title: Agilent CpG array analysis of Methylplex-library of prostate cancer cell lines

status: Public on May 03 2011

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

summary: Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression.  We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS).  Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample.  While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively.  We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters.  Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific, including numerous novel DMRs.   A novel cancer specific DMR in WFDC2 promoter showed heavy methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells.  Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization and these modifications segregated into distinct regions when present on the same promoter.  Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion positive and negative cancers.  This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression. In this data, we are providing Methylplex-PrEC and LNCaP libraries hybridized on Agilent CpG Array, which we chose to perform correlation analysis with deep sequencing result. The LNCaP and PrEC 400bp-5 deep sequencing results were compared with this data and obtained high correlation.

overall_design: Methylplex-array libraries made from LNCaP and PrEC cells were hybridized to Agilent human CGI microarray purchased from Agilent Technologies, Santa Clara, CA.

first: Xuhong

last: Cao

first: Sunita

last: Shankar

first: Saravana

last: Dhanasekaran

first: Arul

last: Chinnaiyan


title: Expression profiling of human mesoangioblasts indicates that S1P induces differentiation towards smooth muscle cells

status: Public on May 01 2011

city: Firenze

first: Alberto

last: Magi

address: Viale Morgagni 50

department: Biochemical Sciences

country: Italy

institute: University of Florence

summary: cDNA microarray study of human mesoangioblasts treated with 1 µM sphingosine 1-phosphate (S1P) at 6 and 24 h.

overall_design: Agilent whole human genome oligonucleotide microarrays (44 K) were used to examine alterations in gene expression of cells after S1P treatment

first: Chiara

last: Donati

first: Giuseppina

last: Marseglia

first: Genni

last: Nannetti

first: Matteo

last: Benelli


title: Reduced expression of RhoE promotes ROCK-dependent invasion in transformed human fibroblasts

status: Public on Apr 20 2011

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary: Cen3tel cells, obtained by telomerase immortalization of human fibroblasts, gradually underwent neoplastic transformation and became metastatic in immunocompromised mice. Neoplastic transformation was associated with a change in cell morphology (from fibroblastic to polygonal). Tumorigenic cells acquired a clear-cut membrane localization of adhesion molecules, a reorganization of the actin cytoskeleton, increased cell motility and invasiveness. In a 3-dimensional environment, tumorigenic cells showed a spherical morphology with cortical actin rings, suggesting a switch from a mesenchymal to an amoeboid ROCK-dependent movement. Accordingly, cell invasion decreased upon treatment with the ROCK inhibitor Y27632, but not with the matrix protease inhibitor Ro28-2653. The increased invasiveness of tumorigenic cen3tel cells was associated with a reduced expression of RhoE, a cellular inhibitor of ROCK. Ectopic RhoE expression decreased cen3tel invasion capability. These results point to RhoE and ROCK as regulators of invasiveness of mesenchymal tumor cells and indicate ROCK as a possible therapeutic target.

overall_design: The cen3tel telomerase immortalized cell line was obtained from primary cen3 fibroblasts, derived from a centenarian individual, by infection with an hTERT-containing retrovirus (Mondello et al., 2003). Cen3tel cells were used at different steps of propagation, reflecting different phases of transformation (Zongaro et al., 2005) to study variations in the migratory and invasive potential accompanying human fibroblast neoplastic transformation. Raw data files: *NORM.txt test is Cy5 and *DS.txt test is Cy3.

first: Cristina

last: Belgiovine

first: Roberta

last: Frapolli

first: Katiuscia

last: Bonezzi

first: Ilaria

last: Chiodi

first: Francesco

last: Favero

first: Maurizia

last: Mello-Grand

first: Angelo

middle: P

last: Dei Tos

first: Elena

last: Giulotto

first: Giulia

last: Taraboletti

first: Maurizio

last: D’Incalci

last: Mondello


title: Gene Expression Profiles in Immature and In vitro matured bovine Oocytes

status: Public on Apr 25 2011

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary:
In cattle, almost all fully grown vesicle stage oocytes (GV) have the ability to resume meisos, develop to Metaphase II stage (MII), support fertilization and progress through the early embryonic cycles in vitro. Yet without intensive selection, the majority fail to develop to the blastocyst stage.
Using the Affymetrix Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of the bovine oocyte and to identify the key pathways associated with oocyte meiotic maturation and developmental potential.

overall_design: Immature and in vitro matured bovine oocytes were collected for RNA extraction and hybridization on Affymetrix GeneChip Bovine Genome array. Careful removal of cumulus and selection of oocytes was carried out under the stereo microscope in order to examine the actual cumulus-free temporal oocyte gene expression profiles. Immature oocytes at time 0 h and in vitro matured oocytes at 24 h were collected for analysis.

first: Solomon

last: Mamo

first: Fiona

last: Carter

first: Claudia

middle: L

last: Leal

first: Abdullah

middle: A

last: Naib

first: Pat

last: Lonergan

first: Trudee

last: Fair


title: Gene expression and H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants

city: Duesseldorf

first: Daniel

last: Schubert

address: Universitaetsstr. 1

department: Institute for Genetics

country: Germany

institute: Heinrich-Heine-University Duesseldorf

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA

status: Public on Apr 12 2011

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

type: Expression profiling by genome tiling array


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

status: Public on Apr 18 2011

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

institute: University Colege Dublin Conway Institute


title: Molecular analysis of the TGF-beta controlled gene expression program in chicken embryo dermal myofibroblasts

status: Public on Apr 15 2011

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

summary: Myofibroblast is a specific type of mesenchymal cell characterized by synthesis of extracellular matrix and contractile activity. While it serves a beneficial function during tissue wound healing under physiological conditions, it can cause devastating damage to organs afflicted with fibrosis. Myofibroblasts are also present in tumor stroma and contribute actively to tumor growth and spreading. Chicken embryo dermal myofibroblasts (CEDM) represent a novel ex vivo model suitable for the analysis of myofibroblastic phenotype as they show strongly pronounced, uniform and self-sustained myofibroblastic phenotype that is stable in time. As myofibroblastic differentiation is controlled chiefly by TGF-beta signaling, the understanding of the differentiation program entails the determination of TGF-beta-regulated genes. To achieve such a goal, we performed oligonucleotide microarray analysis of CEDM cells treated with a selective TGFBR1 kinase inhibitor. Genes reported previously to be under the control of TGF-beta signaling in mammalian cells appeared among the affected genes also in CEDM cells and many so far unknown TGF-beta targets were revealed.

overall_design: Comparison of the expression profiles of chicken embryo dermal myofibroblasts in culture treated with TGFBR1 Kinase Inhibitor II or DMSO only. Three biological replicates were analyzed for each group.

first: Jan

last: Kosla

first: Michal

last: Dvorak


title: Gene expression profiling of rice seedling with 2-azahypoxanthine

status: Public on Apr 14 2011

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

country: Japan

institute: Shizuoka University

summary: Rings or arcs of fungus-stimulated plant growth occur often on the floor of woodlands which are commonly called “fairy rings”. We purified a plant growth-stimulating compound, 2-azahypoxanthine (AHX), from the fairy ring-forming fungus Lepista sordida, and the detection of AHX in the fungus-infected soil near the growth-stimulated turfgrass roots. The growth-promoting activity of AHX towards rice was further analyzed by oligo DNA microarrays.

overall_design:
Immediately after germination, rice seedlings were treated with AHX and incubated for 2 weeks. Total RNA was isolated from the seedlings using an RNeasy plant mini kit (Qiagen). cDNA was synthesized to provide 400 ng of total RNA (Agilent Technologies). This cDNA was used as a template to synthesize cRNA. The cRNA was labeled with Cyanine-3 (Cy3) CTP or Cyanine-5 (Cy5) CTP. Cy3-labeled cRNA was mixed with the same amount of Cy5-labeled cRNA and the mixture was used for hybridization. After hybridization for 17 h at 65°C, the slides were washed and scanned with an Agilent Microarray Scanner. Genes showing a signal value below 300 in the Cy3 channel of the control were excluded from the analysis. Feature extraction and image analysis software (version A.6.1.1; Agilent Technologies) were used to locate and delineate each spot in the array and to integrate each spot’s intensity, filtering, and normalization. We attempted dye swap experiments to estimate the error of technical and dye labelling.
Three-condition experiment, control vs. compound-treated rice (0.05 and 0.2 mM). Biological replicates: control, 0.05 mM AHX-treated,  0.2 mM AHX-treated rice independently grown and harvested. One replicate per array.

first: Jae-Hoon

last: Choi

first: Miyuki

last: Hara

first: Reiko

last: Motohashi

first: Hirokazu

last: Kawagishi


title: Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

status: Public on Apr 07 2011

city: Tokyo

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo

department: Graduate school of agricultural and life Science

institute: University of Tokyo

summary: Normally, rice can elongate the coleoptile under submerged condition. However, reduced adh activity (rad) mutant cannot elongate the coleoptile under submergence. To investigate the change in gene expression,  we  performed microarray analysis. In this analysis, we used 1 day old seedling of rice. But  it is difficult to isolate only coleoptile from rice embryo without any contamination in this stage. Therefore, we applied laser microdissection (LM) technique to this microarray. By use of LM, we isolated coleoptile from rice embryo and use for microarray analysis. As the results, we found that the differences in the gene expression profiles of coleoptile between wild type and rad mutant.

overall_design: Gene expression analysis in coleoptile of wild type and mutant.

