title: Chicken erythrocytes stimulated with LPS, PGN and Poly(I:C)

status: Public on Nov 22 2011

city: Cerdanyola del Vallès

first: Davínia

middle: Morera

last: Capdevila

address: Edifici Biociències, ala sud

department: Biologia cel.lular, Immunologia i Fisiologia

institute: Universitat Autònoma de Barcelona

summary: Erythrocytes represent the most abundant cell type of the bloodstream in all vertebrates. The principal feature that differenciates erythrocytes of non-mammals is that unlike mammals they mantain the nucleus in their terminal differentiation. While the main function associated to erythrocytes is the oxygen and carbon dioxide transport, some other functions, no less important, have been attributed to these cells. The focus of this study was to investigate the response of cultured chicken erythrocytes to bacterial lipopolysaccharide (LPS), bacterial peptidoglycan (PGN) and to the analog viral dsRNA Poly(I:C) using a comercial microarray platform from Agilent.

overall_design: Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 0111:B4, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at  5 μg/ml. All culture plates were incubated for 12h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Nanodrop1000 (ThermoScientific) and Bioanalyzer 2100 (Agilent Technologies) respectively. Three biological replicates were used.

last: Morera

first: Nerea

last: Roher

first: Simon

last: Mackenzie


title: Daphnia magna exposed to narcotics and polar narcotics

status: Public on Feb 01 2012

city: Antwerpen

first: Nathalie

last: Dom

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

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

overall_design: Refer to individual Series


title: Gene expression levels with various artificial mutations and inter-species array

status: Public on Nov 01 2011

city: Koto

first: Jun

last: Sese

state: Tokyo

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: The transcriptome of anthers of  rice gamyb mutant expressing various GAMYB homologs was measured at the microspore stage.

status: Public on Nov 07 2011

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: To confirm the function of the GAMYB homologs for Selaginella moellendorffii and Physcomitrella patens in rice cells, we examined the expression profile in the anthers of transgenic plants, which OsGAMYB, SmGAMYB, or PpGAMYB2 is expressed under the control of the rice GAMYB promoter in rice gamy mutant.

overall_design: Expression profiling was conducted using rice 4x44K microarray RAP-DB (G2519F#15241). The microarray was used to profile gene expression in OsGAMYB:OsGAMYB, OsGAMYB:SmGAMYB, OsGAMYB:PpGAMYB2 and vector transgenic plants. To assess the reproducibility of the microarray analysis, each microarray experiment was performed twice using RNA samples that had been isolated independently (i.e., two biological replicates), and included a dye-swapping test as a technical replicate for each biological replicate.

first: Makoto

last: Matsuoka


title: Comparison of the effects of early pregnancy with human interferon, alpha 2 (IFNA2) on gene expression in bovine endometrium

status: Public on Oct 31 2011

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: Interferon tau (IFNT), a Type I IFN similar to alpha IFNs (IFNA), is the pregnancy recognition signal, produced by the ruminant conceptus. To elucidate specific effects of bovine IFNT and of other conceptus-derived factors, endometrial gene expression changes during early pregnancy were compared to gene expression changes after intrauterine application of human IFNA2. In study one, endometrial tissue samples were obtained on days (D) 12, 15, and 18 post-mating from nonpregnant or pregnant heifers. In study two, heifers were treated from D14 to D16 of the estrous cycle with an intrauterine device releasing IFNA2 or placebo lipid extrudates or PBS only as controls. Endometrial biopsies were collected after flushing the uterus. All samples from both experiments were analyzed with an Affymetrix Bovine Genome Array. Study one revealed differential gene expression between pregnant and nonpregnant endometria on D15 and D18. In study two, IFNA2 treatment resulted in differential gene expression in the bovine endometrium. Comparison of the datasets from both studies identified genes that were differentially expressed in response to IFNA2 but not in response to pregnancy on D15 or D18. Vice versa, genes were found as differentially expressed during pregnancy but not after IFNA2 treatment. In study three, spatiotemporal alterations in expression of selected genes were determined in uteri from nonpregnant and early pregnant heifers using in situ hybridization. The findings of this study suggest differential effects of bovine IFNT compared to human IFNA2 and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT.

overall_design:
Study I: Early pregnancy; day 12 of pregnancy (n=5 heifers), day 15 of pregnancy (n=3), day 18 of pregnancy (n=4), day 12 cyclic controls (n=5), day 15 cyclic controls (n=3), day 18 cyclic controls (n=4).
Study II: Treatment with human interferon alpha (IFNA); IFNA treatment group (IFNA, n=3 heifers), placebo group (PLAC, n=3 heifers), control group (CONT, n=3 heifers).

first: Eckhard

last: Wolf


title: Network inference tools for the human transcriptome

status: Public on Nov 29 2011

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University


title: Regulation of cold-induced gene expression by HY5

status: Public on Nov 23 2011

city: Madrid

first: Rafael

last: Catalá

state: Madrid

address: Ramiro de Maeztu nº9

department: Biologia Medioambiental

country: Spain

institute: CIB-CSIC

summary: Characterization of the role of HY5 in controlling low temperature-regulated gene expression.

overall_design: Two-condition experiment, Ler vs. hy5-1 plants. Biological replicates: 3 cold-exposed replicates

last: Catala

first: Joaquin

last: Medina

first: Julio

last: Salinas


title: R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions

status: Public on Nov 09 2011

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: Transcriptional profiling of R. sphaeroides Δirr under iron limitation (-Fe) compared to control R. sphaeroides Δirr under normal growth conditions (+Fe).

overall_design: Two strain experiment under normal iron (+Fe) and iron limitation (-Fe) conditions. 6 Biological replicates, independently grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

first: Verena

last: Peuser

first: Sebastian

last: Metz


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus)

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC


title: Transcriptional response of  endometrium and the bovine preimplantative embryo to subclinical inflamation of the uterine environment

city: Bonn

first: Michael

last: Hoelker

address: Endenicher Allee 15

institute: Universtity of Bonn

summary: Combining the cytological as well as gene expression changes in the endometrium is required to understand the effects of subclinical endometritis on endometrium as well as embryo. Hence, the present study was aimed to investigate the gene expression profiles of subclinical endometrium as well the effect of the inflamed environment on the gene expression profile of the developing preimplantative embryo.

overall_design: Endometrial samples were collected from each 49 cow using the cytobrush technique, 2 h before insemination (Day 0 of the estrous cycle after superovulation) and immediately before flushing (Day 7 of the estrous cycle after superovulation). The endometrial samples were categorized based on the PMN value as healthy endometrium (HE, PMN = 0) and subclinical endometritis (SE, endometrial PMN > 0).  Flushed embryos were snap frozen for later molecular genetic analysis. Finally, endometrial samples were pooled according to the endometrial health status of the donor cows (HE vs. SE) at the time of insemination and at the time of flushing. The corresponding samples were subjected global gene expression profile. Moreover embryos flushed from HE and SE cows were pooled together according to the health status of their donors at time of flushing. Those embryos were also used for global embryonic gene expression analysis in relation to the health status of the donor cows.

first: Dessie

last: Salilew-Wondin

first: Marc

last: Drillich

first: Grosse-Brinkhaus

last: Christine

first: Franca

last: Rings

first: Nasser

last: Ghanem

first: Leopold

last: Goetze

first: Dawit

last: Tesfaye

first: Karl

last: Schellander

first: Wolfgang

last: Heuwieser


title: Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

status: Public on Oct 19 2011

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

institute: University of Bielefeld


title: Transcriptional Profiles Induced by the Aryl Hydrocarbon Receptor Agonists 2,3,7,8-Tetrachlorodibenzo-p-dioxin, 2,3,7,8-Tetrachlorodibenzofuran and 2,3,4,7,8-Pentachlorodibenzofuran in Primary Rat Hepatocytes

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

summary: Transcriptional profiling of primary rat hepatocytes exposed to high and low doses of three compounds, as well as untreated cells.  All samples were co-hybridized with DMSO controls.

overall_design: A direct two-color experiment design, with each treated sample co-hybridized with a DMSO control. Hepatocytes derived from two animals were used as biological replicates. Four microarrays were completed for each chemical/dose combination. The four replicate arrays represent two dye-swapped microarrays for each of the two animals.

