title: Induced Pluripotent Stem Cells From Pancreatic Ductal Adenocarcinoma Can Recapitulate Early Developmental Stages of Cancer

status: Public on Jun 20 2013

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

summary: Pancreatic ductal adenocarcinoma (PDAC) has one of the worst prognoses of any human malignancy and there are few human cellular models of disease progression. When human PDAC cells are injected into immunodeficient animals, they create tumors of the late stage from which they were derived. We hypothesized that if human pancreatic cancer cells were converted to pluripotency and then allowed to differentiate back into pancreas, the developmental progression would recapitulate early stages of the cancer. To that end, we have generated isogenic matched sets of induced pluripotent stem (iPS) cell-like lines from epithelial cells of human pancreatic tumors and from histologically normal epithelial cells at the resected pancreatic margins. Notably, when injected into immunodeficient mice, at low or high passages, a human pancreatic cancer iPS-like line, but not the corresponding margin iPS-like line, slowly generates intra-epithelial neoplasia (PanIN) ductal structures that typically reflect the early stages of human pancreatic cancer. The PanIN-like ducts can be isolated and cultured. They secrete protein products reflective of PanINs and provide new insights into underlying regulatory networks. An additional iPS-like line from histologically normal cells at a pancreatic resection margin, but containing a mutation that predisposes to PDAC, does not generate PanIN ductal structures. These studies demonstrate that iPS technology can be exploited to recapitulate early progression events of a human epithelial cancer.

overall_design: Study includes a single experiment (#10): a tumor-adjacent pancreatic tissue control (10N); tumor tissue (10C); IPS-transformed tissue control (10N12); and IPS-transformed tumor tissue (10C22).

first: Jungsun

last: Kim

first: John

last: Hoffman

first: R

middle: K

last: Alpaugh

first: Maximilian

last: Reichert

first: Emma

middle: E

last: Furth

first: Antonia

last: Sepulveda

first: Chao

middle: X

last: Yuan

first: Kyoung

last: Won

first: Greg

last: Donahue

first: Jessica

last: Sands

first: Andrew

last: Gumbs


title: Effect of treatment for three months with chemical carcinogen and non-carcinogens on liver miRNAome

status: Public on Jul 03 2013

city: London

first: Nigel

middle: J

last: Gooderham

address: South Kensington Campus

department: Biomolecular Medicine

country: United Kingdom

institute: Imperial College London

summary: Here, we examined the liver microRNA profile of male Fischer rats exposed through their diet to genotoxic (2-acetylaminofluorene) and epigenetic (phenobarbital, diethylhexylphthalate, methapyrilene HCL, monuron, and chlorendic acid) chemical hepatocarcinogens, as well as to non-hepatocarcinogenic treatments (benzophenone, and diethylthiourea) for three months. The aim of the study was to investigate how liver miRNA profiles relate to mode of action and carcinogenic potential of chemicals.

overall_design: In total miRNA profiles from 38 liver samples were examined. These included 3-5 samples for animal fed control diets or diet supplemented with designated chemicals. For each chemical a carcinogenic or a maximum tolerated dose was chosen  based on published literature. The treatments were Diethylthiourea (DETU) 2500 ppm; Benzophenone (BP) 1250 ppm ; Monuron (MON) 1500 ppm ; Diethylhexylphthalate (DEHP) 12000 ppm ; Phenobarbital (PB) 1000 ppm; Chlorendic acid (CA) 1250 ppm; Methapyrilene HCl (MP) 250 ppm; 2-Acetyl aminofluorene (2-AAF) 40 ppm.

first: Costas

last: Koufaris

first: Jayne

last: Wright

first: Richard

middle: A

last: Currie


title: Vitamin C Stimulon in Mycobacterium tuberculosis

status: Public on May 24 2013

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

country: USA

institute: Trudeau Institute

summary: The emergence of drug resistance among tuberculosis (TB) patients is often associated with their non-compliance to the length of the chemotherapy, which can reach up to 2 years for the treatment of multi-drug-resistant (MDR) TB.  Drugs that would kill TB faster and would not lead to the development of drug resistance could shorten chemotherapy significantly. In Escherichia coli, the common mechanism of cell death by bactericidal antibiotics is the generation of highly reactive hydroxyl radicals via the Fenton reaction.  Since ascorbic acid (vitamin C) is known to drive the Fenton reaction, we tested whether the Fenton reaction could lead to a bactericidal event in Mycobacterium tuberculosis by treating M. tuberculosis cultures with vitamin C.  Here, we report that the addition of vitamin C to drug-susceptible, MDR and extensively drug-resistant (XDR) M. tuberculosis strains results in sterilization of the cultures in vitro. We show that the sterilizing effect of vitamin C on M. tuberculosis was dependent on the production of high ferrous ion levels and reactive oxygen species.  Although, this potent sterilizing activity of vitamin C against M. tuberculosis in vitro was not observed in mice, we believe this activity needs further investigation.

