP) xenograft model of oligometastatic and polymetastatic progression by conducting three consecutive rounds of experimental lung colonization assays.  In the first round, we generated oligometastases-like lung derivative MDA-MB-435-L1-GFP (L1) or polymetastases-like MDA-MB-435-L1Mic-GFP (L1Mic) cell lines.   We subsequently generated three oligometastatic L1 lung cell lines as well as four polymetastatic L1Mic lung cell lines from seven distinct animals of the second in vivo passage for further biological characterization and for microRNA expression analysis.

first: H.

middle: R

last: Xing

first: Yves

last: Lussier

first: Qingbei

last: Zhang

first: Yong

last: Huang


title: Salmonella Typhimurium: control vs. Deoxynivalenol (DON) treatment

status: Public on May 20 2011

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

summary: Transcriptional profiling of log and stationary phase S. Typhimurium, comparing untreated controls with Deoxynivalenol treated samples.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

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

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: Each array used labelled cDNA against a common genomic DNA reference. Triplicate arrays were carried out for each of the 4 conditions: untreated log phase, untreated stationary phase, DON treated log phase and DON treated stationary phase

first: Arthur

last: Thompson

first: Virginie

last: Vandenbroucke


title: Piperaquine Resistance is Associated with a Copy Number Variation on Chromosome 5 in Drug-Pressured Plasmodium falciparum Parasites

status: Public on May 23 2011

city: La Jolla

first: Neekesh

middle: V

last: Dharia

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

type: Genome variation profiling by genome tiling array

summary: The combination of piperaquine and dihydroartemisinin has recently become the official first-line therapy in several Southeast Asian countries. The pharmacokinetic mismatching of these drugs, whose plasma half lives are ∼20 days and ∼1 hr respectively, implies that recrudescent or new infections emerging shortly after treatment cessation will encounter piperaquine as a monotherapy agent. This creates substantial selection pressure for the emergence of resistance. To elucidate potential resistance determinants, we subjected cloned Plasmodium falciparum Dd2 parasites to continuous piperaquine pressure in vitro (47 nM, ∼two-fold higher than the Dd2 IC(50) value). The phenotype of outgrowth parasites was assayed in two clones, revealing an IC(50) value against piperaquine of 2.1 μM and 1.7 μM, over 100-fold greater than the parent. To identify the genetic determinant of resistance, we employed comparative whole-genome hybridization analysis. Compared to the Dd2 parent, this analysis found (in both resistant clones) a novel single nucleotide polymorphism in pfcrt, deamplification of an 82 kb region of chromosome 5 (that includes pfmdr1), and amplification of an adjacent 63 kb region of chromosome 5. Continued propagation without piperaquine selection pressure resulted in derivation of "revertant" piperaquine-sensitive parasites. These retained the pfcrt polymorphism and further deamplified the chromosome 5 segment that encompasses pfmdr1; however, these two independently generated revertants both lost the neighboring 63 kb amplification. These results suggest that a copy number variation event on chromosome 5 (825600-888300) is associated with piperaquine resistance. Transgenic studies are underway with individual genes in this segment to evaluate their contribution to piperaquine resistance.

overall_design: Genome DNA from in vitro Piperaquine-Resistant Parasites vs. Parental Dd2

first: Richard

middle: T

last: Eastman

first: Elizabeth

last: Winzeler

last: Fidock


title: Comprehensive genomic map of cytosine methylation for wild-type (WT) and Lsh-/- mouse embryonic fibroblasts

status: Public on May 19 2011

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

type: Methylation profiling by genome tiling array

summary:
DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a high-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences. We provide evidence that Lsh also controls genome-wide cytosine methylation at nonrepeat sequences and relate those changes to alterations in H4K4me3 modification and gene expression. Deletion of Lsh alters the allocation of cytosine methylation in chromosomal regions of 50 kb to 2 Mb and, in addition, leads to changes in the methylation profile at the 5′ end of genes. Furthermore, we demonstrate that loss of Lsh promotes—as well as prevents—cytosine methylation. Our data indicate that Lsh is an epigenetic modulator that is critical for normal distribution of cytosine methylation throughout the murine genome.
We used microarrays to detail a high-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences

overall_design: To investigate how genome-wide DNA methylation patterns are established in mice and how they may specifically depend on Lsh, we generated a comprehensive genomic map of cytosine methylation for wild-type (WT) and Lsh−/− mouse embryonic fibroblasts (MEFs) using methylated DNA immunoprecipitation (MeDIP) combined with whole-genome tiling microarray. In addition, we generated a histone 3 lysine 4 trimethylation (H3K4me3) chromatin map using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) and also evaluated genome-wide gene expression using cDNA microarrays

first: Alika

last: Maunakea

first: Anney

last: Che

first: Victorino

last: Briones

first: Eunice

middle: Y

last: Lee

first: Theresa

last: Geiman

first: Jiaqiang

first: Robert

last: Stephens

middle: M

last: Leighty

first: Keji

last: Zhao

first: Kathrin

last: Muegge


title: A DNA Methylation Fingerprint of  1,628 Human Samples

status: Public on May 24 2011

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

summary: DNA methylation is the best characterized of the different layers that make up the epigenetic setting. Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. The recently arrived single-base-resolution technologies for DNA methylation are extremely helpful tools, but are not yet applicable and affordable for studying large groups of subjects. Herein, we present a compromise between an extremely comprehensive study of a human sample population with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1,628 human samples where we interrogated 1,505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around transcription start sites that are not within a CpG island. For disease, the generated DNA methylation fingerprints show that, during tumorigenesis, human cancer cells underwent a progressive gain of promoter CpG island hypermethylation and a loss of CpG methylation in non-CpG island promoters. Although transformed cells are those where DNA methylation disruption is more obvious, we observed that other common human diseases, such as neurological and autoimmune disorders, had their own distinct DNA methylation profiles. Most importantly, we provide proof of principle that the obtained DNA methylation fingerprints might be useful for translational purposes by showing that are able to identify the tumor type origin of Cancers of Unknown Primary (CUPs). Thus, the DNA methylation patterns identified across the largest spectrum of samples, tissues and diseases reported to date constitute a baseline for developing higher-resolution DNA methylation maps, and provide important clues concerning the contribution of CpG methylation to tissue identity and its changes in the most prevalent human diseases.

overall_design: It was studied the genomic DNA from 1,628 human samples corresponding to 424 normal tissues (180 leukocytes, 97 colon mucosa and 227 other normal samples), 1,054 tumorigenic samples (premalignant lesions, primary tumors and metastases) and 150 non-cancerous disorders, such as brain lesions from Alzheimer’s disease, dementia with Lewy bodies, aortic atherosclerotic lesions, myopathies and autoimmune disorders.