first: J

middle: C

first: Alan

last: Dombkowski


title: Effects of pregnancy and progesterone supplementation on endometrial gene expression in cattle

status: Public on Oct 18 2011

first: Jai Prakash

last: Mehta

address: Veterinary Science Center, University College Dublin

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

country: Ireland

institute: University College Dublin, Ireland

summary: An increase in circulating progesterone (P4) concentrations is associated with increased pregnancy success in beef and dairy cattle. Our objective was to ascertain differential effects of elevated P4 concentrations following conception on endometrial gene expression in beef heifers on Days 5, 7, 13 and 16 of pregnancy, corresponding to the morula, blastocyst, elongation and maternal recognition of pregnancy stages, respectively. Estrus was synchronized in beef heifers (N=263). Two-thirds (N=140) were inseminated (Day 0), and all animals were randomly assigned to one of the following treatments: (i) pregnant, high P4; (ii) pregnant, normal P4; (iii) cycling, high P4; (iv) and cycling, normal P4. All high P4 groups received a P4 release intravaginal device (PRID) on Day 3 post-estrus/mating. Tissue was collected on Days 5, 7, 13 or 16 of the cycle or pregnancy, and pregnancy was confirmed by the presence of an appropriately developed embryo/conceptus.  PRID insertion elevated (P<0.05) P4 concentrations from Day 3.5 to 8 compared with untreated animals and conceptus size was larger (P<0.05) in animals with elevated P4 on Days 13 and 16 compared with normal P4. Total RNA was extracted from predominantly intercaruncular endometria from the ipsilateral uterine horn. Samples from individual heifers were selected on the basis of their P4 profiles and gene expression was analyzed using bovine Affymetrix microarrays (N=5 per treatment per time point). Microarray data from analyses using Bioconductor GCRMA and Limma packages were subjected to a modified t-test and P-values were adjusted for multiple testing using the Benjamin and Hochberg false discovery rate method. Differentially expressed genes were selected on the basis of an adjusted P-value of <0.01. There were no detectable differences in gene expression in endometria from pregnant and cyclic heifers on Days 5, 7 and 13 post-estrus, but, the expression of 764 genes was altered due to the presence of the conceptus at maternal recognition of pregnancy (Day 16). On Days 5 and 7, elevated P4 in pregnant heifers, altered the expression of 36 and 124 genes respectively but on Days 13 and 16 there were relatively few DEG between high and normal P4 heifers (15 and 25). Of the genes that were differentially regulated by P4, the majority were unique to a specific day of the estrous cycle/early pregnancy. In conclusion, gene expression in endometria did not differ between pregnant and cycling heifers until Day 16 of pregnancy (i.e. the time of maternal recognition of pregnancy and production of interferon tau by conceptus trophectoderm); however, elevating P4 in early pregnancy programmed changes in gene expression in endometria that are hypothesized to impact early conceptus growth and development. Thus, on Days 5, 7 and 13 differential gene expression was affected by P4, but on Day 16 the conceptus primarily influenced gene expression in uterine endometria of heifers.

overall_design: Endometiral samples were taken from estrous synchronized beef heifers that were either cyclic or confirmed pregnant with either normal or high concentrations of progesterone on Day 5, 7, 13 and 16 of the estrous cycle/early pregnancy.

first: Niamh

last: Forde

first: James

middle: F

last: Roche

first: Pat

last: Lonergan


title: CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae

status: Public on Oct 01 2011

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen


title: ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae

status: Public on Nov 02 2011

first: Tomas

last: Kloosterman

department: Natural Sciences

institute: University of Groningen


title: Effect of cryopreservation on rabbit late blastocyst transcriptome

status: Public on Sep 23 2011

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

institute: Universidad Politécnica Valencia

summary: Studies on embryo cryopreservation efficiency had been focused mainly on technical and embryo factors. While structural damages can be easily evaluated, physiological damages only can be estimated by analyzing their in vitro and in vivo development to later stages. In order to determine how cryopreservation process affect embryo pre-implantory development, a transcriptional microarray study has been performed comparing gene expression of 6 days old rabbit embryos, previously vitrified or frozen and transferred into recipients rabbit females, to their in vivo counterparts. For each experimental group, control, vitrified and frozen late blastocysts, total RNA was extracted from 3 pools of approximately 10 embryos and labeled with Cy3 or Cy5 dyes. Then, six competitive hybridizations were carried out including two dye-swaps to compensate dye-bias. A specifically microarray designed to study rabbit gene expression profiling, the Rabbit 44K oligonucleotide array (Agilent Technologies), was used in this study. Identification of differentially expressed transcripts from 6 day old blastocysts was achieved using the Limma algorithm, and functional annotation was performed by Blast2GO software. Compared to 6 day old in vivo derived embryos, viable vitrified embryos only present 3 differentially expressed genes, in contrast to frozen viable embryos with 24 genes upregulated and 46 genes downregulated. These results reveal that effects of cryopreservation still remain in late blastocyst pre-implantatory gene expression, and potential damage and alterations produced by vitrification and slow-freezing procedures are differentially resolved after 3 days of in vivo development.

overall_design: Transcriptional microarray study that compares gene expression of viable 6 day old rabbit embryos, previosly vitrified or frozen and tranferred into recipient rabbit females, to their in vivo counterparts. Experiment 1: Control embryos vs. Vitrified embryos and Experiment 2: Control embryos vs. Frozen embryos. Biological replicates used: 3 replicates for control embryos, 3 replicates for vitrified embryos and 3 replicates for frozen embryos.

first: M

middle: D

first: F

last: Marco-Jiménez

middle: S

last: Vicente


title: Chip-on-chip analysis of direct Nkx2.1 target genes in proliferating and differentiating epithelium in mouse lung development.

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

type: Genome binding/occupancy profiling by array

summary: Nkx2.1 is a critical regulator of mammalian lung development. It is expressed in epithelial cells at the initiation of lung organogenesis, becoming progressively restricted during development to bronchiolar and alveolar type II epithelial cells. In humans, it is a common marker of carcinomas of lung and thyroid origin and is highly amplified in 10-15% of lung adenocarcinomas. Despite its key role in development and disease only a few genes directly regulated by Nkx2.1 are known. To identify direct Nkx2.1target genes and pathways controlled by this transcription factor in vivo we analyzed, by chromatin immuno-precipitation (chip)-on-chip method, Nkx2.1 binding to DNA cis-elements in developing mouse lung. We analyzed embryonic day E11.5 lungs, when Nkx2.1 expressing cells are undergoing predominantly proliferation, and day E19.5, when Nkx2.1 expressing cells are undergoing predominantly differentiation. Many highly bound targets are known and well described, such as surfactant proteins and secretoglobins. Unique or common target genes involved in a variety of developmental and tumorigenic pathways were identified at each developmental time point. Positive regulation of cell proliferation was the highest overrepresented biological process at E11.5 while ion transport was the highest overrepresented biological process at E19.5. New identified targets include proliferation related genes such as E2F3, Met, Ccnb1, and Ccnb2. Nkx2.1 downregulation in mouse epithelial and human carcinoma cell lines reduced cell proliferation by arresting cells in the G2/M phase. Reduced expression of Nkx2.1 target genes in both cell lines supports a direct role of Nkx2.1 in regulation of cell proliferation genes. The identification of these transcriptional regulatory pathways in vivo aid us to understand Nkx2.1 function in lung development and link it to disease, since many of the identified targets are aberrantly up regulated in cancer cells.

overall_design: Developing mouse lung, 2 developmental time points E11.5 and E19.5, genomic DNA fragments immunoprecipitated with a-Nkx2.1  (07-601, Upstate-Millipore) vs input, E11.5, 2 biological replicates and E19.5, 3 biological replicates

first: Jean-Bosco

last: Tagne

first: Summet

last: Gupta

first: Steve

last: Shen

first: Meenakshi

last: Lakshminarayanan

first: Yuxia

last: Cao

first: Tom

last: Volkert

middle: I


title: Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka) muscle tissue

status: Public on Sep 10 2011

city: King Salmon

first: Scott

last: Pavey

state: Alaska

address: PO Box 7

department: Natural Resources

institute: Katmai National Park

summary: We sampled lake-type and riverine sockeye in the pristine natural habitats of Aniakchak National Monument and Preserve, Alaska USA.

overall_design: Samples were taken on the same day and close proximite in time. We sampled 17 riverine individuals from Albert Johnson Creek and 13 individuals from Surprise Lake. cDNA from a single individual on the Cy5 was compared with a reference of aRNA on the Cy3.


title: Comprehensive gene expression profiling of the rice root system based on developmental stages and tissue types

status: Public on Oct 26 2011

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: The root system is a crucial determinant of plant growth potential because of its important functions, e.g., acquisition of water and nutrients, structural support, and interaction with symbiotic organisms. Elucidating the molecular mechanisms of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants including rice. As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray analysis approach.

overall_design: We performed comprehensive microarray analysis of a rice crown root using laser microdissection and collected a total of 13 samples (3 replicates for each sample except for one sample, 38 total microarray data) representing 8 different developmental stages along the longitudinal axis and 3 distinct tissue-types along the radial axis at 2 different developmental stages. The 8 developmental stages represent root cap, division zone, elongation zone and maturation zone_I, II, III, IV and V. The 3 tissue-types represent epidermis/exodermis/sclerenchyma, cortex, and endodermis/pericycle/stele. In the maturation zone_V, the cortex consisted largely of aerenchyma (non-living cells) and was not used for the microarray analysis.

first: Hinako

last: Takehisa

first: Baltazar

last: Antonio

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: Substrate selectivity for semisynthetic CK2 proteins

status: Public on Oct 25 2011

city: Baltimore

first: Mary Katherine

last: Tarrant

state: MD

address: 725 N. Wolfe Street, 317 Hunterian Bldg.