overall_design: Comparison of vitamin C treated Mycobacterium tuberculosis transcriptome relative to untreated; Three biological replicates, second is a dye flip

first: Catherine

last: Vilcheze


title: TCA1 Stimulon in Mycobacterium tuberculosis

summary: A cell-based phenotypic screen for inhibitors of biofilm formation in Mycobacterium tuberculosis (Mtb) identified the small molecule TCA1, which has bactericidal activity against both drug susceptible and drug resistant Mtb, and synergizes with rifampicin (RIF) or isoniazid (INH) in sterilization of Mtb in vitro. In addition, TCA1 has bactericidal activity against non-replicating Mtb in vitro and is efficacious in acute and chronic Mtb infection mouse models, both alone and in combination with INH or RIF. Transcriptional analysis revealed that TCA1 down-regulates genes known to be involved in Mtb dormancy and drug tolerance. Mutagenesis and affinity-based methods identified DprE1 and MoeW, enzymes involved in cell wall and molybdenum cofactor biosynthesis, respectively, as the targets responsible for TCA1’s activity. These in vitro and in vivo results indicate that TCA1functions by a novel mechanism and suggest that it may be the first product of a promising new approach for the development of anti-tuberculosis drugs.

overall_design:
Transcriptional profile of TCA1-treated cells relative to DMSO-treated control.
Three biological replicates, third is a dye flip.

first: Dhinakaran

last: Sambandan


title: Differentially expressed genes analysis by cDNA microarray during liver regenration after partial hepatectomy and different stages of liver development in rats.

status: Public on May 17 2013

city: Delhi

first: aparna

last: dixit

address: New Meharuli Road,

country: India

institute: JNU

summary:
Liver transcriptome codes for diverse metabolic functions and involves several pathways. During different developmental stage of rat liver, differential  expression of specific genes occur and allow the liver cells to enter into the further developmental stage. In regenerating rat liver, the mass of the lost liver is regained by a highly synchronized multi-step process involving  expression of specific genes in a temporal manner.
In our study, the transcriptional profile of developing liver (2wks and 4 wks), regenerating liver and adult liver based on microarray data has been systematically compared. Also the biological relevance of differentially expressed genes were also analysed through gene ontology (GO) and pathway analysis.

overall_design: Rat liver was excised out from the animals of different age groups (2 weeks, 4 weeks and 12 weeks) and partially hepatectomized rats at 8 h post surgery, for RNA extraction and hybridization on affymetrix microarray. Each sample was processed in duplicate and checked for quality of total RNA. The RNA was used as a starting template to synthesize double-stranded cDNA with random hexamers tagged with T7 promoter sequence. The fragmented DNA was labeled and used for overnight hybridization with Rat Gene ST 1.0 arrays, followed by washing, staining and scanning.

first: Preeti

last: Gupta

first: Aparna

last: Dixit


title: Identification of Rat foreskin biomarkers of in utero dibutyl phthalate exposure [Affymetrix]

status: Public on Jun 04 2013

city: Wilmington

first: Jack

last: Pike

address: 1600 Rockland Road

department: Urology Research

institute: AI duPont Hospital for Children

summary: Dibutyl phthalate was administered to pregnant Sprague Dawley rats from gestational days 16-20 at either a 100 mg/kg/day or 500 mg/kg/day dose level.  This timeframe covers the reproductive masculinization window which corresponds to increased androgen signalling.  Dibutyl phthalate has been shown to disrupt testosterone production leading to male reproductive abnormalities.  As such, we selected this exposure window for our study and examined gene expression changes in the male rat foreskin, which expresses the androgen receptor.  We collected tissue samples at both gestational day 20 to identify gene expression changes immediately after exposure, and postnatal day 5 to identify gene expression changes persisting after birth using microarray analysis (Illumina RatRef 12 Bead Chips).  To determine whether gene expression changes were brought on by decreased androgen signalling or additional effects of dibutyl phthalate exposure, we exposed rats to the potent androgen receptor antagonist flutamide (5 mg/kg/day) during the same period of development.  Gene expression changes were compared to determine which were brought on by disruption of androgen signalling and which were the result of other aspects of chemical exposure.

overall_design: The flutamide exposure study consisted of seven control dams administered corn oil and seven dams treated with 5 mg/kg/day flutamide.  Two foreskin samples per litter were pooled for gene expression microarray analysis using the Affymetrix Gene 1.0 ST Array.

first: Erin

last: McDowell

first: Kamin

last: Johnson


title: Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum

status: Public on Jun 15 2013

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

type: Methylation profiling by genome tiling array

summary:
Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions.
DNA methylation and its role in gene regulation is conserved in stramenopile.

overall_design: Methylome of the whole genome of diatom phaeodactylum tricornutum.

first: Xin

last: Lin

first: Florian

last: Maumus

first: Jean-Yves

last: Sgro

first: Sue

last: Olson

first: Sandra

middle: S

last: Bondurant

first: Michael

middle: R

last: Sussman

first: Chris

last: Bowler

first: Leïla

last: Tirichine


title: Expression data from E. faecalis Fsr mutants during GBAP induction

status: Public on May 01 2013

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

country: Portugal

institute: ITQB

summary: To rigorously characterize the Fsr regulon, we compared gene expression in V583 isogenic mutants in Fsr genes and each of the Fsr-regulated protease genes using microarrays and purified GBAP, the quorum-sensing molecule. We used microarrays to identified the genes that are regulated directly by Fsr Quorum sensing system.

overall_design: E. faecalis V583 cells were collected at 0 minutes and 10 minutes after GBAP addition, for RNA extraction and hybridization on Affymetrix microarrays. The cells were collected when the number of the cells are ideal for Quorum sensing activation. This procedure was also made without GBAP addition. For each condition were made replicates.