first: Yassen

last: Assenov

first: Jose

middle: I

last: Martin-Subero

first: Balazs

last: Balint

first: Reiner

last: Siebert

first: Hiroaki

last: Taniguchi

first: Hiroyuki

last: Yamamoto

first: Manuel

last: Hidalgo

first: Aik-Choon

last: Tan

first: Oliver

last: Galm

first: Isidre

last: Ferrer

first: Montse

last: Sanchez-Cespedes

first: Alberto

last: Villanueva

first: Javier

last: Carmona

last: Sanchez-Mut

first: Maria

last: Berdasco

first: Victor

last: Moreno

first: Gabriel

last: Capella

first: David

last: Monk

first: Esteban

last: Ballestar

first: Santiago

last: Ropero

first: Ramon

last: Martinez

first: Marta

last: Sanchez-Carbayo

first: Felipe

last: Prosper

first: Xabier

last: Agirre

first: Mario

last: Fraga

first: Osvaldo

last: Graña

first: Luis

last: Perez-Jurado

first: Jaume

last: Mora

first: Susana

last: Puig

first: Jaime

last: Prat

first: Lina

last: Badimon

first: Annibale

last: Puca

first: Stephen

last: Meltzer

first: Thomas

last: Lengauer

first: John

last: Bridgewater

first: Christoph

last: Bock

first: Manel

last: Esteller


title: Large airway epithelial cells from cigarette smokers with and without lung cancer undergoing flexible bronchoscopy in the operating room for resection of a suspicious lung nodule

status: Public on Jun 01 2011

city: Boston

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

summary: mRNA expression was assayed from bronchial epithelial cell samples from smokers with and without lung cancer.  A subset of the samples (2 of the lung cancer samples and 3 of the no cancer samples) were pooled and underwent whole transcriptome sequencing.  The goals were to compare whole transcriptome sequencing gene expression levels to gene expression levels derived from these samples run on the Affymetrix HGU133A 2.0 platform.

overall_design: Current and former smokers with cancer (n=8) and without cancer (n=5) undergoing flexible bronchoscopy in the operating room for resection of a suspicious lung nodule at Boston University Medical Center were recruited.  Patients were classified as having no lung cancer based on the pathological results from the lung biopsy.  Patients with no cancer were diagnosed with alternative benign diseases of the chest including organizing pneumonitis, sarcoidosis and chronic inflammation due to foreign body material.

first: Jennifer

last: Beane


title: Umea Lucidea Experiment

city: Umeå

first: Mattias

last: Landfors

address: Umeå University

department: Clinical bacteriology

country: Sweden

institute: Umeå University

summary:
The experiment was designed to enable validation of pre-processing and test algorithms. The in-house produced cDNA-array contains 44 clones: 19 clones from mice, 4 clones from Pine (involved in photosynthesis) and 21 artificial clones from the Lucidea Universal ScoreCard (Amersham Bioscienses), where each clone was printed 480 times in 48 identically designed sub-grids.
The experiment contains eight arrays with identical experimental design. Total RNA from murine cell line was divided in two samples;  the reference sample was labeled with the fluorophore Cy5 and spiked with the Lucidea Universal ScoreCard reference reaction, the test sample was labeled with Cy3 and spiked with the Lucidea Universal ScoreCard test reaction. The concentrations of the Lucidea reactions are known and consequently so are the true ratios between the reference and test channels. Approximately 40% of the artificial genes were differentially expressed.
The particular design of the experiment makes the data suitable for validating algorithms for pre-processing and tests for identifying differentially expressed genes.
- The 80.I.1 normalization algorithm :  all spots flagged as not found during image analysis considered missing values (complete filtration). Print-tip MA-loess dye normalization based on the calibration clones was applied to the raw data and the B-statistic was calculated.
- The 80.II.1 normalization algorithm : all spots flagged as not found during image analysis considered missing values (complete filtration). Local background correction was applied and all spots with negative values were excluded. Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.
- The 80.II.64 normalization algorithm : all spots flagged as not found during image analysis considered missing values (complete filtration). Local background correction was applied, negative values were excluded and all spots with a value below 64 were set to 64 (censored). Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.
- The 80.V.1 normalization algorithm :  The intensities of all spots flagged not found were treated as missing values during normalization, but prior to calculating test-statistics the spot's log-ratios were set to zero. In the special case when all arrays generated not-found spots, the gene was removed from the experiment (Partial filtration). Local background correction was applied and all negative values were considered missing values. Print-tip MA-loess dye normalization based on the calibration clones was applied to the background corrected data and the B-statistic was calculated.

platform_organism:
Pinus sylvestris
Mus musculus

overall_design: The experiment contains eight arrays with identical experimental design. The reference sample was labeled with the fluorophore Cy5 and spiked with the Lucidea Universal ScoreCard reference reaction, the test sample was labeled with Cy3 and spiked with the Lucidea Universal ScoreCard test reaction.

first: Henrik

last: Andersson

first: Linda

last: Junfors

first: Laila

last: Noppa

first: Patrik

last: Rydén

first: Anders

last: Sjöstedt


title: Global effect of JTV or JTV-Alt overexpression in HeLa cells

status: Public on May 18 2011

city: Bethesda

first: David

last: Levens

address: 10 Center Drive

department: NCI/CCR

institute: NIH

summary: JTV is not only a structural component of multi-aminoacyl-tRNA synthetase complex, but also a regulator of FBP that in turn controls c-Myc expression. In order to identify JTV target genes other than FBP and c-Myc, JTV or JTV-Alt (alternatively spliced form of JTV, enriched in the nucleus) protein was over-expressed in HeLa cells and global gene expression changes were monitored using cDNA expression microarray.

overall_design: JTV or JTV-Alt was expressed in HeLa cells by transient transfection as protein fusion with GFP. After harvesting, only GFP-positive cells were isolated by flow cytometry, and used for RNA extraction. Each JTV or JTV-Alt sample was analyzed by co-hybridizing with control GFP-only samples. Each of the two forms of JTV hybridization was repeated as biological replicate.


title: Gene expression profile of the SVZ of the postnatal mouse brain

city: Washington

first: Vittorio

last: Gallo

state: DC

address: 111 Michigan Av. NW

department: Center for Neuroscience

institute: CNMC

summary: To determine gene expression profiles of neurogenesis, neural stem cell and notch signaling elements in the adult subventricular zone (SVZ) of the WT and CNP-hEGFR mouse, we used SuperArray limited gene array analysis. GEArrayTM expression array systems (cat#OMM404 SuperArray, Bethesda, MD) consisted of spotted cDNA fragments encoding 288 mouse genes related to neurogenesis and neural stem cell differentiation, as well as notch signaling elements. Control sequences (PUC18, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), peptidylpropyl isomerase A (Ppia), and β-actin) were also included. These microarrays were employed to compare SVZ gene expression between WT and CNP-hEGFR mouse SVZ.

overall_design: Total RNA was isolated by Trizol (Invitrogen) and processed for microarray hybridization following the manufacturer’s instructions. Arrays were visualized by autoradiography, and hybridization signals were scanned and analyzed for density in GEArray Expression Analysis Suite 2.0. The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, Ppia, and β-actin. To obtain a gene profile, analysis was performed on three separate RNA samples isolated from different SVZs, with replicate assays conducted on each RNA preparation.

first: Adan

last: Aguirre

first: Maria

middle: E

last: Rubio


title: EucalyptWood

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

summary:
* In response to gravitational stresses, angiosperm trees form tension wood in the upper sides of branches and leaning stems in which cellulose content is higher, microfibrils are typically aligned closely with the fibre axis and the fibres often have a thick inner gelatinous cell wall layer (G-layer).
* Gene expression was studied in Eucalyptus nitens branches oriented at 45° using microarrays containing 4 900 xylem cDNAs, and wood fibre characteristics revealed by X-ray diffraction, chemical and histochemical methods.
* Xylem fibres in tension wood (upper branch) had a low microfibril angle, contained few fibres with G-layers and had higher cellulose and decreased Klason lignin compared to lower branch wood. Expression of two closely related fasciclin-like arabinogalactan proteins and a B-tubulin was inversely correlated with microfibril angle in upper and lower xylem from branches.
* Structural and chemical modifications throughout the secondary cell walls of fibres sufficient to resist tension forces in branches can occur in the absence of G-layer enriched fibres and some important genes involved in responses to gravitational stress in eucalypt xylem are identified.
Keywords: tissue comparison

overall_design: Two nine-year-old Eucalyptus nitens trees were used as a source of biological material. RNA was isolated from xylem from the vertical main stem and from the upper and lower quarter of branches oriented at approximately 45° from vertical. For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.