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins University School of Medicine


title: Role of a short LOV protein in blue light- and singlet oxygen-dependent gene regulation in Rhodobacter sphaeroides

city: Giessen

first: Sebastian

middle: Harald Michael

last: Metz

department: Institut für Mikro- und Molekularbiologie

institute: Justus-Liebig-Universität Giessen

summary:
The facultatively photosynthetic bacterium Rhodobacter sphaeroides harbors an unusual LOV (light, oxygen, voltage) domain protein, RsLOV. While showing a characteristic photocycle, the protein misses a C - terminal output domain, similar to PpSB2 in Pseudomonas putida. Oxygen tension and light quantity are the two main responsible factors controlling the expression of photosynthesis genes in Rhodobacter sphaeroides. Two photoreceptor proteins are known to be involved in this regulation: the intensively studied AppA protein and the more recently identified cryptochrome-like protein CryB. Here we show by transcriptome and physiological studies that RsLOV is also involved in the regulation of photosynthetic gene expression. Our data further hint to a connection between RsLOV and the carbon hydrate metabolism, chemotaxis, as well as to the cellular response to photooxidative stress. RsLOV does not only affect blue light dependent gene expression but also redox-dependent regulation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: aCGH analysis of familial Alzheimer’s disease with presenilin 2 mutation patient-specific induced pluripotent stem cells

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

institute: Keio University

type: Genome variation profiling by genome tiling array

summary: We established two clones of induced pluripotent stem cells (iPSC) with the presenilin 2 mutation, N141 (PS2-1 iPSC and PS2-2 iPSC) by retroviral transduction of primary human fibroblasts. To detect the copy number dependent gene expression profiles in primary fibroblast carrying the presenilin 2 mutation N141(before reprogramming) and PS2-1 iPSC and PS2-2 iPSC(after reprogramming), this experiment was designed.

overall_design: Genomic DNA of primary fibroblasts carrying the presenilin 2 mutation N141 and undifferentiated PS2-1 iPSC and PS2-2 iPSC were collected. Then, they were applied in this experiment.

first: Daisuke

last: Ito


title: Lysyl oxidase-like 2 (LOXL2) a new regulator of cell polarity required for metastatic dissemination of basal-like breast carcinomas

status: Public on Oct 21 2011

first: Gema

last: Moreno-Bueno

address: Arturo Duperier

department: Biochemistry

institute: IIB

summary:
Basal-like breast carcinoma is characterized by the expression of basal/myoepithelial markers, undifferentiated phenotype, highly aggressive behaviour and a frequent triple negative status (ESR-, PR-, Her2neu-). We have previously shown that epithelial-mesenchymal transition (EMT) occurs in basal-like breast tumours and identified Lysyl- Oxidase-Like 2 (LOXL2) as an EMT player and  a poor prognosis marker in squamous cell carcinomas.  We now show that LOXL2 mRNA is overexpressed in basal-like human breast carcinomas.
Identification of new molecular markers in basal breast carcinomas

overall_design: 58 (IDC) infiltrative breast ductal carcinoma samples (Grade 3)

first: G

first: F

last: Salvador

first: A

last: Martin

last: Floristan

first: E

middle: P

last: Cuevas

first: V

last: Santos

last: Montes

first: S

last: Morales

first: M

last: Castilla

last: Rojo-Sebastian

last: Martínez

first: D

last: Hardisson

first: K

last: Csiszar

last: Portillo

first: H

last: Peinado

first: J

last: Palacios

last: Cano


title: Expression analysis of various fungi grown in glucose or xylose

status: Public on Oct 20 2011

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

institute: Dickinson College

type: Expression profiling by genome tiling array

sample_organism:
Candida albicans WO-1
Scheffersomyces stipitis CBS 6054
Lodderomyces elongisporus NRRL YB-4239
Yamadazyma tenuis ATCC 10573
Spathaspora passalidarum NRRL Y-27907


title: Genes regulated by TGF-beta in bovine articular chondrocytes

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

summary: Bovine articular chondrocytes were grown in micromass culture and were either untreated or treated with 5 ng TGF-b1/ml for 8 hours to identify genes regulated by TGF-b.

overall_design: Six total samples were analyzed. Three biological replicates of untreated bovine articular chondrocytes grown in micromass culture and three biological replicates of bovine articular chondrocytes grown in micromass culture and treated with 5ng TGF-b1/ ml for 8 hours.


title: Jasmonic acid-responsive genes in suspension-cultured rice cells

status: Public on Oct 06 2011

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Jasmonic acid (JA) is involved in various developmental processes and defense responses against abiotic and biotic stresses. We identified JA-responsive genes in suspension-cultured rice cells 2-12 h after treatment using rice 44k microarray.

overall_design: Expression profiling in rice cells treated with JA for 2, 4, 6, 8 and 12 h was compared with that in untreated control using two-color method with two biological replicates.

first: Koji

last: Miyamoto

first: Takafumi

last: Shimizu

first: Hideaki

last: Nojiri

first: Hisakazu

last: Yamane


title: Jasmonic acid-responsive genes in rice leaves

summary: Jasmonic acid (JA) is involved in various developmental processes and defense responses against abiotic and biotic stresses. We identified JA-responsive genes in rice leaves 6-48 h after treatment using rice 44k microarray.

overall_design: Expression profiling in rice leaves treated with JA for 6, 12, 24 and 48 h was compared with that in the corresponding mock control using two-color method with two biological replicates.

first: Fengqiu

last: Lin


title: Salivary cytokine alterations in HIV infection

status: Public on Sep 09 2011

city: New York

first: Minal

last: Dalvi

state: NY

address: 345 East 24th Street, Rm 917

department: Department of Basic Science

institute: New York University

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

overall_design: Refer to individual Series


title: Jasmonic acid-responsive genes in rice


title: Dll1 acts as a tumor suppressor in neural stem cells to induce an astroglial lineage-restricted glioblastoma

status: Public on Sep 24 2011

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: There is increasing evidence for tissue stem cells as potential source for cancers. However, the cellular and molecular mechanisms at the origin of this transformation remain elusive. Here we show that Delta-like1 (Dll1) mutation induces the oncogenic transformation of neural stem cell–derived neurospheres into oncogenic spheres capable of generating histological and molecular human glioblastoma (GBM)-like tumors upon subcutaneous and intracranial transplantations into nude mice. Serial transplantation assays suggest that Dll1 spheres tumorigenicity results from the oncogenic transformation of normal neural stem cell into GBM-producing stem cell. Compared differentiation of Dll1 vs. WT spheres shows the presence in Dll1 spheres of a subpopulation of cells which although fated to a glial lineage fail to differentiate terminally, in keeping with the astrocytic promoting function of Delta-Notch. This population of astrocyte progenitors proliferates actively and fails to down-regulate EGFR phosphorylation. These studies suggest that Dll1-induced tumorigenesis is restricted to the astrocytic lineage thereby providing a model for human GBM as well as an explanation for the duality of Notch signaling acting either as an oncogene or a tumor suppressor in stem/progenitor cells derived tumors, depending on the lineage commitment.

overall_design: Comparison between control (WT) and mutants (Dll1-3 and Dll1-5) cells was performed. Two biological replicates (n=3 each replicate) were used, and each replicate (n=3, total RNA pooled) was dye-swaped.

first: Anne-Sophie

last: Laurenson

first: Adrien

last: Lacaud

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Yoshinori

last: Masuo

first: Vincent

last: Lelièvre

first: Eliane

last: Mohier


title: Transcriptional signatures in leaves of adult European beech trees in an experimentally enhanced free air ozone setting

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München


title: Gene expression profiling of human atherosclerotic plaque

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories


title: Functional analysis of Arabidopsis HSFB transcription factor

status: Public on Sep 07 2011

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology


title: Analysis of gene amplification at DAFC-34B

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by genome tiling array


title: BRCT phosphoprotein recognition, but not E3 ligase activity, is essential for BRCA1 tumor suppression

status: Public on Aug 26 2011

city: Cold Spring Harbor

first: Jude

last: Kendall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: It has been recognized that BRCA1, in the form of the BRCA1/BARD1 heterodimer, acting as an ubiquitin E3 ligase offered a possible mechanism to explain its pleiotrophic nature of BRCA1 activity.  Our observation that mice lacking BRCA1 enzymatic activity are viable apart from male sterility was unexpected.  Our results suggest that the E3 ligase activity of BRCA1 is largely dispensable for normal development and is not essential for all BRCA1 functions.  Thus, many of the known and unknown functions of BRCA1 are likely to be mediated independent of its ability to catalyze ubiquitination.  The genome copy number patterns were studied on the mice tumors that lacks E3 ubiqitin ligase activity of BRCA1 and were compared to copy number profile of mice lacking p53 and both brca1 and p53.

overall_design: Array CGH was performed using Agilent mouse CGH microarray 244K kit.  Genomic DNA isolated from tumor tissue and its corresponding mouse tail were labelled with two different dyes and hybridized simultaneously on to microarray slides to perform comparitive genomic hybridization.

first: Reena

last: Shakya

first: Latarsha

last: Reid

first: Francesca

last: Cole

first: Colleen

last: Reczek

first: Dieter

last: Egli

first: Chyuan-Sheng

first: Dirk

last: deRooij

first: Steffen

last: Hirsch

first: Ravi

last: Kandasamy

first: James

last: Hicks

first: Matthias

last: Szabolcs

first: Maria

last: Jasin

first: Richard

last: Baer

first: Thomas

last: Ludwig


title: Effect of sigH in the growth phase transition of Clostridium difficile

status: Public on Aug 22 2011

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary:
This study is based on two microarray datasets, in one hand a phase transition comparison using the expression profiles of 630E strain after 4h and 10h of growth. In other hand a comparison at 10h of growth between a mutant of the sigH gene and the WT strains. This experimental procedure was designed to investigate the effect of sigH in the growth phase transition of Clostridium difficile.