first: Hiroaki

last: Saika

first: Hideo

last: Matsumura

first: Yoshiaki

last: Nagamura

first: Nobuhiro

last: Tsutsumi

first: Naoko

middle: K

last: Nishizawa

first: Mikio

last: Nakazono


title: Gene expression patterns in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction

city: Amherst

first: Derek

last: Lovley

state: MA

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

department: Microbiology

institute: University of Massachusetts Amherst


title: miR-1245 induce genomic instability

status: Public on Mar 24 2011

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

type: Genome variation profiling by genome tiling array

summary: This experiment is design to evaluate genomic alteration following stably expression of miR-1245, stably knock down of BRCA2 is setup as a positive control

overall_design: Primary normal breast epithelial cells (NBEC) were collected from the mammoplasty material of a 30-year-old woman at the Department of Plastic Surgery, the First Affiliated Hospital of Sun Yat-sen University (P. R. China), in accordance with rules and regulations concerning ethical issues on research use of human subjects in China, and were cultured in the Keratinocyte serum-free medium (Invitrogen, Carlsbad, CA) supplemented with epithelial growth factor, bovine pituitary extract and antibiotics (120 µg/mL streptomycin and 120 µg/mL penicillin).  NBEC were infected with virus produced from retro vector pMSCV-miR1245 or empty pMSCV vector; or pSuper Retro BRCA2 shRNA, or pSuper Retro empty vector.  After 2 days infection and 3 days culture, genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGENE, Valencia, CA).  CGH microarray hybridization, data generation and normalization were performed in Shanghai Biochip Corporation.

first: Zhe

last: Ying

first: Jun


title: Human meningioma fixed tumour tissue

status: Public on May 11 2011

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University


title: Caulobacter crescentus starved for carbon

city: Stanford

first: Leticia

last: Britos

state: CA

address: 279 Campus Dr.

institute: Stanford University


title: Expression data from human healthy and lupus EPCs/CACs, and healthy CD133+ bone marrow EPCs

status: Public on Apr 13 2011

first: Celine

middle: C

last: Berthier

address: 1150 W. Medical Center Dr, MSRB2

summary:
Systemic lupus erythematosus (SLE) is characterized by increased vascular risk due to premature atherosclerosis independent of traditional risk factors. We previously proposed that interferon-α plays a crucial role in premature vascular damage in SLE. IFN-α alters the balance between endothelial cell apoptosis and vascular repair mediated by endothelial progenitor cells (EPCs) and myeloid circulating angiogenic cells (CACs). Here we demonstrate that IFN-α promotes an antiangiogenic signature in SLE and control EPCs/CACs, characterized by transcriptional repression of IL-1α and β, IL-1 receptor 1 and vascular endothelial growth factor A (VEGF-A) and upregulation of IL-1 receptor antagonist (IL-1RN) and the decoy receptor IL1-R2. IL-1β promotes significant improvement in the functional capacity of lupus EPCs/CACs, therefore abrogating the deleterious effects of IFN-α.

We used microarrays to analyze the effect of IFNα on peripheral blood EPCs/CACs and on bone marrow EPCs exposed to proangiogenic stimulation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Human healthy and lupus EPCs and CACs from PBMCs, and healthy EPCs from bone marrow, were isolated and cultured under proangiogenic stimulation; after IFN-α incubation or not, RNA was extracted and processed for hybridization on Affymetrix microarrays.

first: Seth

middle: G

last: Thacker

first: Deborah

last: Mattinzoli

first: Maria

last: Rastaldi

first: Matthias

last: Kretzler

first: Mariana

middle: J

last: Kaplan


title: miRNA genes in HMEC and HMF

status: Public on Apr 05 2011

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona


title: Microarray studies of darkness stress and bleaching in the Caribbean corals Acropora palmata and Montastraea

status: Public on Mar 23 2011

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

sample_organism:
Acropora palmata
Orbicella faveolata

platform_organism:
Acropora palmata
Orbicella faveolata


title: Effect of HdIV or MdBV injection on the Spodoptera frugiperda hemocyte and fat body transcriptomes

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA


title: Chromosome conformation capture-on-chip of glucocorticoid receptor-responsive loci in mouse cells

status: Public on Apr 21 2011

first: Myong-Hee

last: Sung

address: 41 Library Dr

department: NCI

institute: NIH

summary: The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression.  Contradicting results have been reported to date, with little consensus about the dynamics of nuclear organization and the features of the contact loci.  In this study we investigated the properties and dynamics of genomic loci that are in contact with glucocorticoid receptor (GR)-responsive loci.  We took a systematic approach, combining genome-wide interaction profiling by the chromosome conformation capture-on-chip (4C) technology with expression, protein occupancy, and chromatin accessibility profiles.  This approach allowed a comprehensive analysis of how distinct features of the linear genome are organized in the three-dimensional nuclear space in the context of rapid gene regulation.  We found that the transcriptional response to GR occurs without dramatic nuclear reorganization.  Moreover, contrary to the view of transcription-driven organization, even genes with opposite transcriptional responses co-localize.  Regions contacting GR-regulated genes are not particularly enriched for GR-regulated loci or for any functional group of genes, suggesting that these subnuclear environments are not organized to respond to a specific factor.  The contact regions are, however, highly enriched for DNaseI hypersensitive sites which represent the entire cell type-specific regulatory sites.  These findings indicate that the nucleus is pre-organized in a conformation allowing rapid transcriptional reprogramming, and suggest that a major force in shaping genome architecture is the repertoire of chromatin binding factors.  Numerous open chromatin loci may be arranged in nuclear domains that are poised to respond to diverse signals in general, and to permit efficient gene regulation.

overall_design:
Fourteen arrays total: Eight microarrays from individual biological replicates, and six microarrays each from a pool of two biological replicates.

This submission represents the chromosome conformation capture-on-chip component of the study. The expression data are included in GSE26189.

first: Gordon

last: Hager

first: Ofir

last: Hakim


title: Expression analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants

status: Public on Mar 21 2011

first: Daniel

last: Schubert

summary: For the expression analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. Tissues for expression and H3K27me3 ChIP-chip analyses were simultaneously harvested.

overall_design: Meristem enriched samples (XMe1 and XMe2) and young leaf samples (XLe1 and XLe2) of clavata3-9 plants were isolated and hybridised to Agilent 44 k arrays [G2519F, V4 (Agilent, Santa Clara)]. Two biological replicates were performed.

first: Marcel

last: Lafos

first: Phillip

last: Kroll


title: Integration of a splicing regulatory network within the meiotic gene expression program of Saccharomyces cerevisiae

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary:
Splicing regulatory networks are essential components of eukaryotic gene expression programs, yet little is known about how they are integrated with transcriptional regulatory networks into coherent gene expression programs. Here we define the MER1 splicing regulatory network and examine its role in the gene expression program during meiosis in budding yeast. Mer1p splicing factor promotes splicing of just four pre-mRNAs. All four Mer1p-responsive genes also require Nam8p for splicing activation by Mer1p, however other genes require Nam8p but not Mer1p, exposing an overlapping meiotic splicing network controlled by Nam8p. MER1 mRNA and three of the four Mer1p substrate pre-mRNAs are induced by the transcriptional regulator Ume6p. This unusual arrangement delays expression of Mer1p-responsive genes relative to other genes under Ume6p control. Products of Mer1p-responsive genes are required for initiating and completing recombination, and for activation of Ndt80p, the transcriptional network that controls subsequent steps in the program. Thus the MER1 splicing regulatory network mediates the dependent relationship between the UME6 and NDT80 transcriptional regulatory networks in the meiotic gene expression program. This work reveals how splicing regulatory networks can be interlaced with transcriptional regulatory networks in eukaryotic gene expression programs.

This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide analysis of H3K27me3 and H3K4me3 deposition in the fie mutant

status: Public on Mar 28 2011

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

last: Bouyer

last: Roudier

first: Vincent

last: Colot

first: Arp

last: Schnittger


title: Analysis of the human endothelial cell response to Borrelia burgdorferi wild-type and deleted in the gene encoding the integrin ligand P66

status: Public on Mar 18 2011

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

institute: Medical College of Wisconsin


title: Establishing a reference epigenome in arabidopsis seedlings

status: Public on Apr 19 2011


title: Profiling of prostate tissues in prostate cancer progression

status: Public on Mar 30 2011

city: Detroit

first: Laila

middle: M

last: Poisson

address: 1 Ford Place

department: Biostatistics and Research Epidemiology

institute: Henry Ford Health Systems

summary:
Samples of benign prostate tissue, localized prostate cancer tissue, and metastatic prostate cancer tissue are profiled to study expression changes in diagnosis and progression of prostate cancer.
Each tissue sample is also profiled for metabolomics data
Keywords: Cancer Progression

overall_design: 41 samples were analyzed (16 benign prostate tissue, 12 local prostate cancer tissue, 13 metastatic prostate cancer tissue)

first: Arul

last: Chinnaiyan


title: Transcriptional profiling of rice salt sensitive 1 (rss1) mutant

status: Public on Mar 11 2011

city: Nagoya

first: Daisuke

last: Ogawa

address: Furou-Chou, Chikusa

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: RSS1 is required for maintenance of meristematic activity under salinity conditions in rice. We carried out transcriptome analysis using shoot basal tissues in wild type and rss1-2 grown under non-stress and salt-stress conditions.

overall_design: WT (-NaCl), WT (+NaCl), rss1-2 (-NaCl), rss1-2 (+NaCl). Three biological replicates.