first: Deyou

last: Qiu

first: Simon

last: Southerton


title: Diverse Environmental Stresses Elicit Distinct Responses at the Level of Pre-mRNA Processing in Yeast.

status: Public on Jul 01 2011

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

institute: Washington and Lee Unversity

summary: Gene expression in Eukaryotic cells is profoundly shaped by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways.  Here we report the use of a splicing isoform specific microarray platform to investigate the effects of a host of diverse stress conditions on both splicing pre-mRNA fate.  Interestingly, We find that diverse stresses cause distinct patterns of changes at the level of pre- mRNA processing. The responses we observed are most dramatic for the RPGs and can be categorized into three major classes. The first is characterized by accumulation of RPG pre-mRNA and is seen in multiple types of amino acid starvation regimes; the magnitude of splicing inhibition correlates with the severity of the stress. The second class is characterized by a rapid decrease in both pre- and mature RPG mRNA and is seen in many stresses that inactivate the TORC1 kinase complex. These decreases depend on nuclear turn-over of the intron-containing pre-RNAs. The third class is characterized by a decrease in RPG pre-mRNA with only a modest reduction in the mature species; this response is observed in hyperosmotic and cation-toxic stresses. We show that casein kinase 2 (CK2) makes important contributions to the changes in pre-mRNA processing, particularly for the first two classes of stress responses. In total, our data suggest that complex post-transcriptional programs cooperate to fine-tune expression of intron-containing transcripts in budding yeast.

overall_design: Splicing-specific microarrays were used to assay the changes to splicing caused by a wide variety of environmental stresses and nutrient conditions.

first: Megan

last: Bergkessel

middle: B

first: Christine

last: Guthrie


title: h3k4me2_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

status: Public on May 17 2011

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

summary: a2e_heterosis - h3k4me2_cvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Cvi

overall_design: 4 dye-swap - chip-chip

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: h3k27me3_c24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_c24 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in C24


title: h3k4me2_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k4me2_col(cvi) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Col-0


title: h3k27me3_colxc24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_colxc24 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxC24 hybrids


title: h3k27me3_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_cvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Cvi seedlings


title: h3k27me3_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxCvi hybrids


title: h3k4me2_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k4me2_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in ColxCvi hybrids


title: h3k4me2_c24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k4me2_c24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in C24


title: h3k27me3_col(c24)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_col(c24) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Col


title: The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5: iron(II) chloride

status: Public on May 16 2011

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

summary: Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing iron(II) chloride supplemented grown culture against non-iron treated grown culture in M9 minimal media

overall_design: Two-condition experiment, iron(II) chloride supplemented culture versus non-iron treated culture. 4 biological replicates including 3 technical replicates for one of the biological replicates. Swap-dye experiments were performed

first: Chee

first: Karl

middle: A

last: Hassan

first: Sasha

last: Tetu

first: Joyce

last: Loper

first: Ian

last: Paulsen


title: Loss of DNA replication control is a potent initiator of gene amplification

city: San Francisco

first: Brian

last: Green

address: 600 16th Street, S376 Genentech Hall

department: Department of Biochemistry

institute: University of California, San Francisco

summary: Eukaryotic cells use numerous mechanisms to ensure that no segment of their DNA is re-replicated within a single cell cycle. Despite longstanding speculation that such tight regulation is needed to protect cells from genomic alterations, this notion has never been experimentally tested. Here we show that even just transient and limited re-replication in Saccharomyces cerevisiae can strongly induce the critical first step of gene amplification, increasing gene copy number from one to two or more. The amplified units, or amplicons, consist of large internal chromosomal segments that are bounded by Ty repetitive elements and are intrachromosomally arrayed at their endogenous locus in direct head-to-tail orientation. The presence of hybrid Ty elements at inter-amplicon junctions together with the dependence of amplification on RAD52 indicate that in budding yeast these re-replication-induced gene amplifications (RRIGA) are mediated by homologous recombination between re-replicated non-allelic repetitive elements. These results finally establish the importance of stringent replication control for genome stability and suggest that re-replication should now be considered as a possible contributor to gene copy number changes in fields as diverse as cancer biology, evolution, and human genetics.

overall_design: The arrays in this series are primary comparative genomic hybridizations to determine genomic changes after re-replication or other genomic stresses. Genomic DNA was purified from reference Saccharomyces cerevisiae cells or survivors of re-replication or other genomic stresses, differentially labeled with Cy3 and Cy5, and competitively hybridized to a spotted microarray containing ORF and intergenic PCR products. Cy5/Cy3 ratios are normalized so that the average ratio of all elements was 1. A small number of the arrays were used to determine the extent and location of re-replication under different conditions. For those, genomic DNA was purified from non-replicating and re-replicating cells and treated as above. Series contains a total of 203 hybridizations.

first: Kenneth

middle: J

last: Finn

first: Joachim

last: Li


title: h3k27me3_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k27me3_col(cvi) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Col


title: Bj Paraquat fulminant shock vs. non-treatment

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

institute: University of Texas at Arlington

summary: Genome-wide transcriptional profiling of cells subjected to a paraquat fulminant shock treatment (5mM for 10 minutes).

overall_design: Three independent biological materials were prepared for cells shock treated with paraquat and non-treated cells. A total 6 arrays which includes dye swap were analyzed.

first: Andrew

last: Donati

first: Jeong-Min

last: Jeon

first: Dipen

last: Sangurdekar

first: Jae-Seong

last: So


title: Differential sensitivity of coral larvae to natural levels of ultraviolet radiation (UVR) during the onset of larval competence

status: Public on May 15 2011

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Scleractinian corals are the major builders of the complex structural framework of coral reefs. They live in tropical waters around the globe where they are frequently exposed to potentially harmful ultraviolet radiation (UVR). Coral eggs and early embryonic stages are thought to be the most sensitive life stages of corals to UVR given that they are highly buoyant and remain near the sea surface for prolonged periods of time. Here we analyzed gene expression changes in different larval stages of the Caribbean coral Montastraea faveolata to natural levels of UVR using high-density cDNA microarrays (10,930 clones). We found that larvae exhibit low sensitivity to natural levels of UVR during most time points analyzed as reflected by comparatively few transcriptomic changes in response to UVR. However, we identified a time window of high UVR sensitivity that coincides with the motile planula stage and the onset of larval competence. These processes have been shown to be affected upon UVR exposure, and the transcriptional changes we identified explain these observations well. Our analysis of differentially expressed genes indicates that UVR induces a stress response and affects the expression of neurogenesis-related genes that can be linked to swimming and settlement behavior at later stages. Taken together, our study provides further data to the impact of natural levels of UVR on coral larvae. Furthermore, our results might allow a better prediction of settlement and recruitment rates after coral spawning events based on UVR climate data.

overall_design:
Gamete capture and larval rearing
Montastraea faveolata gametes were captured and reared as described in Voolstra et al. 2009 (2009a). Briefly, gametes from 10 colonies were captured during a spawning event on the night of the 10th of September 2009 at approximately 22:00 hours using collecting nets attached to plastic enclosures at “La Bocana Chica” (20º50´N, 86º52´W) located in the “Parque Nacional Arrecife de Puerto Morelos”. Within 10 minutes the gametes were brought to the research vessel “Carybdea”, where they were placed in 5 µm filtered sea water (FSW), large zooplankton was removed, and the egg-sperm mixture was mixed gently to enhance the process of fertilization during transportation to the research station (Unidad Académica Puerto Morelos). After 1 hour, the egg-sperm mixture was repeatedly washed with 5 µm FSW to ensure that all unused sperm and remaining zooplankton were removed. The embryos were placed in round, bottomless, incubation bins fitted with 100 µm mesh, which were housed in abundant 5 µm FSW. Fertilization success, measured 6 hours after the washing procedure, was estimated at 95% by counting the number of eggs undergoing division as a proportion of the total number of eggs (dividing + non-dividing).