This SuperSeries is composed of the SubSeries listed below.


title: Genomic profiles of mouse liver tissue harboring deletion of RB and/or p53, untreated or post-hepatocarcinogen treatment [CGH data]

status: Public on Sep 20 2011

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: The retinoblastoma (RB) and p53 tumor suppressors are critical regulators of the cell cycle with profound impact on both normal cell biology and disease etiology. In the context of human cancers, compound inactivation of RB and p53 is a frequent occurrence; however, the cooperation of these tumor suppressors in driving tumorigenesis has proven to be intricate and dependent on both the tissue and type of cancer. Hepatocellular carcinoma (HCC) is a highly complex disease characterized by numerous molecular abnormalities (e.g. p53, RB, TGFβ) and chromosomal aberrations associated with environmental factors (e.g. Hepatitis B/C Virus, Aflatoxin B1). Despite extensive research, how each of these facets of disease development cooperates in promoting tumorigenesis is ultimately unknown.  In the current study, we present a mouse model of liver tumorigenesis, in which the impact of RB and p53 loss is modified by the tissue environment. While loss of RB and p53 promotes deregulation of transcriptional programs associated with advanced disease, these changes are not sufficient to drive spontaneous tumorigenesis in the liver. However, in response to carcinogen-induced damage, distinct and cooperative roles of RB and p53 are revealed, which critically impact cell cycle control, checkpoint response, genome stability, and ultimately tumor development.

overall_design: Mice that are transgenic for Cre recombinase under the albumin promoter and harboring loxP sites within the Rb and/or p53 genes. For gene expression microarray analysis, mice were aged to 14 days, and treated for 24 hours with diethylnitrosamine (DEN) or saline as a control. For CGH analysis, mice were aged to 6 months post-DEN treatment. Liver tissue was obtained from dissected tumors and compared to normal liver tissue of 6-month old, saline-treated littermates. CGH analysis includes 5 individual tumor samples and 2 control samples (each consisting of a pool of 3 normal mouse liver DNA).

first: A

middle: K

last: McClendon

first: Erik

last: Knudsen

first: Sankar

last: Addya


title: Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung

status: Public on Sep 01 2011

city: Seattle

first: Donald

middle: O.

last: Chaffin

state: WA

institute: Seattle Children's Research Institute

summary: Microarray expression profiling of S. aureus lavaged from murine lungs after residence times between 30 minutes and 6 hours compared to post-exponential phase or early log phase growth in Luria-Betani broth.

overall_design: 21 samples analyzed, all replicates are biological replicates (independent biological experiments): 8 replicates of the overnight culture used for intranasal inoculation, 4 each from lavage at 0.5 hours and 2.0 hours, 3 from lavage after 6 hours and 2 from growth in fresh LB for 30 minutes.

middle: O

first: Destry

last: Taylor

first: Shawn

middle: J

last: Skerrett

first: Craig

middle: E

last: Rubens


title: Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

institute: Laboratoire Biométrie et Biologie Evolutive


title: Transcriptional Control by the FATC Domain of Saccharomyces cerevisiae Tra1

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

country: Canada

institute: University of Western Ontario

summary: Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase (PI3K) related kinase family that contain a C- terminal PI3K domain followed by a ~ 35-residue FATC domain. We have characterized four alleles with single residue changes in the FATC domain. Of these tra1-L3733A had the most pronounced effects with phenotypes including temperature and cold sensitivity, and reduced growth in media containing ethanol, Calcofluor white, rapamycin, chloramphenicol and geneticin. Tra1-L3733A interacted at normal levels with components of the NuA4 and SAGA complexes, and did not significantly alter histone acetylation patterns. The tra1-L3733A allele resulted in two-fold or greater change in expression of approximately 11% of yeast genes in rich media. Of the 279 genes with increased expression, 175 were ribosomal subunits or involved in ribosomal function or biogenesis. Elevated levels of Pol I and Pol III transcripts were also observed. The phenotypes of the tra1-L3733A overlapped with but were not identical to strains containing deletions of SAGA or NuA4 components or with strains containing mutations in the PI3K domain. Our finding that the double mutant allele, tra1-SRR3413/L3733A with alterations in the PI3K and FATC domains, resulted in wild type growth, suggests a model whereby the FATC domain negatively regulates the activity of the PI3K domain. Expression of genes involved in ribosome biosynthesis, other than the ribosomal subunits themselves, returned to near normal levels in the double mutant strain.  We also characterized tra1-G3745, which contains an additional glycine residue following the normal C-terminal phenylalanine. This allele did not support viability and showed severe dominant negative effects. In contrast to what was observed for tra1-L3733A, tra1-G4745 resulted in decreased expression of genes required for ribosome biogenesis and did not interact with Esa1 or Spt7.

overall_design: Three biological replicate experiments including one dye-swap were performed for yeast strains CY3003(TRA1::Tn10LUK with IB150(myc9-tra1_L3733A-YCplac111)) and CY3015(TRA1::Tn10LUK with IB157(myc9-tra1_SRR3413_L3733A-YCplac111)) with reference to CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111)).  Similarly, three biological replicate experiments including one dye-swap were performed for yeast strain CY3019(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB162(myc9-tra1_G3745-YCplac111)) with reference to CY3020(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB160(myc9-TRA1-YCplac111)).

first: Ana

last: Mutiu

first: Stephen

middle: M

last: Hoke

first: Julie

last: Genereaux

first: Michael

last: Buck

last: Yu


title: Expression pattern in HaHB1 overexpressor plants under normal growth conditions

status: Public on Aug 02 2011

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

state: Santa Fe

address: Ciudad Universitaria

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

summary: Plants deal with cold temperatures via different signal transduction pathways. To elucidate the molecular mechanisms by which HaHB1 conferred tolerance to cold temperatures, we performed an exploratory transcriptome analysis comparing RNAs of 3-week-old transgenic and WT plants. Several transcripts encoding glucanases and chitinases were induced. Notably, there was not a considerable overlap with CBF regulon genes previously described in cold tolerance molecular mechanism. We propose that HaHB1 is involved in plant cold tolerance via the induction of proteins able to stabilize cell membranes and inhibit ice growth.

overall_design: Transgenic vs WT experiment under normal conditions. Two independent transgenic lines. Two biological replicates for each line.

first: Julieta

middle: V

last: Cabello

middle: L

first: Raquel

last: Chan


title: Delineation of AR oncogenic functions in hepatocellular carcinoma

status: Public on Aug 08 2011

city: Hong Kong

first: Hai

last: Feng

address: The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The goal of this study was to delineate the important AR direct target genes that mediate the oncogenic properties of AR in HCC. The AR direct target genes in two HCC cell lines were identified by chromatin immunoprecipitation microarray (ChIP-chip) analysis and later confirmed by independent ChIP-PCR. The functions of the target genes were further examined.

overall_design: Two human HCC cell lines, Huh7 and PLC/PRF/5 (PLC5), were grown in DMEM supplemented with 10% fetal bovine serum. ChIP assays were performed using anti-AR antibody. The immunoprecipitated and input DNA were used to probe the Agilent human ChIP-chip arrays.

first: Alfred

last: Cheng


title: Molecular studies on sex-different control of the hepatic metabolism in relations to insulin sensitivity

status: Public on Aug 10 2011

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet


title: LATE-REPLICATING HETEROCHROMATIN IS CHARACTERISED BY DECREASED CYTOSINE METHYLATION IN THE HUMAN GENOME

status: Public on Aug 06 2011

city: Bronx

first: John

last: Greally

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array


title: Transcriptional profiling of 29 cases of diffuse large B cell lymphoma

city: Madrid

first: Santiago

last: Montes-Moreno

address: C/ Melchor Fernández Almagro, 3

department: Molecular Pathology

institute: CNIO

summary: 29 cases of RCHOP treated DLBCL were profiled for gene expression. Different integrated annalysis were performed, including mirNA differential expression between cases classified according to the COO signature (see later) and correlation tests between gene and miRNA expression.

overall_design: After transcriptional profiling the cases were classified according to the cell of origin based on the classifier proposed by Wright et al (Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:9991-6.).

first: S

last: Montes Moreno

first: N

last: Martinez


title: Gene and microRNA expression data of diffuse large B cell lymphoma from human diagnostic frozen samples

type:
Expression profiling by array
Non-coding RNA profiling by array


title: Distinct roles of ComK1 and ComK2 in gene regulation in Bacillus cereus

status: Public on Jul 28 2011

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena


title: C. elegans: Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

summary:
Transcriptional profiling of C. elegans worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage.
This data was then compared to data generated for corresponding developmental stages in the  nematode Pristionchus pacificus (see NCBI GEO series GSE31861) , to study evolution of developmental pathways regulating dauer development.

overall_design:
Two-condition experiments.
Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps.
Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps.
Total samples from both experiments 1 and 2 = 8.

first: Christoph

last: Dieterich

first: Ralf

last: Sommer


title: Burkholderia cepacia complex and cystic fibrosis (CF) patients

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

type:
Expression profiling by array
Other

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616


title: Effects of diazepam on gene expression and link to physiological effects in different life stages in zebrafish Danio rerio

status: Public on Jul 23 2011

city: Muttenz

first: Daniela

middle: Maria

last: Oggier

address: Gründenstrasse 40

department: School of Lifesciences

institute: University of Applied Sciences Northwestern Switzerland

summary: We applied zebrafish whole genome microarrays to identify molecular effects of diazepam, a neuropharmaceutical encountered in wastewater-contaminated environments, and to elucidate its neurotoxic mode of action. Behavioral studies were performed to analyze for correlations between altered gene expression with effects on the organism level. Male zebrafish and zebrafish eleuthero-embryos were exposed for 14 d or up to 3 d after hatching, respectively, to nominal levels of 273 ng/L and 273 μg/L (determined water concentrations in the adult experiment 235 ng/L and 291 μg/L). Among the 51 and 103 altered transcripts at both concentrations, respectively, the expression of genes involved in the circadian rhythm in adult zebrafish and eleuthero-embryos were of particular significance, as revealed both by microarrays and quantitative PCR. The swimming behavior of eleuthero-embryos was significantly altered at 273 μg/L. The study leads to the conclusion that diazepam-induced alterations of genes involved in circadian rhythm are paralleled by effects in neurobehavior at high, but not at low diazepam concentrations that may occur in polluted environments.

overall_design: Gene expression in male zebrafish brain was measured after exposure for 14 d to 273 ng/L and 273 ug/L diazepam or to the water control. A total of 11 arrays (Agilent 4 × 44 K Zebrafish microarray) were used, including three for the water control group,  four for the 273 ng/L and four for the 273 μg/L diazepam dose group.