first: Sriram

last: Varahan

first: Matthew

last: Gorman

first: Kelli

middle: L

last: Palmer

first: Ryoji

last: Yokohata

first: Jiro

last: Nakayama

first: Lynn

last: Hancock

last: Gilmore

first: MariadeFátima

last: Lopes


title: Expression data from Bacillus subtilis 168 during growth

status: Public on Apr 10 2013

city: Atlanta

first: CHun-Kai

last: Yang

state: GA

address: 166 Jesse Hill Jr. Dr.

department: Biology

institute: Georgia state University

summary:
The gene expression of Bacillus subtilis 168 showed 3 major patterns including early expression, transition expression and late expression
We monitored Bacillus subtilis gene expression by using microarray at differernt time points

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Bacillus subtilis 168 was choosed as model for gram-positive to study gene expression at different stages

first: Chun-Kai

first: Sonja

last: Young


title: miR expression profiling of mouse hematopoietic stem and progenitor populations [miRNA]

status: Public on Jul 24 2013

city: Baltimore

first: Curt

middle: I

last: Civin

state: Maryland

address: BRB 14-021, 655 W Baltimore St

department: Center for Stem Cell Biology & Regenerative Medicine

institute: University of Maryland School of Medicine

summary: Several individual miRNAs (miRs) have been implicated as potent regulators of important processes during normal and malignant hematopoiesis.  In addition, many miRs have been shown to fine-tune intricate molecular networks, in concert with other regulatory elements.  In order to study hematopoietic networks as a whole, we first created a comprehensive map of global miR expression during early murine hematopoiesis.   Next, we determined the copy number per cell for each miR in each of the examined stem and progenitor cell types.  As data is emerging indicating that miRs function robustly mainly when they are expressed above a certain threshold (~100 copies per cell), our database provides a resource for determining which miRs are expressed at a potentially functional level in each cell type.   Finally, we combine our miR expression map with matched mRNA expression data and external prediction algorithms, using a Bayesian modeling approach to create a global landscape of predicted miR-mRNA interactions within each of these hematopoietic stem and progenitor cell subsets.  This approach identifies several interaction networks comprising a “stemness” signature in the most primitive hematopoietic stem cell (HSC) populations, as well as “myeloid” patterns associated with two branches of myeloid development.

overall_design: Six populations of mouse hematopoietic stem and progenitors have been analyzed (LT-HSC, ST-HSC, MPP, CMP, GMP, MEP).  2-3 replicates are included for each sample.

first: Diane

last: Heiser

first: Brian

last: Godsey

first: Ian

middle: M

last: Kaplan

first: YeeSun

last: Tan

first: Sebastien

last: Morisot

first: Wen-Chih

last: Cheng

first: Donald

last: Small


title: Pellicle Stimulon in Mycobacterium tuberculosis

last: Weinrick

summary: Triplicate 10mL cultures of M. tuberculosis grown in Sautons media without detergent in planktonic (exponential growth phase at OD600 0.2) compared to pellicle (3 weeks growth without shaking in 5% CO2) conditions.

overall_design: comparison of pellicle growth transcriptome to planktonic growth transcriptome, 3 biological replicates, third is dye-flip

first: Dhinakaran

last: Sambandan


title: Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals and AT patients

status: Public on Apr 09 2013

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

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

overall_design: Refer to individual Series


title: Gene expressioin signatures in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes post sham- or IR-treatment

summary: Transcriptional profiling of human lymphoblastoid cell lines  with different ATM genotypes 6h post sham- or 1.5 Gy IR-treatmentl was compared to extract IR-related gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients.

overall_design: Biological replicates: 6 or 4;  Technical replicates: 2 with C3 and C5 dye swap.

first: Zhou

last: Tong

first: Kaufmann

last: William


title: Gene expressioin signatures at basal level in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes

summary: Transcriptional profiling of human lymphoblastoid cell lines  with different ATM genotypes at basal level was compared to extract gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients.

overall_design: Biological replicates: 4;  Technical replicates: 2 with C3 and C5 dye swap.


title: Overexpression of PLIN5 in skeletal muscle promotes oxidative gene expression and intramyocellular lipid content without compromising insulin sensitivity

status: Public on Jan 29 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Aims/hypothesis: While lipid deposition in skeletal muscle is considered to be involved in obesity-associated insulin resistance, neutral intramyocellular lipid (IMCL) accumulation per se does not necessarily induce insulin resistance. We previously demonstrated that overexpression of the lipid droplet coat protein perilipin 2 augments intramyocellular lipid content while improving insulin sensitivity. Another member of the perilipin family, perilipin 5 (PLIN5), is predominantly expressed in oxidative tissues like skeletal muscle. Here we investigated the effects of PLIN5 overexpression – in comparison with effects of PLIN2 – on skeletal muscle lipid levels, gene expression profiles and insulin sensitivity. Methods: Gene electroporation was used to overexpress PLIN5 in tibialis anterior muscle of rats fed a high fat diet. Eight days after electroporation, insulin-mediated glucose uptake in skeletal muscle was measured by means of a hyperinsulinemic euglycemic clamp. Electron microscopy, fluorescence microscopy and lipid extractions were performed to investigate IMCL accumulation. Gene expression profiles were obtained using microarrays. Results: TAG storage and lipid droplet size increased upon PLIN5 overexpression. Despite the higher IMCL content, insulin sensitivity was not impaired and DAG and acylcarnitine levels were unaffected. In contrast to the effects of PLIN2 overexpression, microarray data analysis revealed a gene expression profile favoring FA oxidation and improved mitochondrial function. Conclusions/interpretation: Both PLIN2 and PLIN5 increase neutral IMCL content without impeding insulin-mediated glucose uptake. As opposed to the effects of PLIN2 overexpression, overexpression of PLIN5 in skeletal muscle promoted expression of a cluster of genes under control of PPARα and PGC1α involved in FA catabolism and mitochondrial oxidation.