Experimental procedure
 After 12 hours, the majority of the embryos were in the late blastula stage. A subsample of embryos was taken from different incubation bins and divided into twelve 1 liter containers with 5 µm FSW added to the brim. Each container held approximately 3,000 embryos. All of the containers were placed in 800 L fiber glass aquaria filled with flowing sea water and exposed to natural solar radiation from 9am to 3pm (6h) at 29ºC and 3.5% salinity. Six of the containers were placed under a sheet of 6mm thick Plexiglass G UVT that has a full width at half maximum (FWHM) at 282 nm and is therefore transparent to UVR. The other six containers were placed under a sheet of 4 mm thick Plexiglass G UF-3 that has a FWHM at 390 nm and is therefore opaque to UVR. At the end of the exposure period, the embryos were harvested and preserved in RNAlater (Ambion), placed at 4ºC for 24 hours to ensure infiltration of the fixative and frozen at -80ºC until further processing. The same exposure and fixation procedures were repeated on 36 hours old embryos (late gastrula stage), on 60 hours old non-motile, floating larvae, on 84 hours old motile planulae, and on 132 hours old planulae that are motile, diving, and ready for settlement.

first: Manuel

last: Aranda

first: Anastazia

last: Banaszak

first: Till

last: Bayer

first: James

last: Luyten

first: Monica

last: Medina


title: The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary:
Expression and alternative splicing data from 1-month-old Rbfox1 KO brain.
Rbfox1 regulates the alternative splicing of many transcripts in neurons. We have characterized the Rbfox1-dependent changes in expression and alternative splicing by comparing Rbfox1-KO brain to WT brain. In this dataset, we include the splicing and expression data obtained from dissected WT and Rbfox1 KO mouse brains.

overall_design: 6 total samples were analyzed: brains from 3 WT male mice and 3 Rbfox1 KO male mice, all 1 month of age.

first: Lauren

last: Gehman

first: Douglas

middle: L

last: Black


title: Bj Paraquat prolonged exposure vs. non-treatment

summary: Genome-wide transcriptional profiling of cells exposed to 0.1 mM paraquat from time of inoculation.

overall_design: Three independent biological materials were prepared for cells exposed to 0.1 mM  paraquat during growth and non-treated cells. A total 6 arrays which includes dye swap were analyzed.


title: Conversion of Mouse Fibroblasts to Sphere Cells with Differentiation Potential Induced by AlbuMAXI-containing Medium

status: Public on May 13 2011

city: dayton

first: yiling

last: hong

state: OH

address: 300 college park

department: biology

institute: university of dayton

summary: Analysis of gene expression levels during Fibroblast to sphere cell conversion induced by albumax I containing medium. Murine embryonic fibroblasts (MEF) can be converted to sphere cells in the presence of arachidonic acid and pluronic - F 68. The converted cells exhibit stem cell like properties and and have the potential to differentiate into all the three embryonic germ layers. Our results provide important information on genes that are up- or down-regulated during the reprogramming/conversion process.

overall_design: Total RNA was isolated from murine embryonic fibroblasts, normal mouse embryonic stem (MES) cells and converted sphere cells. MES cells were taken as a control/reference population. Three replicated were included for each sample.

first: Pavan

last: Rajanahalli

first: Kyle

last: Meyer

first: Lin

last: Zhu

first: Brad

middle: D

last: Wagner

first: Michael

last: Robinson

first: David

last: King

first: Yiling

last: Hong


title: Time course expression data from E.coli cells induced with differential amounts of IPTG

city: Newark

first: Kelvin

middle: H.

last: Lee

state: DE

address: 15 Innovation Way

department: Biotechnology Institute

institute: University of Delaware

summary:
In this work expression of two rhsA elements, ext-a1 and daORF-a1, was differentially induced using IPTG. RhsA is a member of multigene rhs family and can code for five different open reading frames (ORFs), referred to as genetic elements. The functions of rhsA and the different ORFs it codes are not well understood.
We used microarrays to study the effect of over-expression of two rhsA elements, ext-a1 and daORF-a1, on E. coli cells.

Keywords: time course

overall_design: E. coli cells were harvested from biological replicate cultures at 0 hrs (0 mM IPTG) and at 1.5 and 3.5 hrs (0, 0.1, and 1 mM IPTG) after IPTG induction for RNA extraction and hybridization on Affymetrix arrays. A total of seven different conditions were analysed. Two biological replicates and two technical replicates were performed for each condition (a total of 28 microarray hybridizations).

first: Kunal

last: Aggarwal

middle: H


title: NsaRS is a Cell-Envelope-Stress Sensing Two-Component System of Staphylococcus aureus

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

summary: S. aureus possesses 16 two-component systems (TCS), two of which (GraRS & NsaRS) belong to the intramembrane-sensing histidine kinase (IM-HK) family, conserved within the firmicutes. NsaRS has recently been documented as being important for nisin-resistance in S. aureus. In this study we present a detailed characterization of NsaRS and reveal that, as with other IM-HK TCS, it responds to disruptions in cell-wall stability. Analysis using a lacZ reporter-gene fusion demonstrated that nsaRS expression is upregulated by a variety of cell-wall damaging antibiotics, including Phosphomycin, Ampicillin, Nisin and Penicillin G. Additionally; we reveal that NsaRS regulates a downstream transporter, NsaAB, during nisin-induced stress. NsaS mutants also display a 200-fold decreased ability to develop resistance to the cell-wall targetting antibiotic bacitracin. Microarray analysis reveals the transcription of 245 genes is altered in a nsaS mutant, with the vast majority down-regulated. Included within this list are genes involved in transport, drug-resistance, cell-envelope synthesis, transcriptional regulation, amino acid metabolism and virulence. Using ICP-MS we observed a decrease in intracellular divalent metal ions in an nsaS mutant when grown under low affinity conditions. Characterization of cells using electron microscopy reveals that nsaS mutants have alterations in both cell-wall and cell-envelope structure. Finally, a variety of virulence related phenotypes are impaired in nsaS mutants, including biofilm formation, resistance to killing by human macrophages and survival in whole human blood. Thus NsaRS is important in sensing cell-wall instability in S. aureus, and functions to reprogram gene expression to modify cell-envelope architecture, facilitating adaptation and survival.

overall_design: We did four hybridizations for this experiment, including a biological replicate and a dye-swap experiment for each replicate to account for dye-bias. Spots flagged as empty or bad were excluded and the raw data from each slide was normalized using LOWESS method, with background correction. The data from the replicates were combined (using the median value) and a one-sample t-test was performed. The volcano plot was used with a fold change cut-off of >= 2 and a p-value of <0.05, to filter the genes that were differentially expressed.