first: Christin

last: Weisbrod

first: Andrea

last: Stoller

first: Armin

last: Zenker

first: Karl

last: Fent


title: Comparative Expression Profiling of E. coli and S. aureus inoculated primary Mammary Gland Cells sampled from Cows with different genetic Predisposition for Somatic Cell Score

status: Public on Jul 27 2011

city: Dummerstorf

first: Bodo

last: Brand

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute of Farm Animal Biology

summary:
Establishment of an in vitro system to explore molecular mechanisms of mastitis susceptibility in cattle by comparative expression profiling of Escherichia coli and Staphylococcus aureus inoculated primary cells sampled from cows with different genetic predisposition for somatic cell score
Primary bovine mammary gland epithelial cells (pbMEC) were sampled from the udder parenchyma of cows that were selected for high and low mastitis susceptibility by applying a marker assisted selection strategy considering QTL and molecular marker information of a repetitively confirmed QTL for SCS in the telomeric region on BTA18
The cells were cultivated and subsequently inoculated with heat inactivated mastitis pathogens Escherichia coli and Staphylococcus aureus, respectively. After 1, 6 and 24 hours the cells were harvested and comparatively analyzed using microarray expression chip technology to identify differences in mRNA expression profiles attributed to cultivation, inoculation or to genetic predisposition.

overall_design: Six heifers inheriting the favorable paternal QTL allele and five heifers inheriting the unfavorable QTL allele were selected by applying a marker assisted selection strategy. All heifers were kept under the same environmental conditions, had no clinical mastitis and did not show any indication of bacterial infection at slaughter. Primary bovine mammary gland epithelial cell cultures were established from cells sampled from the udder parenchyma of each cow. The cells were challenged with heat inactivated Escherichia coli and Staphylococcus aureus or with PBS for control. After 1, 6 and 24 hours the cells were harvested and mRNA expression was comparatively analyzed between time points for each treatment and each paternally inherited SCS-BTA18-QTL allele, respectively. In addition, the differences in gene expression at time points 1, 6 and 24h between inoculated and respective uninoculated control cells were investigated using the short time series expression miner STEM for co-expression profiling and GO cattegory enrichment analyses.

first: Manfred

last: Schwerin


title: Oxidative and electrophilic stress conditions and the sor1 mutant

status: Public on Jul 15 2011

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

institute: Eawag


title: TEAD4 occupied genes in differentiated C2C12 myoblasts

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

summary: The TEAD (1-4) transcription factors comprise the conserved TEA/ATTS DNA binding domain recognising the MCAT element in the promoters of muscle-specific genes. Despite extensive genetic analysis, the function of TEAD factors in muscle differentiation has proved elusive due to redundancy amongst the family members. Expression of the TEA/ATTS DNA binding domain that acts a dominant negative repressor of TEAD factors in C2C12 myoblasts inhibits their differentiation, while selective shRNA knockdown of TEAD4 results in abnormal differentiation characterised by the formation of shortened myotubes. Chromatin immunoprecipitation coupled to array hybridisation (ChIP-chip) shows that TEAD4 occupies 867 promoters including those of myogenic miRNAs. We show that TEAD factors cooperate with MYOD1 to directly induce Myogenin, CDKN1A and Caveolin 3 expression to promote myoblast differentiation and fusion. RNA-seq identifies a novel set of TEAD4 target genes encoding muscle structural and regulatory proteins and those required for the unfolded protein response. In contrast, TEAD4 represses expression of the growth factor CTGF and Cyclin D1 to promote differentiation. Together these results show that TEAD factor activity is essential for C2C12 cell differentiation and define a novel and nonredundant role for TEAD4 in regulating the unfolded protein response.

overall_design: C2C12 cells were infected with  retrotiviral vector expressing Flag-HA-Tagged TEAD4 or with empty control vector and selected in the continouos presence of puromycin. Infected cell populations were then differentiated for 5 days in DMEM medium with 2% horse serum and fixed in 0.4% formaldehyde.

first: Attaailah

last: Benhaddou

first: Tao

last: Ye

first: Aurore

last: Morlon

first: Isabelle

last: Michel

first: Bernard

last: Jost

first: Gabrielle

last: Mengus

first: Irwin

last: Davidson


title: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus

status: Public on Jul 20 2011

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

first: Carla

last: Risso

first: Jessica

middle: A

last: Smith

first: Derek

middle: R

last: Lovley


title: Poly(ADP-ribose) polymerase 3: a key regulator of ectodermal specification and neural crest development.

status: Public on Aug 18 2011

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

summary: Poly(ADP-ribose) polymerase 3 (PARP3) is a member of the PARP family of enzymes. It is structurally related to the well characterized type member PARP1 that orchestrates DNA strand break repair and cell death by the synthesis of poly(ADP-ribose). In contrast, the functions of PARP3 are undefined. We have used several in vitro and in vivo approaches to examine the possible functions of PARP3 as a transcriptional regulator, a function suggested from its previously reported association with several Polycomb group (PcG) proteins. A ChIP-chip analysis of PARP3 gene occupancy in the human neuroblastoma cell line SK-N-SH reveals that PARP3 is preferentially associated with developmental genes and is significantly enriched around the transcriptional start site of several genes encoding neuronal and sensory placodes specifiers, such as SOX9, DLX3 and DLX4. Using zebrafish as a vertebrate animal model, we demonstrate that Parp3 plays a key role in ectodermal and neural crest specification. Morpholino oligonucleotide-directed inhibition of parp3 expression in zebrafish impairs the expression of the neural crest cell specifier sox9a and of dlx3b/dlx4b, the formation of cranial sensory placodes, inner ears and pectoral fins. It delays pigmentation and severely impedes the development of the median fin fold and tail bud. Our findings demonstrate that Parp3 is crucial in the early stages of zebrafish development, possibly by exerting its transcriptional regulatory functions as early as during the specification of the neural plate border.

overall_design: ChIP were conducted as described (Rodrigue et al. 2006). PARP3 was immunoprecipitated from 3 x 10^7 SK-N-SH cells with a commercial anti-PARP3 (Enzo Life Sciences ALX-210-541). In control ChIP, PARP3 antibodies were replaced by rabbit IgG. Two independent PARP3 and control ChIP-chip experiments were achieved. The DNA was amplified using LM-PCR and labelled with Cy5 (PARP3) and Cy3 (IgG) before hybridization on Agilent Human promoter arrays (two 244k chip per ChIP for a total of 4 chips). Detailed protocols can be found at http://www.ircm.qc.ca/microsites/francoisrobert/en. Regions significantly enriched for PARP3 relative to IgG were identified as described (Lee et al. 2006).

first: Michèle

last: Rouleau

first: Vishal

last: Saxena

first: Amélie

last: Rodrigue

first: Abbie

last: Gagnon

first: Michael

last: Hendzel

first: Jean-Yves

last: Masson

first: Marc

last: Ekker

first: Guy

middle: G

last: Poirier


title: Effect of Advanced Paternal Age on Copy Number Variation in Offspring

status: Public on Jul 12 2011

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

country: Australia

institute: The University of Queensland


title: Development of Laser Capture Microdissection to study the gene expression of the sheep early ovarian folliculogenesis

status: Public on Jul 01 2011

city: Castanet-Tolosan Cedex

first: Agnes

last: Bonnet

address: Chemin de Borde-Rouge  BP 52627

institute: INRA

summary: Background Correct achievement of early ovarian folliculogenesis is a crucial phase for further ovarian function. This process is closely regulated by cell-cell interactions and coordinated expression of genes from oocyte and granulosa cells. But, despite of the large number of studies, little is known about the precise gene expression patterns driving early folliculogenesis. The experimental limitations concerned the very small size of these follicles and the mixture of the different developmental stages within an ovary that make the study of isolated follicular components much more difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarrays experiments is promising in addressing the molecular specificity of each follicular compartment. Nevertheless, the isolation of unique cells or group of cells is still challenging to maintain RNA quality during this process and to obtain sufficient amount of RNA. In this study, we described a method allowing the analysis of oocyte and granulosa cells gene expression during the first stages of sheep early folliculogenesis. Results First we developed a new fixation protocol using a frizzed 70% ethanol fixation solution that ensures correct single cell capture and RNA integrity during microdissection time.  After LCM capture of the compartments and follicular stages, RNA extraction and amplification, the expression of 6 oocyte-specific genes (SOHLH2, MAEL, MATER, VASA, GDF9, BMP15) and 3 granulosa cell-specific genes (KITLG, GATA4, AMH) confirmed the purity of the samples and documented their ovine expression profiles. Then, using bovine Affymetrix chip, we identified for the first time, a global gene expression for each follicular compartment during early developmental stages. Particularly the granulosa cell data set is quite unique. 1050 granulosa cell specific transcripts compared to oocyte and 759 oocyte specific transcripts were detected. The analysis of the expression of 2 genes (SIRT7, FST) confirmed this specificity of expression. Finally, the integration of the data stated the 3 main physiological events involved in early folliculogenesis and provided descriptive elements that confirmed the relevance and the potential of the LCM-derived RNAs.  Conclusions This method should contribute through an additional genome wide expression profiling to give insights on molecular mechanisms involved in stage transitions and cell type interplays.