overall_design: Rats received a high fat diet for 3 weeks; 2 weeks after start of the diet intervention Plin5 (OXPAT) or Plin2 (ADRP) were overexpressed in either the right or left tibialis anterior muscle. One week later pooled tibialis anterior muscle samples were analysed on microarrays.

first: Madeleen

last: Bosma

first: Lauren

last: Sparks

first: Johanna

last: Jorgensen

first: Sander

last: Houten

first: Patrick

last: Schrauwen

last: Kersten

first: Matthijs

last: Hesselink


title: Expression Analysis of Bisphenol A (0.1 uM), 17beta-estradiol (0.1 uM), and GSK4716 (0.1 uM) Exposure in Embryonic Zebrafish

status: Public on Mar 25 2013

city: Corvallis

first: Robert

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: Investigation of whole genome expression pattern of 24 hours post fertilization Danio rerio embryos exposed to bisphenol A, 17beta-estradiol, GSK4716, or 0.1% DMSO vehicle control

overall_design: Embryos were exposed to 0.1 uM BPA, 0.1 uM E2, 0.1 uM GSK4716, or control from 8 hpf to 24 hpf. Three biological replicates were collected for each treatment. 40 embryos were pooled to comprise a replicate.

first: Katerine

last: Saili

first: Susan

middle: C

last: Tilton

first: Katrina

last: Waters

first: Jiangfei

last: Chen

first: Qiaoxiang

last: Dong

first: Changjiang

last: Huang


title: Effects of polyglutamine expansion and subcellular localization of C-terminal fragment of Cav2.1 in PC12 rat pheochromocytoma cells

status: Public on Mar 13 2013

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Polyglutamine(polyQ) expansion of α1A voltage-dependent calcium channel (Cav2.1) is the causative mutation of spinocerebellar ataxia type 6 (SCA6). The C-terminal fragment (CTF) of Cav2.1 makes aggregates in the cytoplasm of SCA6 Purkinje cells and may relate to the pathogenesis. In order to identify genes associated with polyQ expansion and subcellular localization of CTF, we analyzed gene expression profiles of PC12 rat pheochromocytoma cells using Tet-off system.

overall_design: We exmined gene expression profiles of Tet-off PC12 cells using the following four recombinant C-terminal fragments (rCTFs): rCTF-Q13-NLS, rCTF-Q13-NES, rCTF-Q28-NLS and rCTF-Q28-NES. We obtained gene expression data of both Dox (+) and Dox (-) conditions for each CTF. All assays were performed in duplicate.

first: Makoto

last: Takahashi

first: Masato

last: Obayashi

first: Taro

last: Ishiguro

first: Nozomu

last: Sato

first: Yusuke

last: Niimi

first: Yasen

last: Mahamut

first: Hiroshi

last: Tanaka

first: Fuminori

last: Tsuruta

first: Ricardo

last: Dolmetsch

first: Mitsunori

last: Yamada

first: Hitoshi

first: Yoshinobu

last: Eishi

first: Hidehiro

last: Mizusawa

first: Kinya

last: Ishikawa


title: Expression data from cyclically stretched engineered neonatal rat ventricuar myocyte (NRVM) tissues

status: Public on Jan 30 2013

city: Cambridge

first: Megan

middle: Laura

last: McCain

state: MA

address: 60 Oxford St Room 332

department: Engineering and Applied Sciences

institute: Harvard University

summary:
Mechanical overload in the heart induces pathological remodeling that typcially leads to heart failure. We sought to build an in vitro model of heart failure by applying cyclic stretch to engineered isotropic (iso) and anisotropic (aniso) NRVM tissues.
We used micoarrays to determine the effects of longitudinal and transvserse cyclic stretch on gene expression in engineered NRVM cardiac tissues. We found that cyclic stretch induced up-regulation of several known indicators of heart faliure, independent of the direction of stretch.

overall_design: NRVMs were seeded on silicone membranes coated with isotropic (iso) fibronectin (FN) or micropatterned with FN (aniso), cultured statically for 1h (t=0h), and stretched for increasing amount of time (t=6h, 24h, 96h) before RNA extraction and hybridization on Affymetrix microarrays. For aniso tissues, stretch was applied in either the longitudinal (long) or transverse (trans) direction. RNA was collected over six primary NRVM harvests and thus RNA was also extracted and analyzed from samples seeded for 1h (at t=0h) on iso FN to be used to normalize across cell harvests.