first: Stacey

last: Kolar

first: Vijayaraj

first: Anna

last: Oszmiana

first: Frances

last: Rivera

first: Halie

middle: K

last: Miller

first: Jessica

last: Davenport

first: Alexander

last: Ulanov

first: Zhong

last: Li

last: Riordan

first: Jan

last: Potempa

middle: S

last: Barber

first: Joanna

last: Koziel

first: Mohamed

middle: O

last: Elasri

first: Lindsey

middle: N

last: Shaw


title: Gene expression profiling of developing cassava storage roots

city: Shanghai

first: Jun

last: Yang

address: 300 Fenglin Road

institute: SIPPE

summary: Mechanisms related to the development of cassava storage roots and starch accumulation remain largely unknown. To evaluate genome-wide expression patterns during cassava tuberization, a 60-mer oligonucleotide microarray representing 20,840 cassava genes was designed to identify differentially expressed transcripts in fibrous root, developing storage root and mature storage root. Using a random variance model and the traditional two-fold change method for statistical analysis, 912 and 3386 differentially expressed genes were identified related to the three different phases. Among 25 significant pathways identified, glycolysis/gluconeogenesis was the most important pathway signature due to its effects on other pathways. Rate-limiting enzymes were identified from each individual pathway, such as pectinesterase, enolase, L-lactate dehydrogenase and aldehyde dehydrogenase in glycolysis/gluconeogenesis, and ADP-glucose pyrophosphorylase, starch branching enzyme and glucan phosphorylase in sucrose and starch metabolism. This study revealed that dynamic changes in at least 16% of the transcriptome, including hundreds of transcription factors, oxidoreductases/transferases/hydrolases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this biological process. The reliability of differentially expressed genes in microarray analysis was further verified by quantitative real-time RT-PCR. The genome-wide transcription analysis facilitates our understanding of the formation of the storage root and deciphers key genes for further cassava improvement.

overall_design: Fibrous roots (FR), developing storage roots (DR) and mature storage roots (MR) were collected for RNA extractions from three independent healthy 4 month-old cassava (cultivar TMS60444) plants in the field .Two RNA samples extracted from stored storage root slices were used as technical repeats (TR) for quality control.

first: Dong

last: An

first: Peng

last: Zhang


title: Widespread RNA and DNA Sequence Differences in the Human Genome

city: Philadelphia

first: Mingyao

state: PA

address: 213 Blockley Hall, 423 Guardian Drive

department: Biostatistics and Epidemiology

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: The transmission of information from DNA to RNA is a critical process.  It is assumed that DNA is faithfully copied into RNA.  However, when we compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals, we uncovered more than 20,000 sites where the RNA sequences do not match that of the DNA.  Validations using RNA sequences from another laboratory and re-sequencing of the DNA and RNA samples confirmed these findings.  All 12 possible categories of discordances were found, with A-to-G and C-to-U being the most common.  About 50% of the differences involved conversions between purines and pyrimidines.  These differences were non-random as many sites were found in multiple individuals.  The same differences were also found in primary skin cells in a separate set of 20 individuals.  In addition, when these differences were found, they were seen in nearly all transcripts.  Thus, these widespread RNA-DNA differences in the human genome provide a yet unexplored aspect of genome variation that affect gene expression and therefore phenotypic and disease manifestations.

overall_design:
identification of RNA and DNA differences

For alignment of the short reads sequences to the human transcriptome(Gencode NCBI36 version 3c), we used the program BOWTIE (version 0.12.7).

***This submission represents the RNA-seq component of the study

first: Vivian

middle: G

last: Cheung

first: Yun

first: Alan

last: Bruzel

first: Allison

last: Richards

first: Jonathan

middle: M

last: Toung

first: Isabel

middle: X

last: Wang


title: Folsomia candida exposed to different 2-phenylethyl isothiocyanate concentrations in soil

status: Public on May 12 2011

city: Amsterdam

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Ecological Science

country: Netherlands

institute: VU University Amsterdam

summary: Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism.   Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level.

overall_design: Four-exposure experiment; Control vs. Acetone control vs.EC10 vs.EC50 exposed animals. Biological replicates: 4 replicates for each exposure.

first: A

middle: E

first: Cornelis

last: van Gestel

first: Bjarne

last: Styrishave

first: Martin

last: Hansen

first: Jacintha

last: Ellers

first: Dick

last: Roelofs


title: h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

first: François

last: ROUDIER

summary: a2e_heterosis - h3k4me2_col_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Col

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: h3k4me2_colxc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

summary: a2e_heterosis - h3k4me2_colxc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in ColxC24 hybrids


title: Comparative genomic hybridization of human induced pluripotent stem cell lines.

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

summary: The Purpose of this series of experiments is to identify copy number variations, duplications, and deletions in human induced pluripotent stem (hiPSC) cell lines.

overall_design: Genomic DNA of different human induced pluripotent stem cell lines are extracted and hybridized to NimbleGen CGH microarray, using genomic DNA of hESC H1 or H9 as common reference. Difference between different stem cell lines will be revealed.

first: Karen

last: Montgomery


title: The effect of Iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5: iron(III) chloride

first: Chee Kent

last: Lim

summary: Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing iron(III) chloride supplemented grown culture against non-iron treated grown culture in M9 minimal media

overall_design: Two-condition experiment, iron(III) chloride supplemented culture versus non-iron treated culture. 3 biological replicates including 3 technical replicates for one of the biological replicate and 2 technical replicates for another biological replicate. Swap-dye experiments were performed

first: Chee

first: Karl

last: Hassan

first: Sasha

last: Tetu

first: Joyce

last: Loper

first: Ian

middle: T

last: Paulsen


title: Identification of p53-regulated microRNAs in Hapatocellular Carcinoma (HCC).

status: Public on May 11 2011

city: Columbus

first: Jeff

last: Palatini

state: Ohio

address: 460 West 12th Ave.

institute: The Ohio State University

summary: p53 suppresses tumor progression and metastasis by regulating a large set of genes and microRNAs. By profiling 92 primary hepatocellular carcinomas (HCCs) and 9 HCC cell lines, we found that p53 upregulates microRNAs including miR-200 and miR-192 family members.

overall_design: By sequencing TP53 in 92 HCC samples, we classified the 92 samples into two groups (wt and mut). We also classified 9 HCC cell lines by testing p21 expression after DNA-damage mediated p53 activation. We then profiled microRNA expression in 92 HCC tissue samples and 9 HCC celll lines to identify p53-regulated microRNAs.

first: Taewan

last: Kim

first: Angelo

last: Veronese

first: Flavia

last: Pichiorri

first: Tae

last: Lee

first: Young-Jun

last: Jeon

first: Stefano

last: Volinia

first: Pascal

last: Pineau

first: Agnès

last: Marchio

first: Sung-Suk

last: Suh

first: Hansjuerg

last: Alder

first: Chang-Gong

last: Liu

first: Anne

last: Dejean

first: Carlo

last: Croce


title: Rhesus macaque aCGH

city: Buffalo

first: Omer

last: Gokcumen

state: New York

address: 109 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

summary: Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations.

overall_design: a custom designed Agilent array-based comparative genomic hybridization (aCGH) platform, which comprises 950,843 unique 60-mer oligonucleotide probes specific to the rhesus macaque reference genome (rheMac2), to compare the genomic DNAs of 17 unrelated rhesus macaques of Indian origin to the genome of an unrelated sample from the same species.


title: Global gene expression analysis of embryos with spina bifida after maternal exposure to retinoic acid

status: Public on May 10 2011

city: Beijing

first: Liuyan

last: Zhang

address: 4A Dutun Rd., Chaoyang District

institute: Institute of Psychology, Chinese Academy of Sciences

summary:
Background
The vitamin A derivative, retinoic acid (RA), is a potent teratogenic agent that induces a variety of congenital abnormalities including neural tube defects. The embryopathology of RA has been extensively investigated and retinol receptors play important roles during organogenesis, development and neural tube closure. Still, the mechanisms by which RA influences these processes are not completely understood.