first: Tokunori

last: Hobo

first: Yosuke

last: Toda

first: Tsukaho

last: Hattori

first: Shin

last: Takeda


title: Identification of copy number alterations by array comparative genomic hybridization in patients with late chronic or accelerated phase chronic myeloid leukemia treated with imatinib mesylate

status: Public on Mar 15 2011

city: Kuala Lumpur

first: Veera Sekaran

last: Nadarajan

address: Lembah Pantai

department: Pathology

country: Malaysia

institute: University Malaya

summary: The outcome of treating chronic myeloid leukemia (CML) with imatinib mesylate (IM) is inferior when therapy is commenced in late chronic or accelerated phase as compared to early chronic phase. This may be attributed to additional genomic alterations that accumulate during disease progression. We sought to identify such lesions in patients showing suboptimal response to IM by performing array-CGH analysis on 39 sequential samples from 15 CML patients. Seventy-four cumulative copy number alterations (CNAs) consisting of 35 losses and 39 gains were identified. Alterations flanking the ABL1 and BCR genes on chromosomes 9 and 22, respectively, were the most common identified lesions with 5 patients losing variable portions of 9q34.11 proximal to ABL1. Losses involving 1p36, 5q31, 17q25, Y and gains of 3q21, 8q24, 22q11, Xp11 were among other recurrent lesions identified. Aberrations were also observed in individual patients, involving regions containing known leukemia-associated genes; CDKN2A/2B, IKZF1, RB1, TLX1, AFF4. CML patients in late stages of their disease, harbor pre-existing and evolving sub-microscopic CNAs that may influence disease progression and IM response.

overall_design: Fifteen patients with confirmed CML, on IM for a minimum period of 18-months and showing suboptimal response to IM, as evidenced by failure to achieve major molecular remission (MMolR) at 18 months were identified from a series of patients treated in our centre. Patients received their medication under the auspices of the Glivec International Patient Assistance Program (GIPAP) and were started on an initial dose of 400mg with dose escalations or reductions made according to the patient’s response and tolerance. Archived sequential peripheral blood lysates from the patients were retrieved and DNA/RNA extracted. Thirty-nine DNA samples of sufficient quality and quantity from the 15 patients were subjected to array-CGH analysis to identify recurrent genomic aberrations that occur through the course of disease.

first: Veera

middle: S

first: Chin

last: Phan

first: Zubaidah

last: Zakaria


title: Transcriptome changes at the initiation of elongation in the bovine conceptus

status: Public on Mar 08 2011

first: Jai Prakash

last: Mehta

address: Veterinary Science Center, University College Dublin

department: UCD School of Agriculture, Food Science & Veterinary Medicine

institute: University College Dublin, Ireland

summary:
Temporal changes in the embryo transcriptome between the blastocyst stage (Day 7) and initiation of elongation (Day 13) differ between in vivo- and in vitro-derived embryos and are reflective of subsequent developmental fate.
The aim of this study was to examine the temporal changes in transcriptional profile as the embryo develops from a spherical blastocyst on Day 7 to an ovoid conceptus at the initiation of elongation on Day 13 and to highlight differences in these temporal gene expression dynamics between in vivo- and in vitro-derived blastocysts which may be associated with embryonic survival/mortality using the bovine Affymetrix microarray.

overall_design: All embryos were produced either in vitro by IVF or in vivo by superovulation. A proportion of Day 7 blastocysts were snap frozen and the remainder were transferred (n=10 per recipient) to synchronized heifers, recovered on Day 13 and snap frozen individually. Three pools of Day 7 blastocysts (n=25 per pool for in vitro and in vivo, respectively) and three pools of Day 13 conceptuses (n=5 per pool, for in vivo and in vitro) were used for microarray. analysis.

first: Dimitrios

last: Rizos

first: Patrick

last: Lonergan


title: Delineating the angiogenic gene expression profile prior to pulmonary vascular remodeling in a lamb model of congenital heart disease

status: Public on Mar 10 2011

city: Augusta

first: Jing

last: Tian

state: GA

address: 1459 Laney Walker BLVD

department: Vascular Biology Center

institute: Medical College of Georgia

summary: Disordered angiogenesis is implicated in the pulmonary vascular remodeling secondary to congenital heart disease (CHD). However, the underlying genes are not well delineated. We have previously shown that an ovine model of CHD with increased pulmonary blood flow (PBF, Shunt) has an “angiogenesis burst” between 1-4 weeks of age. Thus, we hypothesized that the increased pulmonary blood flow elicited a pro-angiogenic gene expression profile prior to the onset of vessel growth. To test this we utilized microarray analysis to identify genes that could be responsible for the angiogenic response.  Total RNA was isolated from the lungs of Shunt and Control lambs at 3 days of age and hybridized to Affymetrix GeneChips for microarray analyses (n=8 for each group). A total of 89 angiogenesis-related genes were found to be up-regulated and  26 angiogenesis-related genes down-regulated in Shunt lungs compared to control (cutting at 1.2 fold difference, P<0.05). We then confirmed the up-regulation of pro-angiogenic genes: FGF2, Angiopoietin2 (Angpt2), and Birc5 at both mRNA and protein levels and the up-regulation of ccl2 at mRNA level in the 3-day shunt lungs. Further, we found that pulmonary arterial endothelial cells (PAEC) isolated from juvenile lambs exhibited increased expression of FGF2, Angpt2, Birc5, and ccl2 as well as enhanced angiogenesis when exposed to elevated shear stress (35 dyn/cm2) compared to cells exposed to more physiological level shear stress (20 dyn/cm2). Finally, we demonstrated that blocking FGF2, Angpt2, or Birc 5 signaling, using neutralizing antibodies, significantly decreased the angiogenic response induced by shear stress. In conclusion, we have identified a pro-angiogenic gene expression profile in a lamb model of CHD with increased PBF that precedes the onset of pulmonary vascular remodeling. Further, our data indicate that FGF2, Angiopoietin2, Birc5, and ccl2 may play important roles in the angiogenic response.

overall_design: Total RNA was isolated from the lungs of Shunt and Control lambs at 3 days of age and hybridized to Affymetrix GeneChips for microarray analyses. Eight chips were employed for both control and shunt groups.

first: Yali

last: Hou

first: Qing

last: Lu

first: Sohrab

last: Fratz

first: Agnes

last: Görlach

first: John

last: Hess

first: Sanjeev

last: Datar

first: Peter

last: Oishi

last: Nechtman

first: Robert

last: Podolsky

first: Jin-Xiong

last: She

first: Jeffrey

last: Fineman

first: Stephen

last: Black


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

status: Public on Mar 09 2011

city: Montreal

first: Moshe

last: Szyf

state: Quebec

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

department: Pharmacology

country: Canada

institute: McGill University

type: Methylation profiling by genome tiling array


title: Gene regulation by the Arabidopsis seed maturation master regulator FUS3

status: Public on Feb 21 2011

first: Akiko

last: Yamamoto

address: Furo-cho

summary: The FUSCA3 (FUS3) transcription factor is considered to be a master regulator of seed maturation because a wide range of seed maturation events are impaired in its defective mutant. To comprehensively identify genes under the control of FUS3, two types of microarray experiments were performed. First, transgenic plants in which FUS3 expression could be induced by the application of estrogen (ESTR) were used to identify the genes up-regulated in young seedlings of Arabidopsis in response to ectopic expression of FUS3. Second, transcriptomes were compared between fus3 mutant and wild type developing seeds. Combining the results of these experiments identified genes under relatively immediate and robust control of FUS3 during seed development. The analyses expanded the range of types of genes under the control of FUS3. The genes positively controlled by FUS3 are not confined to previously known seed maturation-related genes and include those for production of secondary metabolites such as glucosinolates, phenylpropanoids and falvonoids, and primary metabolism such as photosynthesis and fatty acid biosynthesis. Furthermore, several different patterns were identified in the manner of ectopic activation by FUS3 including the kinetics and abscisic acid (ABA) requirement of downstream genes depending on their natures of developmental regulation, suggesting mechanistic diversity of gene regulation by FUS3.

overall_design:
This Series contains two different types of microarray experiments.
First, seven-day-old seedlings of the ESTR-inducible FUS3 transgenic plants (ER-FUS3) were cultured for 3, 6, 12, 24, 36 or 48 h in a standard liquid medium or in that containing ESTR, ABA or both. RNA was prepared from each time point sample of each treatment and used to prepare Cy5-labeled cRNA, which was subsequently probed by DNA array with the reference Cy3-labeled cRNA prepared from the time zero untreated seedlings. Two biological replicates per treatment.
Second, transcriptomes were compared between developing seeds of the wild-type (Col-0) and the fus3-3 mutant. This experiment contains two seed developmental stages, 8 days after flowering (DAF; bent cotyledon stage) and at 12 DAF (green cotyledon stage). Sample pairs in three biological replicates were analyzed by the two-color method. Dye-swapped hybridizations were performed in every replicate.

first: Yasuaki

last: Kagaya

first: Haruko

last: Usui

first: Shin

last: Takeda

first: Tsukaho

last: Hattori


title: Transcriptional profiling of adult wild-type IFM and leg muslce in comparison to salm RNAi IFM.

status: Public on Mar 01 2011

city: Vienna

first: Martin

last: Radolf

address: Dr.Bohrgasse 7

country: Austria

institute: IMP

summary: Transcriptional profiling comparing adult wild-type indirect flight muscle (IFM) with wild-type leg muscle and salm RNAi IFM (Mef2-GAL4, UASsalmIR). We used 2 different salm hairpin constructs for the experiments, TF3029 and TF101052, both available from the VDRC Drosophila stock centre.