first: Sean

middle: P

last: Sheehy

first: Kevin

last: Parker


title: Gene expression of rat PSCs cultured on plastic, matrigel and collagen

status: Public on Jan 17 2013

city: Liverpool

first: Minoti

last: Apte

state: NSW

address: Level 4, Ingham Institute

department: Medicine

country: Australia

institute: University of New South Wales

summary: Activated pancreatic stellate cells produce the fibrotic matrix in chronic pancreatitis and pancreatic cancer. In vitro protocols examining PSC biology have usually involved PSCs cultured on plastic, a non-physiological surface. However, PSCs cultured on physiological matrices e.g. MatrigelTM (normal basement membrane) and collagen (fibrotic pancreas), may have distinctly different behaviours compared to cells cultured on plastic. Therefore, we aimed to compare PSC gene expression after culture on plastic, MatrigelTM and collagen I.

overall_design: Total RNA from stellate cells in 10 cm Petri dishes was isolated by Qiagen RNeasy Mini Plus kit as per manufacturer’s instructions. The Agilent 2100 Bioanalyzer (Agilent Technologies Inc. Santa Clara, CA) was used for quality control of the isolated total RNA. Gene expression profiles of rat PSCs cultured on MatrigelTM, collagen I and plastic were analysed by whole rat genome microarray purchased from Affymetrix (Rat Gene 1.0 ST Array). This array was able to detect 27,342 rat genes, with approximately 26 probes on average per gene (referred to as a probe set).

first: Susan

last: Yang

first: Phoebe

last: Phillips

first: Zhihong

last: Xu


title: Effect of live Mycobacterium leprae infection on global gene expression of primary human Schwann cells at 24 hours

status: Public on Jan 03 2013

city: Rio de Janeiro

first: Anna Beatriz

middle: Robottom

last: Ferreira

state: Rio de Janeiro

address: Rua Adolfo Lutz 55 apt 201

country: Brazil

institute: Fundação Oswaldo Cruz

summary: In an attempt to understand M. leprae interaction with the human host, Stanford Genomics HEEBO Arrays were use to identify modulated genes in primary human Schwann cells infected with live M. leprae at a MOI of 100:1 for 24 hours.

overall_design: Dual channel competitive hybridizations between M. leprae infected and non infected Schwann cells including 3 independent biological replicates and a technical replicate in the form of dye swap.

first: Anna

first: Diana

last: Williams

first: Marcelo

last: Alves

first: Milton

middle: O

last: Moraes

first: Edward

last: Shannon

first: Felippe

last: Sandoval


title: Comparative transcriptome analysis of Brucella melitensis 16M and its hfq mutant under acidified minimum medium (GEM4.0) conditions

status: Public on Apr 27 2013

city: Beijing

first: tai

address: Dongdajie

country: China

institute: Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences

summary: Hfq is a bacterial Sm-like protein which serves as a post-transcriptional regulator of global gene expression. It has been shown to be involved in a wide range of cellular processes and pathways. To characterize the regulation roles of Hfq in Brucella melitensis, the in vitro hfq induction conditions simulating intracellular environments were firstly defined, and then, the transcriptome of the hfq mutant was compared to that of the wild type strain. Comparative transcriptome analysis showed that a total of 359 genes showed a>2.0-fold change in transcript abundance in Δhfq when compared to that in 16M.

overall_design: 2 wild type samples and 2 hfq mutant samples were analyzed.

first: Yufei

last: Wang

first: Zeliang

last: Chen

first: Tongkun


title: Gene expression in Drosophila Invadolysin mutant and wild-type

status: Public on Jan 01 2013

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

summary:
We aimed to assess the consequences of loss of the Invadolysin gene on global gene expression by microarray analysis.
Four biological replicates each of Invadolysin mutant and wild-type larvae were used to assess gene expression on FL002 microarrays (GPL5135).

overall_design: Four biological replicates of invadolysin mutant and wild-type Drosophila. Two arrays had wild-type in Cy5 channel and invadolysin in Cy3 channel, the other two were reversed.

first: Margarete

last: Heck

first: Francesca

last: Di Cara


title: Inhibition of Melanoma Growth by Small Molecules that Promote the Mitochondrial Localization of ATF2

status: Public on Dec 28 2012

city: La Jolla

first: Eric

last: Lau

state: CA

address: 10901 North Torrey Pines Road, Rm 6207

department: Signal Transduction

institute: The Sanford-Burnham Medical Research Institute

summary: Effective therapy for malignant melanoma, the leading cause of death from skin cancer, remains an area of significant unmet need in oncology. Increased expression of PKCε in advanced metastatic melanoma, results in the phosphorylation of the transcription factor ATF2 on threonine 52, which causes its nuclear localization and confers its oncogenic activities. The nuclear-to-mitochondrial translocation of ATF2 following genotoxic stress promotes apoptosis, a function that is largely lost in melanoma cells, due to its confined nuclear localization. Therefore, promoting the nuclear export of ATF2, which sensitizes melanoma cells to apoptosis, offers a novel therapeutic modality. We conducted a pilot high-throughput screen of 3,800 compounds to identify small molecules that promote melanoma cell death by inducing the cytoplasmic localization of ATF2.