Methods
We used a custom-made mouse genome 32K oligonucleotide microarray to determine the gene expression profiles of mouse embryo spinal cord samples that had been exposed to vehicle or RA. Then, we performed a GSEA (gene set enrichment analysis) on the gene expression data by searching MSigDB (v2.5) c2 gene sets (canonical pathways) and c5 gene sets (curated GO terms), with set size restraints on the range to avoid over-narrow or over-broad categories.

Results
Using microarray technology, the present study identifies 85 genes in the spinal cord that exhibit at least a 1.5-fold change between control samples and samples with spina bifida aperta. A gene set enrichment analysis showed that maternal exposure to RA induced spinal bifida that were associated with altered expression of genes involved in pro- or anti-apoptosis, cell proliferation, migration, cytoskeleton components, and cell or focal adhesion, indicating that defective functions of these cell components and biological processes preceded the abnormal development of neural tube.

Conclusions
Maternal exposure to RA induced spinal bifida that were associated with altered expression of genes involved in pro- or anti-apoptosis, cell proliferation, migration, cytoskeleton components, and cell or focal adhesion. As shown in previous reports, defective functions of these cell components and biological processes preceded the abnormal development of the neural tube. Our study will help the understanding of the etiology and pathology of spinal bifida. However, it should be noted that the changes in gene expression induced by RA exposure may not be an effect on events other than neural tube closure; further study is required to fully understand the molecular mechanisms and consequence of neural tube defects in embryos exposed to RA.

Our study provides a global analysis of gene expression patterns in spina bifida and will help the understanding of the etiology and pathology of neural tube defects.

overall_design:
We assessed the changes in gene expression that coincide with spina bifida in RA-treated mouse fetuses. After generating an independent list of regulated genes, we analyzed samples by gene set enrichment analysis to expand our results.

A pool of spinal cord tissue from spina bifida fetuses whose mothers were exposed to RA was compared to a pool of spinal cord tissue from fetuses whose mothers were exposed to olive oil vehicle. Three replicates each.

first: Kunlin

first: Wei

last: Dai

first: Shuai

first: Jing

first: Mei

last: Zhao


title: Human meningioma fixed tumour tissue: validation set

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

summary:
Background:  Meningiomas account for about 27% of primary brain tumors, making them one of the most common brain tumor. They are most common in people between the ages of 40 and 70 and are more common in women than in men. Most meningiomas (90%) are categorized as benign tumors, with the remaining 10% being atypical or malignant. Multiple classifications exist today, but the most commonly used is the World Health Organization’s (WHO) which classifies meningiomas into three histological grades: grade I (benign), grade II (atypical), and grade III (anaplastic) in accordance with the clinical prognosis. Most of these subtypes behave similarly, however anaplastics are the most aggressive. The ability to distinguish benign from atypical and anaplastic tumors is important because of its impact on treatment decisions. A molecular based classification system has the likelihood of being a better prognostic indicator and is useful for identifying alterations in pathways and networks that drive tumor progression and growth. The information obtained can potentially be translated into more effective and less toxic targeted therapies. We tested a method for genome wide expression profiling of formalin-fixed, paraffin-embedded tissues. We applied the method to the analysis of the clinical outcome of meningioma tumor.

Materials and Methods:  The training set consisted of tissue samples from 63 patients who were consecutively treated with surgery for meningioma between 1990 and 2005. For each patient data on clinical outcomes and formalin-fixed, paraffin-embedded blocks of tumor were available. The validation set included tissue samples from 189 patients with meningioma who consecutively underwent surgery between 1992 and 2006. We used a custom 60-mer amino modified oligo- array, containing 912 probes, a lot of which specific for genes commonly altered in cancer. Functional annotation was performed by means of gene set enrichment analysis (GSEA, www. broad.mit.edu/gsea/). Survival analyses were performed with the use of the log-rank test and Cox regression modeling. All analyses were performed with the use of GenePattern.

Results: We investigated whether gene-expression profiles of meningioma tumors were associated with the clinical outcome. Using a standard leaveone- out cross-validation procedure, we found the meningioma signature to be significantly correlated with survival (P = 0.0001). The survival correlated signature contained 219 genes and was tested in the validation set.

Conclusion: These results support the validity of the survival signature and highlight the potential role of tumoral meningioma tissue in predicting the outcome for patients with meningioma tumors.

overall_design:
Patients:  The training set consisted of tissue samples from 79 patients who were consecutively treated with surgery for meningioma between 1990 and 2001 at Bari Medical School. For each patient data on clinical outcomes and formalin-fixed, paraffin-embedded blocks of tumor and adjacent tissue were available. The validation set included tissue samples from 210 patients with meningioma who consecutively underwent surgery between 1992 and 2000: 104 patients at the Vito Fazi Lecce Hospital (Italy), 106 at the Sant’Anrea hospital, Rome. Archived formalin-fixed, paraffin-embedded tissues obtained with approval by the local institutional review boards. Formalin fixed, paraffin-embedded blocks obtained at the time of resection were cut into four 10 μm thick sections, macrodissected to isolate tumor, and subjected to RNA extraction as described in the Supplementary Appendix (available with the full text of this article at www.nejm.org).

Analysis of Gene Expression: We used a custom 60-mer amino modified oligo- array, containing 912 probes, a lot of which specific for genes commonly altered in cancer. Microarray data and protocol are available at www.ncbi.nlm.nih.gov/geo/, accession numbers GSE10143 and GPL5474.) Genes whose expression was associated with disease-specific survival and time to recurrence were selected (see the Supplementary Appendix). The value of the signature was assessed on the basis of overall survival.

first: Pietro

middle: I

middle: F

last: D'urso

first: Pasqualino

last: Ciappetta


title: The habitat disruption induces immune-suppression and oxidative stress in honey bees

city: Nagoya

first: Tatsuhiko

last: Kadowaki

address: Chikusa

country: Japan

institute: Nagoya University

summary: Background: Honey bee is a major insect used for pollination of a number of commercial crops worldwide.  However, the number of managed honey bee colonies has recently declined in several countries, and a number of possible causes are proposed.  Although the use of honey bees for pollination can be considered as disruption of the habitat, its effects on honey bees' physiology have never been addressed.  In Japan, more than 100 thousands colonies are annually used for pollination, and intriguingly 80% of them are used in greenhouses.  Recently, honey bee colonies have often collapsed when they are introduced into greenhouses.  Thus, to suppress colony collapses and maintain the number of worker bees in the colonies are essential for successful long-term pollination in greenhouses and recycling honey bee colonies.

overall_design: Honey bee hives were installed into strawberry and eggplant greenhouses, and then the gene expression profiles of the honey bees were examined at the different time periods.  Total 16 samples with two replicates were analyzed.