overall_design: Experiments were done in biological duplicates + 1 technical replicate  (1 labeled sample was hybridized on a different array)

first: Cornelia

last: Schnönbauer

first: Frank

last: Schnorrer


title: Molecular Cytogenetic Analysis of a Gliosarcoma with Osseous Metaplasia

status: Public on Feb 28 2011

city: Oslo

first: Hanne-Sofie

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

summary: Gliosarcoma, a rare glioblastoma variant, is composed of a glial and a mesenchymal component. Though the mesenchymal portion most commonly resembles a fibrosarcoma, other differentiation patterns have been observed. We present the first genomic characterisation (karyotyping followed by FISH and array-CGH analysis) of a gliosarcoma with osseous metaplasia. In addition to chromosomal changes often found in gliomas (+7,-10,-13, and -22), the tumour cells also harboured a hitherto unknown 3q21;21q21~22-translocation. As translocations are very rare in high-grade astrocytic tumours and have not formerly been seen in gliosarcomas, it is possible that the t(3;21) may be characteristic of gliosarcoma with osseous metaplasia.

overall_design: Tumour sample analysed with control DNA (supplied by Agilent)

first: Ludmila

last: Gorunova

first: Francesca

last: Micci

first: David

last: Scheie

first: Petter

last: Brandal

first: Torstein

middle: R

last: Meling

first: Sverre

last: Heim


title: Gene-expression profile of the response to E. coli (k2bh2) infection in the bovine udder

city: Tjele

first: A.J. (Bart)

last: Buitenhuis

address: Blichers allé 20

department: Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology

country: Denmark

institute: Aarhus University

summary: Mastitis in dairy cows is one of the most costly and prevalent diseases affecting dairy cows world wide. Insight in the molecular regulation of the host immune response to an E. coli infection, could help to develop new strategies to prevent cattle from E. coli infection. Here we performed a gene-expression analysis from udder tissue exposed to a controlled E. coli infection at T=24h post infection (p.i.) representing the acute phase response and at T=192h p.i. representing a chronic stage.

overall_design: 49 Samples

first: Peter

last: Sørensen

first: A

first: Christine

last: Røntved

first: Klaus

last: Ingvartsen


title: Genomic mapping of 5-hydroxymethylcytosine in the human brain

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Methylation at the 5-position of cytosine is a well-studied epigenetic pathway. In addition to 5-methylcytosine (5mC), substantial amounts of 5-hydroxymethylcytosine (5hmC) also referred to as the 6th DNA base, have been detected in certain tissues, most notably the brain. However, the genomic distribution of this cytosine modification is unknown. Here, we have developed an immunoprecipitation technique (5hmC-IP) to examine the occurrence of 5hmC in human DNA from brain frontal lobe tissue. The distribution of 5hmC was compared to that of 5mC. We show that 5hmC is more selectively targeted to genes than is 5mC. 5hmC is found at promoters and is particularly enriched in intragenic regions (gene bodies) but is largely absent from non-gene regions. 5hmC peaks at transcription start sites did not correlate with gene expression levels or H3K4me3 peaks. However, presence of 5hmC in gene bodies was more positively correlated  with gene expression levels than was presence of 5mC. Promoters of testis-specific genes showed strong 5mC peaks in brain DNA but were almost completely devoid of 5hmC. Our data provide a first overview of the genomic distribution of 5hmC in human brain and will set the stage for further functional characterization of this novel DNA modification.

overall_design: Comparison between 5hmC and 5mC profiles

first: Seung-Gi

last: Jin

first: Xuejun

last: Li

first: Gerd

last: Pfeifer


title: Gene expression in response to axotomy in organotypical slices co-cultures

status: Public on Feb 25 2011

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
Brain slice cultures offer advantages over other in vitro methods, as they mimic numerous in vivo aspects. For most purposes, slices of the developing brain, termed organotypic slice cultures , preserve a high degree of cellular differentiation and tissue organization. The entorhino-hippocampal connection (EHP) is the main entrance of information to the hippocampus proper and the dentate gyrus. Also it has some specific features that make them particularly interesting in studies of axonal regeneration: (i) the culture method obviates the need for extensive animal surgery and requires less time than other in vivo approaches; (ii) the EHP is reproduced easily in vitro in cultures with a degree of laminar specificity similar to that found in vivo; (iii) the EHP is myelinated both in vitro and in vivo; and (iv) most of the cellular and molecular barriers to axon regeneration are present after the axotomy of the EHP in vitro. Altogether this model is useful to evaluate axon regeneration and putative estrategies to promote axonal growth.

Keywords: organotypic slice cultures; axonal lession; gene expression

overall_design: To evaluate the genes whose transcription was regulated after 1, 3 and 7 days after EHP (Entorhino-Hippocampal Pathway) axotomy, RNA samples were analyzed with Agilent whole genome rat long oligonucleotide (44 K base) probe based microarrays.

first: Oscar

last: Seira

first: Franc

last: Llorens

first: Jose

last: delRio

first: Alejandra

last: Rangel

first: Rosalina

last: Gavin

first: Vanessa

last: Gil


title: Expression of G protein-coupled receptors and related proteins in HEK293, AtT20, BV2, and N18 cell lines as revealed by microarray analysis

status: Public on Feb 01 2011

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Salinity stress inducible genes in rice

city: Tsukuba

first: Hiroshi

last: Mizuno

address: 2-1-2 Kannondai

department: Genome and Biodiversity Research

institute: National Institute of Agrobiological Sciences

summary: 44K oligo microarray analysis was performed for monitoring salinity stress–inducible genes in rice.

overall_design: Two-condition, 0 h or 1 h treatment of 150mM NaCl in shoot or in root. Two dye swapped experiments were performed.

first: Takashi

last: Matsumoto


title: Mapping of H3K4 and H3K27 trimethylation in zebrafish cells

status: Public on Feb 08 2011

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo


title: Tumor-associated stroma derived from primary clinical breast cancer samples (II)

status: Public on Jan 15 2011

first: Greg

last: Finak

state: QC

address: 3775 University

department: Mcgill Center For Bioinformatics

summary: Breast cancer is an extremely heterogeneous disease. This heterogeneity can be observed at multiple levels, including gene expression, chromosomal aberrations, and disease pathology. A clear understanding of these differences is important since they impact upon treatment efficacy and clinical outcome.  Many studies have shown that the tumor microenvironment also plays a critical role in cancer initiation and progression. Although genomic technologies have been used to gain a better understanding of the impact of gene expression heterogeneity on breast cancer outcome by identifying gene expression signatures associated with clinical outcome, histopathological breast cancer subtypes, and a variety of cancer--related pathways and processes, relatively little is known about the influence of of heterogeneity in the tumor microenvironment on these factors. We show that gene expression in the breast tumor microenvironment is highly heterogeneous, identifying at least six different  classes of tumor stroma with distinct expression patterns and distinct biological processes. Two of these classes recapitulate the processes identified in the stroma--derived prognostic predictor, while the others are new classes of stroma associated with distinct clinical outcomes. One of these is associated with matrix remodeling and is strongly associated with the basal molecular subtype of breast cancer. The remainder are independent of the previously published molecular subtypes of breast cancer. Additionally, based on independent data from over 800 tumors, the combinations of stroma classes and breast cancer subtypes identify new subgroups of breast tumors that show better discrimination between good and poor outcome individuals than the molecular breast cancer subtypes or the stroma classes alone, suggesting a novel classification scheme for breast cancer . This further demonstrates an important role for the tumor microenvironment in defining breast cancer heterogeneity, with a consequent impact upon clinical outcome.

overall_design: 49 samples, each replicated at least 2 times in a common reference design using Agilent whole human genome oligonucleotide arrays.

first: Morag

last: Park

first: Michael

last: Hallett

first: Sarkis

last: Meterissian

first: Nicholas

last: Bertos


title: The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome

status: Public on Feb 12 2011

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute


title: p53 regulates epithelial-mesenchymal transition (EMT) and stem cell properties through modulation of miRNAs.

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

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


title: Rat model of MTLE: Animals with epilepsy vs animals without epilepsy (Agilent)

status: Public on Feb 13 2011

city: Boston

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

summary: Neither the molecular basis of the pathologic tendency of neuronal circuits to generate spontaneous seizures (epileptogenicity) nor anti-epileptogenic mechanisms that maintain a seizure-free state are well understood. Here, we performed transcriptomic analysis in the intrahippocampal kainate model of temporal lobe epilepsy in rats using both Agilent and Codelink microarray platforms to characterize the epileptic processes. The experimental design allowed subtraction of the confounding effects of the lesion, identification of expression changes associated with epileptogenicity, and genes upregulated by seizures with potential homeostatic anti-epileptogenic effects. Using differential expression analysis, we identified several hundred expression changes in chronic epilepsy, including candidate genes associated with epileptogenicity such as Bdnf and Kcnj13. To analyze these data from a systems perspective, we applied weighted gene co-expression network analysis (WGCNA) to identify groups of co-expressed genes (modules) and their central (hub) genes. One such module contained genes upregulated in the epileptogenic region, including multiple epileptogenicity candidate genes, and was found to be involved the protection of glial cells against oxidative stress, implicating glial oxidative stress in epileptogenicity. Another distinct module corresponded to the effects of chronic seizures and represented changes in neuronal synaptic vesicle trafficking. We found that the network structure and connectivity of one hub gene, Sv2a, showed significant changes between normal and epileptogenic tissue, becoming more highly connected in epileptic brain. Since Sv2a is a target of the antiepileptic levetiracetam, this module may be important in controlling seizure activity. Bioinformatic analysis of this module also revealed a potential mechanism for the observed transcriptional changes via generation of longer alternatively polyadenlyated transcripts through the upregulation of the RNA binding protein HuD. In summary, combining conventional statistical methods and network analysis allowed us to interpret the differentially regulated genes from a systems perspective, yielding new insight into several biological pathways underlying homeostatic anti-epileptogenic effects and epileptogenicity.