overall_design: For this specific gene expression analysis experiment, we subjected WM793 melanoma cells to treatment with DMSO- or 10µM SBI-0087702 for 24 h. RNA was harvested and subjected to microarray analyses using the Illumina Human HT-12 v4 BeadChip. Raw microarray data were normalized using the lumi package in R (variant stabilizing transformation followed by quantile normalization). Subsequent variant-stabilized, normalized microarray values were sorted by fold-change values and subjected to a 1.5-fold-change cut-off threshold. The fold-change-ranked gene list was subjected to gene ontological enriched functional network clustering using the Ingenuity (IPA) gene ontology platform.

first: Varsano

last: Tal

first: Yongmei

last: Feng

first: Marine

last: Garrido

first: Loribelle

last: Milan

first: Susanne

last: Heynen-Genel

first: Christian

last: Hassig

first: Ze'ev

last: Ronai


title: transcriptomic analysis of phosphatin effect-Phosphatin effect on Arabidopsis

status: Public on Apr 11 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: cea11-02_phosphatin - transcriptomic analysis of phosphatin effect - Identification of transcriptomic modifications promoted by phosphatin (AC6) (a molecule mimicking Pi addition effects on Pi starved plants). - 40 µM Phosphatin was added to MS (diluted 10 times) containing 20µM phosphate medium and controls were grown on MS (diluted 10 times) containing 20µM phosphate or supplemented with 500 µM of Pi. For each ARN extraction their was 3 plates containing each 10 seedlings grown 13 days in vertical petri dishes.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Laurent-

last: Nussaume

first: Marie-Laure

last: Martin-Magniette


title: Modulation of gene expression by complement protein C1q in amyloid-beta injured neurons

status: Public on Dec 21 2012

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

summary: Complement protein C1q is induced after injury in the brain and during Alzheimer's disease and has been shown to protect against amyloid-beta induced neuronal death. In this study, we used microarray approach to identify the pathways modulated by C1q that are associated with neuroprotection.

overall_design:
Immature rat cortical primary neurons are treated with fibrillar amyloid-beta peptides and/or C1q for 3h before RNA extraction and hybridization on rat Affymetrix microarrays.

Supplementary file: Processed/normalized, probe-level signal intensities from neurons treated with amyloid-beta or C1q. Median signal intensity used as global normalization method, done with JMP genomics (v5.0) software.

first: Andrea

last: Tenner


title: Downregulation of the HOPX gene decreases metastatic activity in a chicken sarcoma cell line model and identifies genes associated with metastasis

status: Public on Nov 27 2012

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

summary: Metastatic progression is the leading cause of cancer mortality yet we have an incomplete view of the genetic events governing this process. An investigation was undertaken to explore the role of homeodemain only protein X (HOPX) in metastatic propensity and to identify other genes that may participate in metastasis development. The transcription factor HOPX was assessed for its possible involvement in metastasis formation using a knock-down induced by plasmid-delivered shRNAs. We used our original model system of chicken v-src-transformed tumour cell line PR9692 and its subclone (PR9692-E9) that have lost the ability to induce metastases after inoculation into syngeneic chickens without any significant change in primary tumour formation. We found that also a PR9692 cell line with decreased expression of HOPX gene (PR9692-shHOPX) lost its metastatic capacity in vivo (in chickens) and displayed a reduced cell migration in vitro. We compared the gene expression profiles of control (PR9692-shMOCK) and PR9692-shHOPX cells using oligonucleotide microarrays, assuming that genes with differential expression might be associated with metastasis. The data were compared with a previous study showing differences in gene expression between the PR9692 and PR9692-E9 cells. Bioinformatics was applied to identify gene expression patterns associated with metastasis. 234 genes were identified to show at least 2-fold change in both pairs of cell lines. The results were validated with real-time quantitative RT-PCR and the differential expression was confirmed for several genes. We were also able to demonstrate a significant change at protein level in case of three selected genes (NCAM, FOXG1, ITGA4). shRNA mediated knockdown of one of the identified HOPX regulated genes (integrin alpha 4) in the PR9692 cell line itself showed a marked inhibition of metastasis formation.

overall_design: Comparison of expression profiles obtained from metastatic PR9692-shMOCK and non-metastatic PR9692-shHOPX cells. Two biological replicates were analyzed for each group.

first: Denisa

last: Kovarova

first: Jiri

last: Plachy

first: Katerina

last: Trejbalova

first: Jan

last: Kosla

last: Hejnar


title: Effects of steroid ablation and progestin replacement on the transcriptome of the primate corpus luteum during simulated early pregnancy.