first: Tomomi

last: Morimoto

first: Yuriko

last: Kojima

first: Taku

last: Toki

first: Yayoi

last: Komeda

first: Mikio

last: Yoshiyama

first: Kiyoshi

last: Kimura

first: Keijiro

last: Nirasawa


title: Transcriptome profile of peripheral blood mononuclear cells in patients with type I diabetes and their first grade relatives

status: Public on May 09 2011

city: Prague

first: Katerina

last: Stechova

address: V Uvalu 84

department: Paediatric

country: Czech Republic

institute: Charles University 2nd Medical Faculty

summary: Type 1 Diabetes (T1D) is considered to be a Th1 autoimmune disease characterised by an absolute lack of insulin caused by an autoimmune destruction of the insulin producing pancreatic beta cells. Th1 lymphocytes are responsible for the infiltration of the islets of Langerhans and for the cytokine release that supports cytotoxic (Tc) lymphocytes to mediate destruction of the beta cells. The preclinical disease stage is characterized by the generation of the self-reactive lymphocytes that infiltrate the pancreas and selectively destroy the insulin-producing beta cells present in the islets. Other cellular immune mechanisms regarding immunoregulation and antigen presentation and processing are involved in T1D pathogenesis as well. Our aim was to identify genes involved in the corresponding signalling cascades, especially those which may serve as promising diagnostic tools for the identification of persons in the prediabetic phase of the disease. We addressed the question by analysing gene expression profiles of freshly isolated peripheral blood mononuclear cells in type 1 diabetes patients, their first degree relatives divided according to their autoantibody status, and healthy controls.

overall_design: 9 T1D-patients versus 10 first degree relatives versus 10 healthy controls

first: Radek

last: Blatny

first: Zbynek

last: Halbhuber

first: Jana

last: Vcelakova

first: Miluse

last: Hubackova

first: Lenka

last: Petruzelkova

first: Zdenek

last: Sumnik

first: Barbora

last: Obermannova

first: Pavlina

last: Pithova

first: Vendula

last: Stavikova

first: Maria

last: Krivjanska

first: Dominik

last: Filipp

first: Stanislava

last: Kolouskova


title: Human meningioma fixed tumour tissue: training set

first: Oscar

last: D'Urso

overall_design:
Patients:  The training set consisted of tissue samples from 79 patients who were consecutively treated with surgery for meningioma between 1990 and 2001 at Bari Medical School. For each patient data on clinical outcomes and formalin-fixed, paraffin-embedded blocks of tumor and adjacent tissue were available. The validation set included tissue samples from 210 patients with meningioma who consecutively underwent surgery between 1992 and 2000: 104 patients at the Vito Fazi Lecce Hospital (Italy), 106 at the Sant’Anrea hospital, Rome. Archived formalin-fixed, paraffin-embedded tissues obtained with approval by the local institutional review boards. Formalin fixed, paraffin-embedded blocks obtained at the time of resection were cut into four 10 μm thick sections, macrodissected to isolate tumor, and subjected to RNA extraction as described in the Supplementary Appendix (available with the full text of this article at www.nejm.org).

Analysis of Gene Expression: We used a custom 60-mer amino modified oligo- array, containing 912 probes, a lot of which specific for genes commonly altered in cancer. Microarray data and protocol are available at www.ncbi.nlm.nih.gov/geo/, accession numbers GSE10143 and GPL5474. Genes whose expression was associated with disease-specific survival and time to recurrence were selected (see the Supplementary Appendix). The value of the signature was assessed on the basis of overall survival.

first: Pietro

last: D'urso

first: Pasqualino

last: Ciappetta


title: Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging- Related Transcriptional Networks (ChIP-chip)

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary:
Sirtuins (Sirt) are a family of enzymes that modify chromatin and other proteins to affect gene activity. Loss of Sirt6 leads to a progeria-like phenotype in mice, but the target of SIRT6 action has been elusive. Here we show that Sirt6 binds to thousands of gene promoters in a stress-inducible fashion, guided by the stress-responsive transcription factor NF-κB.
Chromatin profiling by ChIP-chip analysis of Sirt6 and NF-KB component RelA combined with expression array data of wildtype, Sirt6 knockout and Sirt6 RelA double knockout cells demonstrates that RelA recruits Sirt6 to NF-KB targets in response to TNF-a induction and that many of these targets are important for senescence and aging.

overall_design: comparison of wild type, RelA -/- and Sirt6-/- MEF cells

first: Tiara

last: Kawahara

first: Nicole

middle: A

last: Rapicavoli

first: Angela

middle: R

last: Wu

first: Stephan

last: Quake

first: Howard

middle: Y

last: Chang


title: Breast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications (GEX)

city: Helsinki

first: Taru

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital

summary:
Introduction: CHEK2 is a moderate penetrance breast cancer risk gene, whose truncating mutation 1100delC increases the risk about two fold. We pursued to investigate gene copy number aberrations and gene expression profiles that are typical for breast tumors of CHEK2 1100delC mutation carriers.

Materials and methods: A total of 126 breast tumor tissue specimens including 32 samples from patients carrying CHEK2 1100delC were studied in array comparative genomic hybridization (aCGH) and gene expression experiments (GEX). After dimensionality reduction with CGHregions R package, CHEK2 1100delC associated regions in the aCGH data were detected by Wilcoxon rank sum test. Linear model was fitted to GEX data with R package limma. Genes whose expression levels were associated with CHEK2 1100delC mutation were detected by Bayesian method.

Results: We discovered four lost and three gained CHEK2 1100delC related loci. These include losses of 1p13.3-31.3, 8p21.1-2, 8p23.1-2 and 17p12-13.1 as well as gains of 12q13.11-3, 16p13.3 and 19p13.3. Twenty-eight genes located on these regions showed differential expression between CHEK2 1100delC and other tumors nominating them as candidates for CHEK2 1100delC associated tumor progression drivers. These included CLCA1 on 1p22 as well as CALCOCO1, SBEM and LRP1 on 12q13. Altogether 188 genes were differentially expressed between CHEK2 1100delC and other tumors. Of these, 144 had elevated and 44 lowered expression levels.
Our results suggest WNT pathway as a driver of tumorigenesis in breast tumors of CHEK2 1100delC mutation carriers and a role for the olfactory receptor protein family in cancer progression. Differences in the expression of the 188 CHEK2 1100delC associated genes divided breast tumor samples from three independent datasets into two groups that differed in their relapse-free survival time.

Conclusions: We have shown that copy number aberrations of certain genomic regions are associated with CHEK2 mutation 1100delC. On these regions we have identified potential drivers of CHEK2 1100delC associated tumorigenesis, whose role in cancer progression is worth investigating. Furthermore, poorer survival related to the CHEK2 1100delC gene expression signature highlights pathways that are likely to have a role in the development of metastatic disease in carriers of CHEK2 1100delC mutation.

overall_design: 78 samples from breast tumors: 13 tumors from CHEK2 1100delC mutation carriers, 65 other tumors

first: Dario

last: Greco

first: Rainer

last: Fagerholm

first: Outi

last: Kilpivaara

first: Kati

last: Kampjarvi

first: Kristiina

last: Aittomaki

first: Carl

last: Blomqvist

first: Paivi

last: Heikkila

first: Ake

last: Borg

first: Heli

last: Nevanlinna


title: Expression patterns of microRNAs associated with CML phases and their disease related targets