overall_design: Four condition experiment with five samples per condition. The samples include right dentate gyrus from animals with seizures, left dentate gyrus from animals with seizures, right dentate gyrus from animals without seizures, and left dentate gyrus from animals without seizures. A dye swap was included.

middle: D

first: Stanislav

last: Karsten

first: Anatol

last: Bragin

first: Lili

last: Kudo

first: Lauren

last: Gehman

first: Josephine

last: Ruidera

first: Daniel

middle: H

last: Geschwind

first: Jerome

last: Engel Jr


title: Mouse liver gene expression profiling of Cross B6/J x A/J

status: Public on Feb 02 2011

first: Sergey

last: Lezhnin

address: 33 AVENUE LOUIS PASTEUR

department: Molecular Profiling

institute: Merck Research Laboratories


title: Ovarian epithelial carcinoma tumors and cell lines

city: Stanford

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine


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

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg


title: Transcriptomic analysis of rice

status: Public on Jan 13 2011

first: Baltazar

last: Antonio

state: Ibaraki

address: Kannondai 2-1-2


title: In vivo identification of solar-responsive gene network

status: Public on Jan 20 2011

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

institute: CNRS UMR6290

summary: Solar radiation is one of the biggest threats to the skin, eliciting a specific protective cellular response. To descipt the underlying mechanisms, we have chosen to study in vivo, epidermis gene expression of surface solar radiation (SSR)-irradiated skin using whole genome microarray (Agilent 44K).

overall_design: We studied epidermis samples from five healthy Caucasian patients, with phototype II or III, using two different doses (2J/m2 and 4J/m2) and sham-irradiated.

first: Marie-Dominique

last: Galibert


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

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

overall_design: For continuous gene expression profile of leaf, the uppermost fully-expanded leaf, 1st leaf before 83 days after transplanting (DAT) and flag leaf from then on, in the main stem was sampled at 12:00 PM at regular intervals of 7 days encompassing 17 different growth stages with three replicates.

first: Yutaka

last: Sato

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in Atlantic salmon

status: Public on Feb 03 2011

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

platform_organism:
Oncorhynchus mykiss
Salmo salar


title: Comparison of gene expression profile of flag leaf from fertile and sterile lines of rice

summary: To examine the role of formation of a strong sink during leaf senescence, we compared the expression profile of the flag leaf of three different sterile mutant lines with fertile plants. The fertile and sterile lines showed basically similar expression profiles of flag leaves sampled at the same time. However, the fertile lines showed more rapid and enhanced change in transcriptome as compared to the sterile lines indicating that leaf senescence initiated independent of sink formation and is accelerated by sink formation.

overall_design: Three independent mutant lines, namely, pair1, pair2, and mel1-1, and fertile plants (homozygous or heterozygous) derived from each segregating population were used for comparison. The flag leaves were sampled at initiation of heading, 1 week after heading (WAH), 2 WAH, and 3 WAH, with three biological replicates.

first: Makoto

last: Kusaba


title: Human bronchial cells (BEAS-2B) treated with amiodarone (AM)

status: Public on Jan 10 2011

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

summary: AAmiodarone is an antiarrhythmic drug and representatively induce pulmonary phospholipidosis. Amiodarone-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of amiodarone-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray. The expression of these genes are potential biomarker of amiodarone-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents.

overall_design: BEAS-2B cells were seeded and after incubation for 24 h at 37C, the cells were treated with 29.388 μM(IC20) amiodarone for 48 h. And after total RNA isolation, gene expression analysis was conducted using a 44-k whole human genome microarray. Labeling and hybridization were performed using a FairPlay microarray labeling kit, followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye. The hybridized slides were scanned using a GenePix 4000B microarray scanner, and the images were analyzed using GenePix 4.1 software to obtain gene expression ratios. The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000. A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.

first: Jae-Chun

last: RYU

first: Youn-Jung

last: Kim

first: Mee

last: Song


title: Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

summary: An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting.

overall_design: A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.

first: Kazuhiko

last: Sugimoto


title: Identification of fusion genes in breast cancer

status: Public on Jan 11 2011

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

summary: Characterization of genomic copy number changes in breast cancer cell lines BT474, SKBR3, KPL4 and MCF7 compared to a normal human female genomic DNA reference.

overall_design: The experiment utilized four breast cancer cell lines; BT474, SKBR3, MCF7 and KPL4. All cell lines were grown in accordance with the distributor’s instructions. All samples were hybridized once on 1M Agilent Human Genome CGH microarrays according to manufacturers instructions. Genomic DNA pooled from healthy female donors was used as a reference in all hybridizations. DNA from cell line samples were labeled with Cy5 and DNA from reference were labeled with Cy3.

first: Sara

last: Kangaspeska

first: Astrid

last: Murumägi


title: Secreted bacterial effectors that inhibit host protein synthesis are critical for induction of the innate immune response to virulent Legionella pneumophila

status: Public on Jan 08 2011

city: Berkeley

first: Russell

last: Vance

address: 415 Life Science Addition

institute: UC Berkeley


title: Functional characterization of Arabidopsis mutants deficient in cytosolic APX1 and peroxisomal CAT2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Transcriptional profiling of WT, cytosolic ascorbate peroxidase 1 (Apx1) and peroxisomal catalase 2 (Cat2) single mutants and apx1/cat2 double mutant plants, subjected to 0h and 1h of high light irradiation in order to identify molecular mechanisms underlying the observed growth retardation and stress resistance of apx1/cat2 double mutant plants.

overall_design: 4 genotypes x 2 conditions experiment including WT, apx1, cat2, and apx1/cat2 plants treated with 0h and 1h of high light irradiation. Two biological replicates. In total, 16 samples hybridized on 8 Arabidopsis Gene Expression microarrays V3 (Agilent, two-color array) including color swap of replicate samples.

first: Sandy

last: Vanderauwera

first: Frank

last: Van Breusegem


title: Polycomb chromatin domains in Drosophila

status: Public on Jan 31 2011

first: Maarten

last: van Lohuizen

department: Molecular Genetics

institute: NKI-AVL

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: The knockdown of the maternal estrogen receptor-β2 mRNA (ers2a) affects embryo transcript contents and larval development in zebrafish

status: Public on Jan 12 2011

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

country: Italy

institute: University of Padua

summary: In zebrafish, vitellogenic oocytes can incorporate significant amounts of 17β-estradiol released from nearby granulosa cells according to a first-order kinetics, since the steroid low polarity ensures high permeability and affinity for yolk lipids. Estrogen bioactivity is likely, because the maternal mRNA for the estrogen receptor-β2 (ers2a) is highly expressed in ovulated oocytes. This transcript is available for translation in the embryo until its sharp decline from 4 to 8 hours post-fertilization (hpf), being replaced by low levels of zygotic ers2a  mRNA from 24 hpf to hatching at 48 hpf, as determined by qRT-PCR. Estrogen receptors-α and -β1 are only expressed zygotically at low levels from 24 hpf onwards. To test the functional role of maternal ers2a  mRNA, 1- or 2-cell embryos were injected with 10.3 ng each of morpholino to knockdown translation (MO2-ers2a) of both maternal and zygotic ers2a  transcripts, missplicing morpholino (MO3-ers2a) to block post-transcriptionally the zygotic transcript alone, and a nonspecific morpholino (MO-control) as a control. Treatment with MO2-ers2a caused severe malformations in 63% of 1-5 dpf larvae, as compared to 10-11% in those treated with MO3-ers2a and MO2-control. Defects included body growth delay and curved shape, abnormal brain and splanchnocranium development,  enlarged and hemorrhagic pericardial cavity, uninflated swim bladder and rudimentary caudal fin with aberrant circular motion. Affected larvae could survive for only 12-14 days. Co-injection of an anti-p53 MO failed to rescue the MO2-ers2a-phenotypes, eliminating the possibility of off-target effects. Pangenomic microarray analysis revealed that 240 and 219 significantly expressed transcripts were up- and down-regulated, respectively, by maternal Ers2a protein deficiency in 8-hpf MO2-ers2a-embryos. Also at 48 hpf, 162 and 120 presumably zygotic transcripts were up- and down-regulated, respectively, but only 18 were in common with each of the 8-hpf sets. Whole-mount in situ hybridization revealed an intensified expression of the genes six3.1 and emx1 in MO2-ers2a-embryos at 24-48 hpf, as compared to controls. These findings suggest the involvement of maternal ers2a  mRNA in the epigenetic programming of zebrafish development.

overall_design: MO2-ers2a morphants were compared with MO-control at 8 hpf and 48 hpf. MO2-ers2a is a morpholinos selected to knockdown translation of ers2a mRNA

first: Benato

last: Francesca

first: Surachai

last: Pikulkaew

last: Rabbane

first: Lorenzo

last: Colombo

first: Luisa

last: Dalla Valle


title: Sertoli cell specific testicular gene expression of Connexin 43 knockout mice

status: Public on Jan 06 2011

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

country: Germany

institute: Institute for Medical Microbiology

summary: Infertility observed in adult Sertoli cell (SC)-specific Connexin 43 Knockout-mice rather seems to be an effect of the disturbed SC-Germ cell (GC) crosstalk than a direct consequence of the loss of Cx43 protein in SC with important GC specific genes being mostly affected by this deletion.

overall_design: Identification of differentially expressed genes in testis of cx43 KO-mice at developmental stage 8 days post partum when compared with testis of WT-mice

first: Ralph

last: Brehm


title: Expression analysis of benzoate and phenol degradation in the hyperthermophilic archaeon Ferroglobus placidus

status: Public on Jan 05 2011

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

country: USA

institute: University of Massachusetts Amherst


title: Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster during heat shock