status: Public on Dec 01 2012

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

summary: The LH-like molecule chorionic gonadotropin (CG) is secreted by the macaque conceptus during and following implantation, “rescuing” the CL from impending regression and extending its functional lifespan in early pregnancy for approximately two weeks. CG binds to the same receptor as LH; i.e., LHCGR, and promotes production of steroids and other factors such as relaxin (RLN1). Our research group recently used Affymetrix™ rhesus macaque total genome arrays to compare the effects of CG on the luteal transcriptome from rhesus females during simulated early pregnancy (SEP) with changes during luteal regression in the non-fecund menstrual cycle. This analysis demonstrated that CG-rescue affected expression levels of 4,500 mRNA transcripts between days 10 and 15 of the luteal phase. Previous analyses indicated that a portion of the transcriptome in the macaque CL of the menstrual cycle was regulated indirectly by LH via the local actions of steroid hormones, including progesterone (P). Therefore, this study was designed to distinguish CG-regulated luteal genes that are dependent versus independent of local steroid (P) action. A protocol of increasing dosages of hCG (SEP) was begun on day 9 of the luteal phase in rhesus females combined with concurrent administration of the 3BHSD inhibitor trilostane (TRL) +/- the synthetic progestin (P) R5020. CL were collected on day 10 (no treatment) of the luteal phase to serve as a baseline comparison (n=8), 1 day of SEP (Day 10+hCG+/-TRL+/-R5020) and 6 days of SEP (Day 15+hCG+/-TRL+/-R5020); n=4/group. In the presence of CG, treatment with TRL reduced serum P levels to less than 1 ng/ ml after 1 day and all of the Day 15+h+TRL-treated females initiated menses before CL collection. The isolated CL were processed for total RNA and hybridized to microarrays. Compared to hCG treatment alone, 50 significantly altered mRNA transcripts were identified on day 10, rising to 95 on day 15 (P<0.05, ≥ 2-fold change in gene expression). The mRNA levels for several genes were validated in CL by real-time PCR. RNL1 levels increased with CG-treatment, but were not affected by steroid ablation, similar to previously reported relaxin protein expression. Steroid-sensitive genes included CDH11, IL1RN, INSL3, LDLR, OPA1, SERPINE1, SFRP4, and TNSF13B1; however differential sensitivity was observed and effects of steroid ablation and P replacement varied by day. Expression of some genes (e.g., 3BHSD2, ADAMTS1, ADAMTS5, MMP9, STAR, and VEGFA) previously identified as steroid regulated in the macaque CL during the menstrual cycle were not significantly altered by steroid ablation and P replacement during CG exposure in SEP. These data indicate that the majority of CG-regulated luteal transcripts are differentially expressed independently of local steroid actions. The proportion of steroid sensitive mRNA transcripts in the presence of CG is much smaller than in the presence of LH during the non-fecund cycle. Nevertheless, the steroid-regulated genes in the macaque CL may be essential during early pregnancy, based on the previous report that TRL treatment initiates premature structural regression of the CL during SEP. These data reinforce the concept that the structure, function, and regulation of the rescued CL in early pregnancy is different from the CL of the menstrual cycle.

overall_design: A protocol of increasing dosages of hCG (SEP) was begun on day 9 of the luteal phase in rhesus females combined with concurrent administration of the 3BHSD inhibitor trilostane (TRL) +/- the synthetic progestin (P) R5020. CL were collected on day 10 (no treatment) of the luteal phase to serve as a baseline comparison (n=8), 1 day of SEP (Day 10+hCG+/-TRL+/-R5020) and 6 days of SEP (Day 15+hCG+/-TRL+/-R5020); n=4/group.The isolated CL were processed for total RNA and hybridized to Affymetrix Rhesus Genome microarrays.

first: C

middle: V

first: R

last: Aazzarah

first: L

last: Quennoz

first: J

middle: D

last: Hennebold

last: Stouffer


title: Gene Expression in Rats Fed a Western Diet

city: North Ryde

first: Robert

last: Dunne

state: New South Wales

address: Locked Bag 17

institute: CSIRO

summary: Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes  in the expression of DNA damage and repair genes in response to the above dietary treatments.

overall_design:
Distal colon tissues  from Sprague Dawley  rats fed a variety of diets (see summary)  were removed from RNAlater stabilisation reagent (Sigma, Australia) they had been stored in,, placed in 1 ml of TRIzol® Reagent (Invitrogen, Australia) and homogenised usingbeads (mix of 2.5 mm glass and 0.1 - 1.0 mm diameter silicon-zirconian beads) in a MiniBeadbeater-8 (BioSpec Products Inc., USA). Total RNA was extracted (using TRIzol® Reagent manufacturer's instructions) and further purified using RNAeasy mini spin columns (QIAGEN, Australia) with a DNase on-column digestion as per manufacturer's instructions.RNA integrity was checked using a Bioanalyzer 2100 (Agilent Technologies, USA) andquantified using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). RNA samples with insufficinet quality and quantity were not assayed.
The numbers of rats arrayed from each diet were as follows: CON,   5;LAMS,  7; HAMS,  8; HAMSB, 9; LAW,   6; HAW , 8. This gives a total of 43 arrays.

first: Michael

last: Conlon

first: Caroline

last: Kerr

first: Christopher

last: McSweeney

first: Janet

last: Shaw

first: Seungha

last: Kang

first: Anthony

last: Bird

first: Matthew

middle: K

last: Morell

first: Trevor

last: Lockett

first: Peter

last: Molloy

first: Ahmed

last: Regina

first: Shusuke

last: Toden

first: Julie

last: Clarke

first: David

last: Topping


title: Differential gene expression of candidate genes for growth in rainbow trout

status: Public on Nov 29 2012

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

state: Ontario

address: Science Complex, University of Guelph

department: Intergrative Biology

country: Canada

institute: University of Guelph

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

overall_design: Growth in fishes is a complex trait, controlled by both genetic and environmental factors, that impacts many components of fitness.  Gene expression studies may lead to the identification of candidate genes for growth and microarrays offer the opportunity to examine the expression of thousands of genes simultaneously.  Gene expression differences in the liver and white muscle were examined in normally growing, 15 month-old, large and small size-selected rainbow trout (Oncorhynchus mykiss) derived from two different seasonal spawning groups (Sept. and Dec.).  Examination of the gene expression differences in both liver and white muscle tissue allowed us to assess the seasonal influences upon gene expression patterns that occur in this species, and facilitated the identification of genes that may possess similar expression patterns regardless of seasonal effects.  The analysis of global gene expression in large and small fish reared under standard conditions provides an understanding of typical growth patterns that may be observed in this species.  The identification of candidate genes by this study may provide insight into the mechanisms of growth in fishes and may help to identify candidate genes for growth.