sample_organism:
Bos taurus
Ovis aries

overall_design: The 2 ovine follicular compartments (i.e. granulosa cells (G) and oocytes (O) were captured using LCM technology for each early stage (primordial (Pd), primary (Pm), secondary (Sec) follicles. The RNA of each group was extracted using Picopure RNA Isolation kit (Arcturus) and subjected to 2 round T7 amplification (RiboAmp®HS PLUS kit, Arcturus). Ovine microarray experiments were performed using the Affymetrix Bovine Expression Array. First the quality of the cross-species hybridizations was checked by comparison of hybridization data of ovine fetal ovary RNA with bovine fetal ovary ones, generated with the Affymetrix standard protocol (protocole 1). Then, three biotin-labeling protocols were compared from ovine fetal ovary total RNA:  protocol 1; protocol 2 (Biotin-labeled cRNAs were synthesized following Affymetrix protocol using the second-round cDNAs from RiboAmp®HS kit as templates); protocol 3 (Arcturus biotin turboTM labeling kit  from aRNA after the 2 round amplification using RiboAmp®HS kit). Last , one LCM-derived aRNA sample of each group was labeled using the Arcturus biotin turboTM labeling kit (protocol 3) and hybridized to Affymetrix Bovine Expression arrays. Images were interpreted using Microarray Suite version 5.0 (MAS 5.0) in GCOS with scaling (100) and without normalization.

first: Agnès

first: Claudia

last: Bevilacqua

first: Francis

last: Benne

first: Corinne

last: Cotinot

first: Laurence

last: Liaubet

first: Patrice

last: Martin

first: Elodie

last: Poumerol

first: Magali

last: Sancristobal

first: Julien

last: Sarry

first: Gwenola

last: Tosser-Kloop

first: Loys

last: Bodin

first: Beatrice

last: Mandon-Pepin


title: Effects of PKC412 on gene expression and link to physiological effects in zebrafish Danio rerio eleuthero-embryos

first: Daniela

last: Oggier

summary: To identify molecular effects of the antineoplastic agent PKC412 (Midostaurin), we applied gene expression profiling in zebrafish using whole genome microarrays. Zebrafish eleuthero-embryos were exposed for 6 dpf to nominal levels of 2 μg/L and 40 μg/L PKC412. Among the 259 and 511 altered transcripts at both concentrations, respectively, the expressions of genes involved in the circadian rhythm were of interest. Alteration of swimming behaviour was not noted. Pathways of interest affected by PKC412 were angiogenesis, apoptosis, DNA damage response and response to oxidative stress. Angiogenesis was not altered by PKC412 treatment at both concentrations. Apoptosis occurred in olfactory placodes of embryos exposed to 40 μg/L, and DNA damage was induced at both PKC412 concentrations. However, there were no significant effects on reactive oxygen species formation. This study leads to the conclusion that PKC412-induced alterations of gene transcripts are partly paralleled by physiological effects at high, but not at low PKC412 concentrations expected to be of environmental relevance.

overall_design: Gene expression in zebrafish eleuthero-embryos was measured after exposure for 6dpf to 2 ug/L and 40 ug/L PKC412 or to the respective controls. A total of 12 arrays (Agilent 4 × 44 K Zebrafish microarray) were used, including four for the water control group, four for the solvent control group, four for the 2 μg/L and four for the 40 μg/L PKC412 dose group.

first: Anna

last: Lenard

first: Michael

last: Küry

first: Birgit

last: Höger

first: Markus

last: Affolter

first: Karl

last: Fent


title: Epigenomic reprogramming during epithelial to mesenchymal transition

status: Public on Jul 03 2011

city: Baltimore

first: Andrew

last: Feinberg

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

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


title: Genomic Aberrations in Paediatric Gliomas and Embryonal Tumours

city: Oslo

first: Hanne-Sofie

middle: S

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

summary: The pathogenesis of paediatric central nervous system tumours is still poorly understood. In an attempt to increase the knowledge of the genetic mechanisms underlying these tumours, we performed genome-wide screening of 17 paediatric gliomas and embryonal tumours using a combination of G-band karyotyping and array comparative genomic hybridisation (aCGH). G-banding revealed abnormal karyotypes in 56% of tumour samples (9 of 16; one failed in culture), whereas aCGH analysis found copy number aberrations in all 13 tumours that could be examined. Pilocytic astrocytomas (n=3) showed normal karyotypes or simple non-recurrent translocations by karyotyping, but revealed the now well-established recurrent gain of 7q34 by aCGH. Our series included one anaplastic oligoastrocytoma, tumours that have not previously been characterised genomically in children, and an anaplastic neuroepithelial tumour (probably an oligoastrocytoma); both tumours showed losses of chromosomes 14 by G-banding as well as structural aberrations of the long arm of chromosome 6, and loss of 14q, 17p, and 22q by aCGH. Three supratentorial primitive neuroectodermal tumours (n=5) showed aberrant karyotypes; two near-diploid with mainly structural changes and one near-triploid with several trisomies including gains of one copy of chromosomes 1, 2, and 7. aCGH confirmed these findings and revealed additional recurrent gains of 1q21-44, 3p21, and 3q29. We also describe cytogenetically for the first time a cribriform neuroepithelial tumour, a recently identified variant of atypical teratoid/rhabdoid tumour with a favourable prognosis, which showed loss of 1p33, 4q13.2, 10p12.31, 10q11.22, and 22q by aCGH.

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

first: Petter

last: Brandal

first: Ludmila

last: Gorunova

first: Torstein

last: Meling

first: Bård

last: Krossnes

first: Sverre

last: Heim


title: Mytilus galloprovincialis: temporal expression analysis of digestive gland and mantle

status: Public on Jul 11 2011

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

country: Italy

institute: University of Piemonte Orientale "Amedeo Avogadro"

overall_design: Refer to individual Series


title: Transcriptome analysis of epithelial and stromal contributions to mammogenesis in prepartum dry cows

status: Public on Jun 30 2011

city: East Lansing

first: Heather

last: Dover

address: B290 Anthony Hall

department: Animal Science

institute: Michigan State University

summary: Our overall objective is to identify key differences in gene expression signaling pathways in the epithelial and intralobular stromal compartments during prepartum mammary remodeling and development in the dry cow.

overall_design: 2 cell types (epithelia or stroma) from each of 6 animals were collected by Laser Capture Microdissection

first: Theresa

last: Casey


title: Mature and aged Male and female rabbit heart gene expression in global ischemia and cardioplegia

status: Public on Jun 28 2011

city: Boston

first: James

middle: D

last: McCully

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

summary:
Background:  Demographic studies have shown that the mean age of patients requiring coronary artery bypass surgery (CABG) is 68 years with approximately 44% of these patients being female . In recent studies, women have been shown to have a significantly greater operative risk as compared to men  and that women have worse outcomes after cardiac surgery. Recently we have shown that cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms and is significantly decreased with age and in particular is significantly decreased in the aged female.
Methods: The mechanisms through which cardioplegia affords cardioprotection are complex and can not be investigated as a single entity but rather must be investigated using a systems approach. To meet these needs we have used microarray and proteomic analysis.  The combined use of these two techniques allows for the identification of functionally related gene groups and protein biomarkers.   Mature 15 to 20 weeks; 3 to 4 kg) and aged (not senescent, >32 months; 5 to 6 kg) male and female New Zealand White rabbits were used for in situ blood perfused cardiopulmonary bypass.  Control hearts received 30 minutes sham ischemia and 120 minutes sham reperfusion. Global ischemia (GI) hearts received 30 minutes of global ischemia. GI was achieved by crossclamping of the aorta. Cardioplegia hearts received cold blood cardioplegia (Deaconess Surgical Associates (DSA) solution (containing 50 uM diazoxide) prior to GI. Following 30 minutes of GI the crossclamp was released, the cardiopulmonary bypass was ceased and the hearts were reperfused for 120 minutes. The hearts were removed flushed of blood and then quick frozen in liquid nitrogen prior to isolation of RNA and protein. Microarray and high throughput proteomic analysis was performed as previously described.
Results: Our studies demonstrate that the cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms. Our data also show that there are significant differences in the proteins expressed in the mature and aged. Principal component analysis indicated that in the mature male, mature female, and aged male the proteins expressed in control, global ischemia, and cardioplegia were diverse and clustered for individual treatments suggesting that the proteins had different expression levels in each treatment. In contrast, in the aged female the proteins expressed in global ischemia and in cardioplegia were clustered together, suggesting there was no difference in the proteins expressed during global ischemia and with cardioplegia.  Glycolysis/gluconeogensis was a significant functional pathway for the aged male but not the mature male or female. Glycolytic and gluconeogenic proteins were significantly up-regulated in the aged male compared to the female and significantly up-regulated in the aged male with cardioplegia as compared to global ischemia. In the aged female 9 unique mitochondrial proteins were up-regulated with cardioplegia. These proteins were associated with oxidative phosphorylation, the electron transport chain, the formation of pyruvate, and the tricarboxylic acid (TCA) cycle, but not glycolysis nor gluconeogenesis.
Conclusions: Our study demonstrates that the mitochondrion plays a key role in age and gender specific cardioprotection. The identification of these specific pathways and biomarkers should allow for the development of age and gender specific cardioprotection and significantly decrease morbidity and mortality in the aged female.

overall_design: Rabbit heart (atria and ventricles):control vs. global ischemia; control vs. cardioplegia; cardioplegia vs. global ischemia


title: Gene profiling, mutations and expression of epidermal growth factor receptor in androgen-dependent prostate cancer