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

summary: Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA or Mock IP DNA from heat shocked Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.

overall_design: Heat Shock Factor IP or mock IP vs whole cell extract from heat shocked Kc cells.

first: Sarah

last: Gonsalves


title: Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

status: Public on Dec 31 2010

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS).

overall_design: Two-condition experiment, shoots of root-wounded seedlings vs. shoots of control seedlings. Biological replicates: 2 control replicates, 2 treated replicates. Technical replicate: Dyeswap

first: Satoko

last: Hasegawa


title: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci

status: Public on Jan 07 2011

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI


title: Lymphoid function of the tuberculous granuloma

status: Public on Dec 22 2010

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Induced lymphoid structures associated with pulmonary granulomas have been observed during TB in both humans and mice and could orchestrate host defense. In order to determine whether granulomas perform lymphoid functions, mice lacking secondary lymphoid organs (SLOs) were infected with Mycobacterium tuberculosis (MTB). As in wild type mice (WT), granulomas developed, MTB was controlled, and antigen-specific T cell responses including T central memory (TCM) cells were generated in the complete absence of SLOs. Moreover, T cell activation correlated with granuloma formation in these mice and TCM cells accumulated in lungs and participated in protection against secondary MTB infection. Lung granulomas may therefore represent tertiary lymphoid organs (TLOs) capable of priming robust T cell responses and mediating host defense during chronic MTB at the site of infection.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Tracey

last: Walker

first: Stefan

last: Kaufmann


title: Transcriptional profiling of embryonic zebrafish expressing a mutant TNNT2

city: Charlestown

first: Jason

last: Becker

state: MA

address: 13th St, Building 149

department: CVRC

institute: Massachusetts General Hospital

summary: Transcriptional profiling of embryonic zebrafish injected with a control morpholino or a morpholino that causes exclusion of TNNT2 exon 13.

overall_design: Zebrafish embryos were injected with a antisense morpholino oligo that induced missplicing of exon 13 of TNNT2 (TNNT2sp) or a control morpholino. At 96hpf these embryos were euthanized and RNA was collected.

first: Calum

last: MacRae


title: Expression of 50-500nt ncRNAs in silkworm Bombyx mori: developmental time courses

city: Nanyang

first: Yunchao

last: Kan

state: Henan

address: Wolong road 1638

institute: China-UK-NYNU-RRes Joint Libratory of insect biology

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

overall_design: Refer to individual Series


title: Gis2 studies

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology


title: Whole-genome analysis reveals active heat shock factor binding sites are mostly associated with non-heat shock genes


title: Transcriptional properties of the endometrial macrophage in the pregnant cow

status: Public on Dec 21 2010

city: Gainesville

first: Peter

last: Hansen

email: lijoli@ufl.edu, pjhansen@ufl.edu

state: FL

address: 1812 Shealy Drive

department: Animal Sciences

institute: University of Florida

summary: Transcriptional profiling of bovine CD14+ cells comparing endometrial CD14+ cell with blood CD14+ cells from the same pregnant cow . Enzymatically dispersed stromal endometrial cells and peripheral blood mononuclear cells from the same cow were labelled using CD14 antibody as a maker.  The labeling with CD14 makes possible the soring of those CD14 cells by FACS. Goal was to determine the effects of pregnancy and the location of CD14+ on global CD14+ cells gene expression.

overall_design: Two-condition experiment, endometrial vs. blood CD14+ cells. Biological replicates: 4 pairs of blood and endometrial CD14+ cells from each pregnant cow.

first: Lilian

last: Oliveira

first: Steve

last: McClellan


title: Identification of Exposure Biomarkers for Mutagenic Carcinogens in Complex Environmental Matrices

status: Public on Dec 09 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary:
We investigated an in vitro experimental exposure model of the MutaMouse flat epithelial (FE1) cells exposed to a complex mixture of carcinogenic PAHs known as coal tar (SRM 1597a) using an Agilent 22k, oligo mouse array platform.

Keywords: Toxicology, biomarkers discovery, stress response, complex mixture of carcinogens, PAHs

overall_design: The FE1 cells were exposed to two different sub-toxic concentrations of coal tar (SRM 1597a): 1 mg/ml and 4 mg/ml in a serum free media. After 6h exposure, the cells were washed twice with PBS and re-incubated in fresh media without coal tar. After 4h and 8h incubation, the media were collected for proteomic experiment and the cells were collected from the petri dishes for RNA extraction.

first: Natalie

last: Osika

first: Mamady

last: Hapsatou

first: Carole

last: Yauk

first: Paul

last: White


title: Characterization of pathogen specific expression of host immune response genes in Mycobacterium and Anaplasma spp. infection in ruminants

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

summary: Anaplasma and Mycobacterium species are known to modify gene expression in ruminants. The objectives of this study were (a) to characterize global gene expression profiles in European red deer (Cervus elaphus) in response to Anaplasma ovis and A. ovis/Mycobacterium bovis/M. avium sub. paratuberculosis (MAP) infections, (b) to compare the expression of immune response genes between A. ovis- and A. ovis/M. bovis/MAP-infected deer, and (c) to characterize the differential expression of immune response genes identified in red deer in cattle infected with M. bovis and A. marginale. The results of this study showed that global gene differential expression in A. ovis- and A. ovis/M. bovis/MAP-infected deer results in the modification of common and pathogen-specific cellular biological processes. The differential expression of host immune response genes also showed pathogen-specific signatures and the effect of infection with multiple pathogens on red deer host immune response. These results suggested that intracellular bacteria from Anaplasma and Mycobacterium genera use similar mechanisms to infect and multiply within ruminant host cells while pathogen-specific mechanisms underline differences that could contribute to disease characterization and diagnosis in ruminants.

overall_design: A gene expression pre analysis was made in deers naturally infected with Anaplasma ovis and Mycobacterium complex using Affymetrix Bos taurus microarray to detect differentialy expressed genes. The immune response genes with variation in expression were analyzed by real time RT-PCR in the same samples and a bigger group of deers. A real time RT-PCR analysis was also made in Bos taurus naturally infected with Anaplasma marignale.

first: Nieves

last: Ayllon

first: Tania

last: Carta

first: Christian

last: Gortázar

first: Jose

last: de la Fuente


title: Post-transcriptional regulation of stress response in a myo1Δ mutant of the budding yeast Saccharomyces cerevisiae

status: Public on Dec 08 2010

city: San Juan

first: José

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

summary: The microarrays experiments of three biological and one technical replicates were performed in YJR12 (wt) and YJR13 (myo1∆) strains. YJR12 (wild type) and YJR13 (myo1∆) strains were obtained as haploid segregants from a cross between YJR6 (myo1::HIS5 strain) and BY4741 (obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) with continuous shaking at 200 rpm.  RNA  was extracted from ribosomal pellets  using the RNeasy Mini Kit (Qiagen, Valencia, CA) following  the manufacturer’s instructions. RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies). The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following the manufacturer’s instructions. 1.0 µg of RNA extracted form ribosomal pellets from each sample was amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies). The amplified cRNA was labeled with 10mM Cyanine 5-CTP (Cy5) or Cyanine 3-CTP (Cy3) (Perkin Elmer Life Sciences). Labeled cRNA’s were purified with Qiagen RNeasy mini spin columns and dye incorporation was monitored on an Agilent Bioanalyzer. Hybridization of Cy5 and Cy3 labeled cRNA’s were performed using Yeast Oligo Microarray slides and hybridization kit from Agilent Technologies (Sheldon Manufacturing) at 60ºC for 17 hours. Slides were washed and scanned with a VersArray Chip Reader system (BioRad, Hercules, CA) at a resolution of 5mm with detector sensitivity values between 704-800 and laser power at 85%. Scanned images were transferred to the Imagene 3.0 software (Biodiscovery) for further analysis to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 TIFF files. The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity. The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array. After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated. The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change after background correction and normalization. An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.018 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma program.

overall_design: Previous analysis of global mRNA expression in Saccharomyces cerevisiae myosin type II deficient strains (myo1∆) revealed 547 genes related to the stress response that were proposed to be regulated at the transcriptional level. The objective of this study is to explore the post-transcriptional regulation of the stress response in these strains. We have identified 1,271 differentially regulated mRNAs bound to ribosomes extracted from myo1∆ strains compared to wild type controls. To assess the mode of regulation of these putative translationally regulated genes, ribosomal protein (RP) mRNAs were analyzed for their polysomal distribution in sucrose gradient fractions of myo1∆ and wild-type (wt) cells. Our analysis of three representative RP mRNAs showed that RPS8A, RPL7B and RPL3 were recruited from heavy to lighter polyribosome fractions in myo1∆, suggesting that these RP mRNAs were less efficiently translated. Western blot analysis revealed accumulation of the phosphorylated form of eukaryotic translation initiation factor 2 (eIF2α-P) in myo1Δ strains and RPS8A, RPL7B and RPL3 mRNAs were found co-precipitated with immunoprecipitated eIF2α-P, suggesting a direct association between eIF2α-P and translationally regulated RP mRNAs. In yeast, GCN2 codes for the only eIF2α kinase that is directly regulated by TOR (target of rapamycin) pathway. Repression of TOR by rapamycin in a myo1Δ strain did not increase levels of eIF2α-P yet, a gcn2Δmyo1Δ strain exhibited a severe synthetic growth defect suggesting an important survival role for TOR mediated translational regulation in these strains. Reduced steady state levels of the translation initiation factor eIF4G, were also observed in myo1Δ further supporting the regulation of translation by the TOR pathway. These findings support the conclusion that post-transcriptional control specifically by translation inhibition is a key component of the stress response in yeast.