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

summary: Background  MicroRNAs are important regulators of transcription in hematopoiesis. Their expression deregulations were described in association with pathogenesis of some hematological malignancies. This study provides integrated microRNA expression profiling at different phases of chronic myeloid leukemia (CML) with the aim to select CML specific miRNAs and find new possible biomarkers. The functions of in silico filtered targets are in this report annotated and discussed in relation to CML pathogenesis.  Results  Using microarrays we identified differential expression profiles of 49 miRNAs in CML patients at diagnosis, in hematological relapse, therapy failure, blast crisis and major molecular response. The expression deregulation of miR-150, miR-20a, miR-17, miR-19a, miR-103, miR-144, miR-155, miR-181a, miR-221 and miR-222 in CML was confirmed by real-time quantitative PCR and in silico analyses identified targeted genes of these miRNAs encoding proteins that are involved in cell cycle, growth inhibition, MAPK, ErBb, transforming growth factor beta and p53 signaling pathways that are related to CML. Validated miR-150 decreased levels were detected in patients at diagnosis, in blast crisis and 67% of hematological relapses and showed significant negative correlation with miR-150 proved target MYB and with BCR-ABL transcript level.  Conclusions  This study revealed microRNAs that may be related to the CML pathogenesis and may reflect transformation from chronic to accelerated phases. The obtained expression patterns in peripheral blood total leukocytes during the course of CML suggest specific miRNAs as possible biomarkers. The annotated functions of in silico filtered targets of selected miRNAs outline mechanisms whereby microRNAs may be involved in CML pathogenesis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Twenty four patient samples of total leukocytes from peripheral blood were used to prepare pools representing different CML phases for microarray analysis: diagnosis (n=5, Dg), major molecular response (n=5, MMR), therapy failure (n=5, TF), hematological relapse (n=5, Hr), and blast crisis (n=4, BC). Eleven healthy donors of age median 60 (range 45 - 78) and man/woman ratio 3/2 following CML incidence were used to create a control pool.

first: Kateřina

last: Machová Poláková

first: Tereza

last: Lopotová

first: Hana

last: Klamová

first: Pavel

last: Burda

first: Marek

last: Trněný

first: Tomáš

last: Stopka

first: Jana

last: Moravcová

last: Rüberg


title: Gene expression profiling in wild type and In(3LR)sep larval brain tissue (Drosophila)

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

institute: NKI-AVL

summary:
We performed a series of microarray expression profile experiments in central brain tissue from 3rd instar larvae, interrogating expression differences between wild type and In(3LR)sep strains. Since our 4C data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23166), demonstrated dramatic changes in nuclear organization of PcG target genes residing on In(3LR)sep.

Keywords: mRNA expression profiling by oligonucleotide arrays

overall_design: Changes in mRNA expression were recorded on oligonucleotide arrays representing the transcribed genome. Replicate experiments were performed including dye swaps.

first: Bas

last: Tolhuis

first: Marleen

last: Blom

first: Ron

last: Kerkhoven

first: Ludo

last: Pagie

first: Hans

last: Teunissen

first: Marja

last: Nieuwland

first: Marieke

last: Simonis

first: Wouter

last: de Laat

last: van Steensel


title: Differential expression associated with GB virus C in HCV/HIV co-infection

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

institute: University of Melbourne

summary: The aim of this study was to identify differential gene and protein expression associated with GBV-C that may be of importance in reduction of HCV-related liver disease. GB virus C (GBV-C) infection leads to improved outcomes in human immunodeficiency virus (HIV) infection. Furthermore, GBV-C has been shown to reduce hepatitis C virus (HCV)-related liver disease in HCV/HIV co-infection.

overall_design:
We aimed to identify differential gene expression associated with GBV-C in HCV/HIV co-infection by comparing RNA expression from liver biopsies of HCV/HIV co-infected patients with and without GBV-C infection.
Liver biopsies were obtained from 10 Patients with HCV/HIV co-infection; 4 of these patients were positive for GBV-C infection and 6 were negative for  GBV-C infection.  The tissue was stored in RNAlater and RNA was extracted for hybridisation to Affymetrix Human Genome U133 plus 2.0 microarrays at the University of Texas Medical Branch Molecular Genomics Core Laboratory.  The data was analysed for genes differentially expressed between GBV-C positive and negative patients using Partek Genomics suite and applying a custom CDF file (Hs133P_Hs_UG_8), available from Molecular and Behavioural Neuroscience Institute, University of Michigan.

first: Mark

middle: D

last: Berzsenyi


title: Integrated  analysis of genome-wide copy number and matched expression data reveals novel genes in esophageal adenocarcinoma

city: Cambridge

first: Xin Yi

last: Goh

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Hutchison-MRC Research Centre

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

overall_design:
Total DNA isolated from human tissue sections was used to make fluorescently labeled DNA that was hybridized to Illumina HumanCytoSNP-12 Beadarray. All protocols were carried out following Illumina's standard protocols. After hybridization, raw data were recorded and normalized using Illumina's BeadStudio software v2.0.

Matched expression data:

GSE25201      GSE19417
D2   MRC/OEA0022CJ5 (GSM482819)
D3   MRC/OEA0032CJ5 (GSM482817)
D27  MRC/OEA0272CJ1 (GSM482814)
D36  MRC/OEA0362CJ3 (GSM482806)
D37  MRC/OEA0372AJ0 (GSM482800)
D96  MRC/OEA0962BJ0 (GSM482847)
D118 MRC/OEA1172CJ1 (GSM482848)
D138 MRC/OEA1382CJ0 (GSM482844)
D156 MRC/OEA1562CJ2 (GSM482853)

first: X

first: J

last: Rees

first: A

middle: L

last: Paterson

first: S

last: Chin

middle: C

last: Marioni

first: V

last: Save

first: M

last: O'Donovan

first: P

middle: P

last: Eijk

first: D

last: Alderson

first: B

last: Ylstra

first: C

last: Caldas

first: R

last: Fitzgerald


title: Streptococcus mutans UA159 vs. clp mutant strains

status: Public on Jun 10 2011

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

country: USA

institute: University of Florida

summary: Transcriptional profiling to investigate the roles of ClpP and ClpX of S. mutans

sample_organism:
Streptococcus mutans
Streptococcus mutans UA159

overall_design: RNA was extracted from four replicate samples of each strain of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.

first: Jacqueline

last: Abranches

first: Jose

last: Lemos


title: Interactions among Polycomb domains are guided by chromosome architecture

first: Maarten

last: van Lohuizen

summary: Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal interactions in Drosophila melanogaster larval brain tissue. Our results demonstrate that PcG target genes interact extensively with each other in nuclear space. These interactions are highly specific for PcG target genes, because non-target genes with either low or high expression show distinct interactions. Notably, interactions are mostly limited to genes on the same chromosome arm, and we demonstrate that a topological rather than a sequence-based mechanism is responsible for this constraint. Our results demonstrate that many interactions among PcG target genes exist, and that these interactions are guided by overall chromosome architecture.

overall_design: We applied Chromosome Conformation Capture on Chip (4C) to map long-range chromatin interactions among PcDs on a genome-wide scale. Moreover, we implemented a modification of the 4C protocol in which the 4C PCR products are further amplified in a linear fashion using a T7 RNA amplification procedure. Finally, we fluorescently labeled the amplified products with dye and hybridized them to a specially designed microarray, which covers approximately 92% of the non-repetitive fly genome. In this way, we could identify all fragments that are in close contact with a chosen locus with limited material from a single fly tissue (i.e. larval brain).

first: Bas

last: Tolhuis

first: Marleen

last: Blom

first: Ron

last: Kerkhoven

first: Ludo

last: Pagie

first: Hans

last: Teunissen

first: Marja

last: Nieuwland

first: Marieke

last: Simonis

first: Wouter

last: de Laat

last: van Steensel


title: MicroRNA profiling in dorsal root ganglion after sciatic nerve injury

status: Public on May 06 2011

city: Bristol

first: Liang-Fong

last: Wong

address: Whitson Street

institute: University of Bristol

summary: Changes in microRNA (miRNA) expression in the mouse L4 and L5 dorsal root ganglion following unilateral sciatic nerve transection. The timepoint of 7 days post-axotomy was chosen to capture miRNA expression profiles at a time when the injured neurons were beginning to regenerate.

overall_design: Two condition experiment, paired control DRG vs axotomised DRG following unilateral sciatic nerve transection. 3 biological replicates, one replicate per array. Dye swap in Replicate 2.