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary:
We analyzed mutations in Epidermal Growth Factor Receptor (EGFR)  Tyrosine kinase (TK) domain, EGFR expression and gene profiling in prostate carcinoma (PC) in order to find out molecular prognostic markers and supply a proof for EGFR targeted therapies. 100 glyofixx-fixed, paraffin-embedded PC specimens were recovered after radical prostatectomy from locally advanced PC patients. Exons from 18 to 21 of EGFR TK domain were amplified and sequenced. For the entire cohort, EGFR protein evaluation by immunohistochemistry was performed. Gene expression profile was analyzed on 51 out of 100 samples by whole genome microarray. Statistical tests were performed in order to detect any significant association between EGFR iperexpression and prognosis. None out of 100 specimens presented mutations in exon 18; 2 point mutations were identified in exon 19, 5 in exon 20 and 6 in exon 21. In addiction, 58 out of 100 patients had the same silent mutation, at codon 787 in exon 20. EGFR iper-expression was found in 36% of specimens and was significantly associated with biochemical relapse. Gene profiling analysis on mutated samples selected 29 modulated genes differentially expressed between mutated EGFR+ and mutated EGFR- samples; 4 down-regulated genes, EAF2, ABCC4, KLK3 and ANXA3 and one up-regulated gene, FOXC1, are involved in prostate cancer progression. Our findings suggest that a subgroup of PC patients could potentially benefit of EGFR targeted therapies. The EGFR protein evaluation could contribute to identify PC relapsers.
Keywords: EGFR expression, TK mutations, target therapy, microarray data.

overall_design: In this work we studied mutation status and expression of Epidermal Growth Factor Receptor (EGFR) in a case series of 100 primary prostate cancer tissue specimens. Results indicate that 13% and 36% of PC patients presents EGFR tyrosine kinase domain mutations and iperexpression respectively, suggesting that this receptor could be a therapeutic target in progressive prostate cancer.  The analysis of correlation between EGFR protein expression, mutations, clinical parameters and outcome allow us to identify EGFR as significantly associated with biochemical relapse and high Gleason score.   Gene expression profiling in 51 of PC tissues led to the identification of a gene list which separated EGFR mutated patients according to EGFR protein expression. These results could give more information on clinical outcome and possible development of new targeted therapies.

first: Caterina

middle: P

last: Neia

first: Giorgia

last: Migliardi

first: Maurizia

last: Grand

first: Raffaella

last: Segir

first: Ymera

last: Pignochino

first: Giuliana

last: Cavalloni

first: Bruno

last: Torchio

first: Luciano

last: Mosso

first: Giovanna

last: Chiorino

first: Massimo

last: Aglietta


title: Prostate Cancer Recurrence

status: Public on Jun 15 2011

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

department: Biochemistry

country: Brazil

institute: Universidade de Sao Paulo

first: Egidio

last: Camila

first: Miguel

last: Srougi

first: Katia

last: Leite

first: Luiz

middle: H

last: Camara-Lopes

first: Eduardo

last: Reis

first: Sergio

last: Verjovski-Almeida


title: Cooperativity of Rb, Brca1, and p53 and malignant breast cancer evolution

status: Public on Dec 17 2011

city: Worcester

first: Karl

last: Simin

address: 364 Plantation St.

institute: UMass Medical School

type:
Expression profiling by array
Third-party reanalysis

summary: Breast cancers that are “triple-negative” for the clinical markers ESR1, PGR, and HER2 typically belong to the Basal-like molecular subtype. Defective Rb, p53, and Brca1 pathways are each associated with triple-negative and Basal-like subtypes. Our mouse genetic studies demonstrate that the combined inactivation of Rb and p53 pathways is sufficient to suppress the physiological cell death of mammary involution. Furthermore, concomitant inactivation of all three pathways in mammary epithelium has an additive effect on tumor latency and predisposes highly penetrant, metastatic adenocarcinomas. The tumors are poorly differentiated and have histologic features that are common among human Brca1-mutated tumors, including heterogeneous morphology, metaplasia, and necrosis. Gene expression analyses demonstrate that the tumors share attributes of both Basal-like and Claudin-low signatures, two molecular subtypes encompassed by the broader, triple-negative class defined by clinical markers. These studies establish a unique animal model of aggressive forms of breast cancer for which there are no effective, targeted treatments. Rb, p53, and Brca1 are associated with inherited forms of cancer, but defects in these pathways are also found together in a subset of breast cancer patients without a family history of the disease. Simultaneous inactivation of all three pathways causes more aggressive disease than do pair-wise combinations, indicating that the pathways play non-overlapping roles in tumor prevention.

overall_design: Gene expression analysis of mouse mammary tumors with perturbation of Rb family pathways, p53, and/or Brca1 are compared to other mouse model tumors (n=152)

first: Simin

last: Karl


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (1X1M)

city: Toronto

first: Stephen

middle: W

last: Scherer

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 36 Samples

first: Dalila

last: Pinto

first: Jeffrey

last: MacDonald


title: Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells [CGH data]

status: Public on Jun 04 2011

city: Phoenix

first: Jonathan

middle: J

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

summary:
Copy number and Gene expression profiling of HT-29 wild-type and bortezomib resistant cell lines
Identification of mechanisms of bortezomib resistance

overall_design: Copy number differences between HT-29 cell line variants and a HapMap control population of 9 female samples were identified using the Agilent 1M Human CGH microarray

first: Christopher

last: Kirk


title: Genome-wide analysis of promoter methylation in pancreatic adenocarcinoma

first: AUDREY

last: VINCENT

address: 1550 Orleans Street, CRBII

department: Pathology

summary: Methylation profiles of pancreatic adenocarcinoma cell lines were compared with normal pancreatic ductal tissues

overall_design: Methylated CpG island amplification was followed by CpG island microarray

first: Audrey

last: Vincent

first: Noriyuki

last: Omura

first: Seung-Mo

last: Hong

first: Andrew

last: Jaffe

first: James

last: Eshleman

first: Michael

last: Goggins


title: Parallel evolution of transcriptome structure during genome reorganization

status: Public on Jun 27 2011

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

summary:
Genome reorganization by large scale indels, gene displacements, and horizontal gene transfers allow an organism to re-organize genes into operons (“operonization”) and explore novel strategies for adapting to its changing environment. We have characterized the process of operonization by mapping and comparing transcriptome structures (TSs) of four phylogenetically diverse exptremophilic archaea: a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an anaerobic thermophile (Pyrococcus furiosis DSM 3638), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and a photoheterotrophic halophile (Halobacterium salinarum NRC-1). We demonstrate how the evolution of new transcriptional elements (promoters and terminators) is utilized as a mechanism to incorporate translocated, inverted, and newly acquired genes into existing gene regulatory programs.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Pyrococcus furiosus DSM 3638
Methanococcus maripaludis S2
Saccharolobus solfataricus P2

first: Sung-Ho

first: David

last: Reiss

first: J

middle: C

last: Bare

first: Dan

last: Tenenbaum

first: Min

last: Pan

first: Joseph

last: Slagel

first: Sujung

last: Lim

first: Murray

last: Hackett

first: Angeli

last: Menon

last: Adams

first: Adam

last: Barnebey

first: Steven

middle: M

last: Yannone

first: John

last: Leigh

first: Nitin

last: Baliga


title: Dose dependent response of liver gene expression and lipoperoxidation to dietary long chain omega 3 PUFA

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

summary:
The cardioprotective effects of long chain (LC) 3PUFA can be achieved at the gene expression level, notably in liver. However, the complexity of biological pathways modulations and the nature of the bioactive molecules are still under investigation. The present study aimed to investigate the dose-response effects of LC 3PUFA on the production of peroxidated metabolites and on global gene expression in liver.

The intake of LC ω3PUFA increased, in a dose-dependent manner, their incorporation in liver phospholipids but also the hepatic production of 4-HHE. Pathways related to inflammation were dose-dependently associated with the 3 groups but Group 2 was rather associated with inflammatory effects while Group 3 was anti-inflammatory. LC ω3PUFA had no effect on PPAR-controlled genes. However, they modified, in a dose-dependent manner, the expression of major genes related to lipoprotein metabolism (LDLR, VLDLR, INSIG1 and MTTP), possibly through the FXR signaling pathway. In conclusion, the effect of LC ω3PUFA is dependent on the dose possibly because of the production of peroxidated metabolites such as 4-HHE.

overall_design: New-Zealand white rabbits were fed (7 wk) a high cholesterol diet and received by daily oral gavages either oleic acid rich oil or a mixture of oils providing 0.1% (Group 1), 0.5% (Group 2) or 1% (Group 3) of energy as docosahexaenoic acid. Specific peroxidated metabolite issued from LC 3PUFA (4-hydroxyhexenal or 4-HHE) were measured by GC/MS/MS and transcription profiling was conducted in liver. Differentially expressed genes were identified using Bioconductor (Moderated p<0.05, Fold Change>1.20) and clustered into pathways (Ingenuity Pathway Analysis 7.0).

first: Cecile

last: Gladine


title: Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon

status: Public on Jun 03 2011

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University


title: Phanaerochaete chrysosporium and Postia placenta gene expression in ball-milled aspen or ball-milled pine medium

status: Public on Jun 02 2011

city: Madison

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

sample_organism:
Rhodonia placenta
Phanerodontia chrysosporium

platform_organism:
Rhodonia placenta
Phanerochaete chrysosporium RP-78


title: Cultured human amniotic fluid-derived mesenchymal stromal cells

status: Public on Jun 18 2011

city: Malaga

first: Jose Maria

last: Miranda-Sayago

state: Malaga

address: Campus Teatinos, SN

department: Biochemistry, Molecular Biology and Immunology

country: Spain

institute: University of Malaga

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Delineation of EZH2 oncogenic functions in hepatocellular carcinoma

status: Public on May 31 2011

city: Shatin

first: Richard

middle: KW

last: CHOY

address: 1/F, Block E, Prince of Wales Hospital

department: Obstetrics & Gynaecology

institute: The Chinese University of Hong Kong

summary: The goal of this study was to delineate the important EZH2 direct target genes that mediate the oncogenic properties of EZH2 in HCC. The EZH2 direct target genes in two HCC cell lines were identified by chromatin immunoprecipitation microarray (ChIP-chip) analysis and later confirmed by independent ChIP-PCR. The functions of the target genes were further examined.