first: M

last: Rivera-Ruiz

first: J


title: Genome-wide methylation analysis of esophageal squamous cell carcinoma

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

summary: Genome-wide methylation analysis was performed by methylated DNA immunoprecipitation-CGI microarray analysis.

overall_design: A pool of four cancer samples without lymph node metastasis, two pools of four cancer samples with lymph node metastasis, and three metastatic lymph nodes were prepared from the patients, and analyzed by MeDIP-CGI microarray.

first: Ken

last: Gyobu

first: Toshikazu

last: Ushijima


title: Chromatin-associated protein kinase C-0 regulates an inducible gene expression program and microRNAs in human T lymphocytes

status: Public on Dec 14 2010

city: Forest Hill

first: Russell

middle: Leigh

last: McInnes

state: Vic

address: 347 Burwood Hwy

department: LSCA

country: Australia

institute: Agilent Technologies

summary: Studies in yeast have demonstrated that signalling kinases with well known cytoplasmic functions have a surprisingly active role in the nucleus, where they are tethered to chromatin and modulate gene expression programs. Here we provide evidence for a novel function of the signal transduction kinase, protein kinase C-theta (PKC-0) that physically associates with the proximal regulatory regions of key inducible immune response genes in human T cells. Chromatin-anchored PKC-q forms hitherto undescribed nuclear complexes by interacting with active RNA polymerase II, the histone kinase MSK-1 and the adaptor molecule 14-3-3z. ChIP-on-Chip analysis reveals that PKC-0 binds directly to both the promoter and transcribed regions of genes, as well as to the promoters of microRNA genes implicated in cell migration and invasion. Moreover, enforced expression of these microRNAs is associated with heightened production of mRNAs encoding a distinct subset of inducible immune response genes. Collectively, these data suggest that in addition to its well known role as a cytoplasmic signalling kinase, PKC-0 controls immune gene expression within the nucleus of T cells by participating in chromatin-associated signalling complexes

overall_design: PKC-0 and Pol II ChIP DNA were pooled from five independent ChIP assay experiments that were first individually validated by real-time PCR. Pooled ChIP samples were subsequently amplified based on one round of the whole genome amplification method using the WGA2 kit (Sigma-Aldrich), as described previously (O'Geen, Hollenhorst, Dindot). An alternate random primed and linker-mediated PCR amplification protocol was compared with the WGA2 kit using quantitative real-time PCR, which generated similar yields of amplified material, but failed to preserve the degree of enrichment after the linker-mediated PCR amplification (data not shown). Labelling, hybridization and scanning were performed as described in the Mammalian ChIP-on-chip protocol (version 9.1; Agilent Technologies). Briefly, the control and PKC-0 or Pol II ChIP DNA were labelled with 5 ug cyanine-3 and 5 ug cyanine-5 (Invitrogen BioPrime CGH labeling kit), respectively. Samples were hybridised on each microarray slide for 40 h at 65°C. Agilent human promoter microarrays were utilised comprising of two slides per set defined to cover ~17,000 promoters of human transcripts from -5.5 to +2.5 Kb relative to transcriptional start site. The microarrays were scanned on an Agilent scanner (G2565BA) at 100% PMT gain. Two replicates of each ChIP-on-chip experiment were performed.

first: Elissa

last: Sutcliffe

first: Karen

last: Bunting

first: Yi

middle: Q

last: He

first: Jasmine

last: Li

first: Anjum

last: Zafar

first: Elizabeth

last: Hindmarsh

first: Christopher

last: Parish

first: Toshiki

last: Taya

first: Peter

last: Milburn

first: Sudha

last: Rao


title: Effect of changing light regimes on Dinoroseobacter shibae DFL12 growth

status: Public on Dec 03 2010

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493


title: CpG Methylation profile of Invasive Prostate Cancer Cells compared to Non-invasive

status: Public on Dec 04 2010

city: Frederick

first: Lesley

last: Mathews

address: 1050 Boyles Street Bldg 560 Rm 21-81

department: Laboratory of Cancer Prevention

institute: National Cancer Institute

summary:
Two established cell lines, LNCaP and DU145 and two primary prostate cancer cell lines, PCSC1-2 were invaded toward a stem cell media through Matrigel.
DNA was isolated from Non-invasive cells and invasive cells.

overall_design: Methylated DNA was isolated from each sample using the Methyl Collector kit from Active Motif. Methylated and Non-Methylated DNA was dye labeled and applied to 244K Human promoter tiling arrays.

first: William

middle: L

last: Farrar


title: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida

status: Public on Dec 01 2010

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

institute: University of Tromsø


title: A serine protease inhibitor induces necrosis of infected macrophages within granulomas during activation of tuberculosis

first: Hans-Joachim

last: Mollenkopf

summary: Granulomas function in humans during tuberculosis by focusing production of host antimicrobial factors against the causative bacterial agent Mycobacterium tuberculosis to contain infection. We show that mice unable to produce nitric oxide –itself an important antimicrobial molecule- demonstrate functional granulomas in the lung able to control infection after dermal infection. Disease in the lung was activated by administration of neutralising antibody against either TNF-α, which disrupted granuloma integrity, or INF-γ, which resulted in development of caseous necrosis within granulomas reminiscent of active human tuberculosis. In the latter case, the serpin protease inhibitor serpinb3a and its target protease, cathepsin G are highly expressed in cells local to necrotic regions in granulomas and serpinb3a induces necrosis of infected macrophages independently of cathepsin G binding. Therefore a single host protein is capable of inducing necrosis and bacterial growth during intracellular infection.

first: Stephen

middle: T

last: Reece

first: Stefan

last: Kaufmann


title: A mesoderm-derived mesenchymal stem/stromal cells (MSC) precursor

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin


title: Gene expression analysis of 15-Lipoxygenase 2 (15-LOX2) transgenic mice

status: Public on Dec 16 2010

city: Smithville

first: Dean

last: Tang

state: TX

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

summary: 15-Lipoxygenase 2 (15-LOX2), a human-specific lipid-peroxidizing enzyme, is mainly expressed in luminal compartment of the normal prostate and often decreased or lost in prostate cancer (PCa). Previous studies from our lab implicate 15-LOX2 as a functional tumor suppressor. To better understand the biological role of 15-LOX2 in vivo, we established prostate-specific 15-LOX2 transgenic mice using the ARR2PB promoter. Unexpectedly, 15-LOX2 expression resulted in age-dependent prostatic hyperplasia. Interestingly, transgenic expression of 15-LOX2sv-b, a splice variant that lacks the arachidonic acid metabolizing activity, also induced hyperplasia and enlargement of the prostate. Prostatic hyperplasia induced by both 15-LOX2 and 15-LOX2sv-b was associated with an increase in proliferative (i..e., Ki67+) and luminal cells but 15-LOX2-induced hyperplasia was also accompanied by a prominent increase in basal cells. Microarray analysis revealed distinct gene expression profiles that could help explain the prostate phenotypes. Strikingly, 15-LOX2 (but not 15-LOX2sv-b) transgenic prostate showed up-regulation of several well-known stem/progenitor cell molecules including Sca-1, Trop2, p63 and Psca. Prostatic hyperplasia caused by both 15-LOX2 and 15-LOX2sv-b did not progress to PCa over >5 years of observations. Mechanistically, hyperplastic prostate lobes (especially those of the 15-LOX2 mice) showed a dramatic increase in senescent cells revealed by increased SA-ßgal, HP1, and p27Kip1 staining. Collectively, our results suggest that 15-LOX2 expression in mouse prostate leads to hyperplasia that activates the senescence checkpoint, which may in turn function as a barrier to tumor development.

overall_design: RNA was isolated from combined prostatic lobes of 6 mice (to reduce inter-animal variation) from ~2.5 month old (young; y) 15-LOX2 (line fl26), 15-LOX2sv-b (line svb9), wild type (wt) and ~15 month old (old; o) wt mice and hybridized onto Agilent's whole mouse genome oligoarrays arrays (G4122A) in fl26y(vs)wty, svb9y(vs)wty and wto(vs)wty combinations. The hybridizations were carried out in duplicates using an independent set of samples (biological replicates).

first: Mahipal

middle: V

last: Suraneni

first: Robin

last: Schneider-Broussard

first: John

last: Moore

first: Tammy

last: Calhoun-Davis

first: Carlos

last: Maldonado

first: Hangwen

first: Donna

last: Kusewitt

first: Peiying

last: Yang

first: Robert

middle: A

last: Newman

first: Jianhua

last: Hu


title: Validation and copy number variation in inbred and wild mice

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

institute: University of Lausanne

sample_organism:
Mus musculus
Mus musculus domesticus
Mus spretus


title: Geobacter sulfurreducens biofilm transcriptomics

status: Public on Nov 23 2010

city: Washington

first: Sarah

last: Strycharz

state: DC

address: 4555 Overlook Ave.

department: CBMSE

institute: Naval Research Laboratory


title: Genetic abnormalities in GBM brain tumors

status: Public on Nov 21 2010

city: new york

first: Viviane

last: Tabar

state: NY

address: 411 east 67th street

department: neurosurgery

institute: MSKCC

summary: Examine the genetic abnormality in brain tumors

overall_design: Genomic DNA were extracted from frozen brain tumor samples and CGH assay were performed to compare the similarity genomic abnormality among different cell groups.