overall_design: Two human HCC cell lines, Huh7 and PLC/PRF/5 (PLC5), were grown in DMEM supplemented with 10% fetal bovine serum. ChIP assays were performed using anti-EZH2 antibody. The immunoprecipitated and input DNA were used to probe the Agilent human ChIP-chip arrays.

first: Alfred

last: Cheng

last: Choy


title: Mutant telomerase RNAs induce DNA damage and apoptosis via the TRF2-ATM pathway in telomerase-overexpressing primary fibroblasts

status: Public on May 29 2011

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

summary: Mutant template human telomerase RNAs (MT-hTers) have been shown to induce apoptosis in various cancer cells with high telomerase activity. However, the mechanism by which MT-hTers inhibit growth of cancer cells and their effects on normal cells remain unknown. To determine the effects of MT-hTers on normal cells, MT-hTer-47A and -AU5 were introduced into IMR90 lung fibroblasts that have low telomerase levels. Growth of IMR90 cells following MT-hTers infection was not significantly impaired; however, similar treatments in telomerase-overexpressing IMR90 (IMR90 WThTERT) cells inhibited cell proliferation and induced apoptosis. Confocal microscopy showed that MT-hTers induced DNA damage foci i.e. 53BP1 and γ-H2AX in IMR90 WThTERT cells. Microarray analysis revealed that GADD45γ was significantly elevated in MT-hTers treated IMR90 WThTERT cells. MT-hTers also induced ATM phosphorylation at Ser 1981 in IMR90 WThTERT cells, and Western blot analysis revealed high levels of phosphorylated p53 following down-regulation of cellular TRF2 expression in MT-hTers treated IMR90 WThTERT cells. Taken together, we have elucidated that MT-hTers induce double-stranded DNA breaks (DSBs)-like damages in telomerase-positive IMR90 WThTERT cells following phosphorylation of ATM and p53 via suppression of TRF2 which eventually may have led to apoptosis via elevation of GADD45γ.

overall_design: MT-hTer-47A and -AU5 were introduced into IMR90 primary lung fibroblasts and immortalized IMR90 WT-hTERT cells. Through microarray analysis, gene expression of MT-hTer-infected IMR90 WT-hTERT cells were compared against MT-hTer-infected IMR90 control cells.

first: Dashayini

last: Mahalingam

first: LingLee

last: Tay

first: WeiHan

last: Tan

first: JuinHsien

last: Chai

first: Xueying


title: Expression data from chicken embryonic fibroblasts infected with Toxoplasma gondii

status: Public on May 27 2011

city: Stanford

first: Yi-Ching

last: Ong

state: CA

address: 299 W. Campus Dr.

department: Microbiology & Immunology

country: USA

institute: Stanford University


title: Symbiosis in Anemonia viridis sea anemones

status: Public on Jun 01 2011

city: NICE

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

institute: University of Nice


status: Public on May 20 2011

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Genomic profiling of HL60 and U266 blood cancer cell lines with (P as positive) or without (N as negative) CD34 cells using Agilent-014950 Human Genome CGH Microarray 4x44K.

overall_design: HL60 and U266 blood cancer cell lines were extracted and their sub-cell lines (with or without CD34 cells) were compared using Agilent-014950 Human Genome CGH Microarray 4x44K.

first: Klaudia

last: Kuranda


title: Comparison of gene expression in reproductively healthy (offshore) versus reproductively impaired (nearshore) female queen conchs (Strombus gigas) in the Florida Keys.

status: Public on Jun 07 2011

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University


title: The haplo-spliceo-transcriptome of the human Major Histocompatibility Complex

status: Public on May 23 2011

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7


title: Transcription profile of T. thermophilus HB8 strain lacking mutS, mutL, or mutS2 gene

city: Sayo-gun

first: Kenji

last: Fukui

state: Hyogo

address: 1-1-1, Kouto, Sayo-cho

department: SPring-8 Center

country: Japan

institute: RIKEN

summary:
We analyzed the expression profile of mutS, mutL, or mutS2 deletion mutant strain of Thermus thermophils HB8 during the exponential growth phase.  When compared with wild type using t-test (P < 0.01), 8, 111, and 18 genes were over 2-fold up-regulated in mutS, mutL, and mutS2-lacking strains, respectively. Keywords: cell type comparison

This SuperSeries is composed of the SubSeries listed below.

overall_design: Wild-type and the mutant strains were precultured in 3 mL of rich medium for two times at 70°C and then subcultured to 1000 mL of rich medium. These cells were cultured at70°C for 300 min , and then cells were harvested from 50 ml of the culture. Total RNA were extracted from wild-type and mutant strains and used for the cDNA synthesis by SuperScript II (Invitrogen, Carlsbad, CA).  The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions. The 3’-terminal-labeled cDNA was hybridized with a TTHB8401a520105F GeneChip (Affymetrix) which contained probe sets of 25-mer oligonucleotides for 2238 ORFs and 1096 intergenic regions.  After washing and staining with streptavidin-phycoerythrin (Invitrogen) by GeneChip Fluidics Station 450XP (Affymetrix), the array was scanned by a GeneChip Scanner 3000 (Affymetrix).  The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.2 (Affymetrix).  The data analysis was performed on the Subio platform version 1.6 (Subio Inc., Tokyo, Japan).  The genes which had detection call of “presence” more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.01 in the Student’s t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.  For the biological replication, above experiments were performed three times independently.

first: Yoshihiro

last: Agari

first: Akeo

last: Shinkai

first: Seiki

last: Kuramitsu


title: Separated Transcriptomes of Male Gametophyte and Tapetum in Rice

status: Public on May 12 2011

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on the spatiotemporal expression patterns and gene ontology (GO) categories of anther-expressed genes, some noteworthy expression patterns are discussed in connection with various important biological events of anther development.

overall_design: The separated transcriptomes of rice microspore/pollen and tapetum were measured at the premeiosis, meiosis, tetrad, uninuclear, bicellular, and tricelluar stages by using laser microdissection (LM)-mediated microarray.

first: Masao

last: Watanabe

first: Nori

last: Kurata

first: Makoto

last: Matsuoka

first: Mikio

last: Nakazono


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

city: Vancouver

first: Guanggan

last: Hu

email: hug@msl.ubc.ca, kronstad@msl.ubc.ca

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

institute: The University of British Columbia


title: Transcriptional response of Streptococcus pneumoniae to Zn2+-limitation and the repressor/activator function of AdcR

status: Public on May 13 2011

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

summary:
Zinc (Zn2+) is an important trace metal ion that has been shown to regulate the expression of several (virulence) genes in streptococci. Previously, we analyzed the genome-wide response of S. pneumoniae to Zn2+-stress. In this work, we have performed a transcriptomic analysis to identify genes that are differentially expressed under intracellular Zn2+-limitation. This revealed a number of genes that are highly upregulated in the absence of extracellular Zn2+, amongst which the genes belonging to the regulon of the Zn2+-responsive repressor AdcR, like adcBCA, encoding a Zn2+-dependent ABC-uptake system, adcAII, encoding a Zn2+-binding lipoprotein, and also virulence genes belonging to the Pht family (phtA, phtB, phtD and phtE). Using transcriptome analysis, lacZ-reporter studies, in vitro DNA binding experiments, and in silico operator predictions, we show that AdcR directly represses the promoters of adcRCBA, adcAII-phtD, phtA, phtB and phtE in the presence of Zn2+. AdcR can also function as an activator, since in the presence of Zn2+ it directly induces expression of adh that encodes a Zn2+-containing alcohol dehydrogenase. In conclusion, the genome-wide transcriptional response of S. pneumoniae to Zn2+-limitation was established, which is mainly mediated via direct regulation by the Zn2+-dependent regulator AdcR.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Tomas

last: Kloosterman

first: Oscar

last: Kuipers


title: Bj Paraquat

status: Public on May 16 2011

city: Arlington

first: Woo-Suk

last: Chang

state: TX

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

institute: University of Texas at Arlington

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


title: Time-course in rice leaves in the field: WT (cv.Norin8) vs. osgi mutant

status: Public on May 18 2011

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Diurnal time-course transcriptional profiling of rice leaf in the field comparing a circadian clock related mutant, osgi, with the wild-type (WT).

overall_design: Two sample experiments (WT vs. osgi) : 13 time-points (2h interval), 8 replicates (2leaves from individual plants x 4stages(each staggered by tranplanting dates with one week interval)): sampled on Aug. 12th 7:00-Aug.13th 7:00 (2008) at a paddy field in Tsukuba (Japan)

first: Motohiro

last: Mihara

first: Ritsuko

last: Motoyama

first: Yoshiaki

last: Nagamura


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

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

institute: City University of Hong Kong

first: Chee-Kent

first: Karl

last: Hassan

first: Sasha

last: Tetu

first: Joyce

middle: E

last: Loper

first: Ian

middle: T

last: Paulsen


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

status: Public on May 10 2011

city: Helsinki

first: Taru

middle: A

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital


title: Gene expression analyses of mice selectively inbred for trait anxiety

status: Public on May 04 2011

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

country: Germany

institute: Max Planck Institute of Psychiatry


title: Mouse cells cyclophosphamide treated vs untreated

status: Public on Apr 27 2011

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

institute: Istituto Superiore di Sanità

first: Mara

last: Valentini