first: Cameron

last: Brennan


title: Genetic abnormalities in various cell subpopulations of GBM brain tumors

summary: GBM is a heterogenous tumor. Based on membrane protein expression, the GBM single cell dissociates were seperated into different subfractions by FACS assay. The genomic aberration among each populations were compared by analysis of CGH data.

overall_design: Genomic DNA were extracted from sorted cell population and CGH assay were performed to compare the similarity genomic abnormality among different cell groups.

first: Rong

last: Wang


title: Gene expression patterns of biopsies from colonoscopies taken in 2007, 2008, and 2009 of an ulcerative colitis patient infected with Trichuris trichiura

status: Public on Nov 20 2010

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF


title: Characterization of Stem-cell derived Retinal Pigmented Epithelium (RPE)

status: Public on Nov 10 2010

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: To assess the geome-wide similarities between primary fetal retinal pigmented epithelium (RPE) and stem-cell derived RPE, we performed whole genome microarray expression on primary RPE and both embryonic stem cell (ESC) derived RPE and induced pluripotent stem cell (iPSC) derived RPE. We found ES-derived RPE better resembles fetal RPE than iPS-derived RPE.

overall_design: Gene expression was measured in primary fetal RPE, ES-derived RPE, iPS-derived RPE. ES cells and BJ fibroblasts were used as controls.

first: Jo-Ling

last: Liao

first: Juehua

last: Yu


title: RNA profiles of embryonic stem cells generated from in vitro produced or in vivo derived rhesus preimplantation embryos

status: Public on Nov 09 2010

city: Detroit

first: Carol

state: Michigan

address: 275 East Hancock Street

department: Physiology and Obstetrics and Gynecology

institute: Wayne State University

summary: It is often overlooked that human ESCs are generated from in vitro cultured, often surplus/‘discard’, embryos considered unsuitable for transfer in infertility clinics. In vitro culture of preimplantation embryos has been associated with a number of perturbations, including ultrastructure, gene expression, metabolism and post-transfer development. We report here the transcriptional profiles characteristic of ESC lines generated from either in vitro cultured or in vivo derived embryos.

overall_design:
Embryonic stem cell RNAs were prepared from samples collected from 8 different lines. Four lines were generated from preimplantation embryos derived in vivo (R series; Thomson et al 1995) and four lines were generated from in vitro cultured preimplantation embryos (Ormes series; Mitalipov et al 2003).

ChipInspector carries out significance analysis on the single probe level.  Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

first: A

last: Harvey

first: J

last: Byrne

first: S

last: Mao

first: C

last: Lalancette

first: B

last: Bavister

last: Mitalipov

last: Krawetz

last: Brenner


title: Sprouting transcriptome in cortical neurons: aged

status: Public on Nov 15 2010

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

summary: Selective isolation of total RNA and then whole genome expression analysis of sprouting neurons in peri-infarct cortex of the adult rat after stroke, compared to adjacent neurons that have not sprouted a new connection, in young adult (2 months) and aged (2 years) animals.

overall_design: Two different fluorescent conjugates of the tracer cholera toxin B (CTb), CTb-Alexa 488 and CTb-Alexa 647 (Molecular Probes), were sequentially injected into peri-infarct cortex at the sites of post-stroke axonal sprouting using a picospritzer pressure injection system. After survival periods of 7 days and 21 days (separate cohorts of animals), CTb-647 was injected exactly within CTb-488 injection site. Seven days after the second tracer injection, laser capture microdissection (LCM) was used to capture ~300 neurons for each cell type. Total RNA was isolated from captured cells and subjected to two rounds of T7 amplification.

first: Songlin

last: Li

first: Justine

last: Overman

first: Diana

last: Katsman

first: CJ

last: Donnelly

first: Jeffrey

last: Twiss

first: Roman

last: Giger

first: Daniel

last: Geschwind

first: Stanley

last: Carmichael


title: microarray analysis of rat terminal end buds at neonatal diethlstilbestrol administration rats

status: Public on Nov 06 2010

city: sakuragaoka

first: souda

last: masakazu

state: kagoshima/kagoshima

department: tumor pathology, field of oncology

institute: kagoshima university graduate school of medical and dental sciences

summary: Diethlstilbestrol (DES) is a synthetic estrogen prescribed to several millions of pregnant women worldwide. The risk for breast cancer after age 40 in women prenatally exposed to DES has been reported, however, the precise mechanism of susceptibilities to breast cancer remains to be resolved. To understand the mechanism of effect of intrauterine exposure to DES on human mammary glands at peripubertal stage, we investigated the global gene expression profile of terminal end buds (TEBs), the target of carcinogen, in rat mammary glamds at postnatal days (PND) 35 and 49, equivalent to peripubertal stage in human, exposed to low or high dose of DES at neonatal period. In all group, the number of TEBs was gradually increased and peaked at PND35 and decreased at PND49. At PND 35 and 49, low dose of DES-treated group showed highest number of TEBs. At PND35, β- and γ-casein mRNA expression inreased 8.19-fold and 26.05-fold, respectively, and the most significant network revealed by IPA analyses showed relevance of NF-κB in low dose of DES-treated group. The present findings suggested that deregulation of mammary gland differentiation and development-related genes group may contribute to the increase of number of TEBs at critical period of carcinogen susceptibilities.

overall_design: Experiment: We used laser capture microdissection to specifically isolate the cells from terminal end buds (TEBs) in rat mammary gland at 35 and 49 days after birth. Inbred Sprague-Dawley female rats were subcutaneously given 0.05ml sesame oil (group I, control) and either 1 μg (group II) or 100 μg (group III) diethlstilbestrol (DES, Sigma Chemical Co., St. Louis, Mo. USA) dissolved in 0.05 ml sesame oil within 24 hr of birth. Animal were weaned at 21 days of birth and each group of rats was autopsied at 35 and 49 days of birth. From group I (35 days of birth: n=2, 49 days of birth: n=2), group II (35 days of birth: n=2, 49 days of birth: n=2), group III (35 days of birth: n=2, 49 days of birth: n=2), we performed a hybridization, respectively.

first: Masakazu

last: Souda

first: Yoshihisa

last: Umekita

first: Akihide

last: Tanimoto

first: Hiroki

last: Yoshida


title: Confinement stress in HR and LR trout lines

status: Public on Nov 24 2010

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway


title: The effects of novel adjuvant complex and CpG ODN on host immune response to recombinant Eimeria profilin vaccine

status: Public on Oct 28 2010

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

summary: This study investigated the ability of two novel adjuvant formulations, QCDC (Quil A/cholesterol/DDA/Carbopol) and QCDCR (QCDC/Bay R1005), in combination with a recombinant profilin vaccine, to modulate host protective immunity and to alter new gene expression during experimental avian coccidiosis.

overall_design: Four-condition experiment, Profilin only vs. Non-vaccination, Profilin only vs. Co-vaccination of QCDC plus profilin, Profilin only vs. Co-vaccination of QCDCR plus profilin, Biological replicates: 2 profilin only replicates, 2 Non-vaccination replicates, 2 QCDC plus profilin replicates, 2 QCDCR plus profilin replicates with dye-switching.

first: Duk-Kyung

first: Hyun

last: Lillehoj


title: Sprouting transcriptome in cortical neurons: young

first: Giovanni

last: Coppola

first: Songlin

middle: J


title: Hedgehog targets in the Drosophila embryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling

status: Public on Nov 03 2010

first: Brian

last: Biehs

address: 505 Parnassus Ave

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


title: Sprouting transcriptome in cortical neurons


title: Effects of dynamic compressive loading on MSC chondrogenesis

status: Public on Nov 01 2010

city: Philadelphia

first: Alice

last: Huang

state: PA

address: 424 Stemmler Hall, 3450 Hamilton Walk

department: Bioengineering

institute: University of Pennsylvania

summary: Long-term dynamic compression enhanced the mechanical properties of MSC-seeded constructs only when loading was initiated after 21 days of chondrogenic differentiation.  This study examined the molecular differences of chondrogenic MSCs compared to undifferentiated MSCs (TGF-beta vs no TGF-beta) and the effects of dynamic loading on MSC chondrogenesis (loading vs free-swelling).

overall_design: Free-swelling MSC-seeded constructs were cultured for 21 days in chemically defined media. Chondrogenesis was induced with TGF-beta3. Undifferentiated controls were maintained in parallel. After 21 days of chondrogenic differentiation, a subset of constructs were subjected to 21 days of dynamic compressive loading. On days 21 and 42, construct mechanical properties and biochemical content were assessed. Microarray analysis was carried out on day 3, day 21 and day 42 constructs. 6 arrays.

first: Megan

last: Farrell

first: Minwook

first: Robert

last: Mauck


title: A wholly-defined Agilent microarray spike-in dataset

status: Public on Oct 23 2010

city: Buffalo

first: Qianqian

last: Zhu

address: 701 Ellicott St.

institute: State University of New York at Buffalo

summary: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this “Ag Spike”dataset is identical to that of our previous Platinum Spike dataset (GSE21344) and therefore allows direct cross-platform comparison. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.

overall_design: We used the same 28 PCR pools that had been used before to generate the Platinum-Spike dataset (GSE21344). These pools contain PCR products from 5725 Drosophila Gene Collection release 1.0 (DGCr1) cDNA clones. We mixed PCR products from all pools together with specified relative abundance to generate two samples representing the A and B conditions. Both samples were in vitro transcribed and then labeled with Cy3 and Cy5 fluorescent dye. Labeled A samples were hybridized with B samples labeled with reverse dye to three Agilent Drosophila Gene Expression microarrays. The process from in vitro transcription to hybridization was repeated twice. At the end we generated 12 arrays that were randomly placed in three independent slides to remove potential systematic error due to array position.

first: Marc

last: Halfon