first: Moira

last: Ferguson

first: Roy

middle: G

last: Danzmann


title: Role of microRNAs in compensatory b-cell mass expansion associated with pregnancy and obesity

status: Public on Nov 20 2012

city: Lausanne

first: Cécile

last: Jacovetti

address: rue du Bugnon 9

department: DBCM

country: Switzerland

institute: University of Lausanne

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

summary: We found that in rodents, b-cell mass expansion during pregnancy and obesity is associated with changes in the expression of a group of islet microRNAs. We were able to reproduce in isolated pancreatic islets the decrease of miR-338-3p level observed in gestation and obesity by activating the G-protein coupled estrogen receptor GPR30 and the GLP1 receptor. Blockade of miR-338-3p in b-cells using specific anti-miR molecules mimicked gene expression changes occurring during b-cell mass expansion and resulted in increased proliferation and improved survival both in vitro and in vivo. These findings point to a major role for miR-338-3p in compensatory b-cell mass expansion occurring under different insulin resistance states.

overall_design:
GSM880669 - GSM880674
3 biological replicate of INS832/13 cells treated with either a control or an antimiR338 were submitted to RaGene V1,0 affymetrix chip to decipher the role of miR338

GSM896009 - GSM896016
Islets from control (n=4) or 14 days pregnant female rat (n=4) were taken. Total RNA was extracted and microRNA profiling was performed with miRNA Agilent arrays.

first: Cecile

first: Emmanuelle

last: Meugnier

first: Romano

last: Regazzi


title: Chip-chip from Candida albicans cells with HMS1-MYC, RTG1-MYC, RTG3-MYC, GFP-ZCF21, GFP-LYS14, GFP-LYS144

status: Public on Oct 02 2012

city: San Francisco

first: Jose

middle: Christian

last: Perez

department: Microbiology and Immunology

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary:
The transcription regulators HMS1, RTG1, RTG3, ZCF21, LYS14 and LYS144 play roles in the proliferation of C. albicans in a mammalian host.
Chromatin immunoprecipitation (ChIP) of HMS1-MYC, RTG1-MYC, RTG3-MYC, GFP-ZCF21, GFP-LYS14, GFP-LYS144 followed by array hybridization (Agilent) uncovered a network of target genes required for C. albicans to thrive in the host.

overall_design: Comparison of IP/input in tagged strains to untagged cells immuniprecipitated with the same antibody.

first: J

first: Alexander

last: Johnson


title: Sirolimus induced phosphaturia

status: Public on Sep 24 2012

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

summary:
Introduction: The kidney is the major arbiter of extracellular phosphate homeostasis. The vast majority of glomerular filtrated phosphate is reabsorbed in the proximal tubule. Posttransplant phosphaturia is common and aggravated by sirolimus immunosuppression. The cause of sirolimus induced phosphaturia however remains elusive.
Results: The urine phosphate/creatinine ratio was higher and serum phosphate was lower in sirolimus treated rats, fractional excretion of phosphate was elevated and renal tubular phosphate reabsorption was reduced suggesting a renal cause for hypophosphatemia. PTH was lower in sirolimus treated rats. FGF 23 levels were unchanged at day 2 but lower in sirolimus treated rats after 7 days. Brush border membrane vesicle phosphate uptake was not altered in sirolimus treated groups or by direct incubation with sirolimus. mRNA, protein abundance, and subcellular transporter distribution of NaPi-IIa, Pit-2 and NHE3 were not different between groups but NaPi-IIc mRNA expression was lower at day 7. Transcriptome analyses revealed candidate genes that could be involved in the phosphaturic response.
Discussion: Sirolimus caused a selective renal phosphate leakage which was not mediated by NaPi-IIa or NaPi-IIc regulation or localization. We hypothesize that another mechanism such as a basolateral phosphate transporter may be responsible for the sirolimus induced phosphaturia.
Male Wistar rats received sirolimus or vehicle for 7 days (1.5mg/kg) and were placed in individual metabolic cages for eight days allowing a 24 hour adaption period to the metabolic cage environment. At the end of the experiments rats were anesthetized by inhalation of Isoflurane/air and blood samples and kidneys were collected.

overall_design: 4 cases (sirolimus) and 4 controls (vehicle) have been analysed

first: Maria

last: Haller


title: Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Chlamydia trachomatis is a significant human pathogen yet their obligate intracellular nature severe restrictions upon research.  Chlamydiae undergo a complex developmental cycle characterized by an infectious cell type known as the  elementary body (EB) and an intracellular active replicative form called the reticulate body (RB).    EBs have historically been described as metabolically dormant.  A cell-free (axenic) culture system was developed which showed high levels of metabolic and biosynthetic activity from both EBs and RBs.  EBs preferentially utilized glucose-6-phosphate as an energy source whereas RBs required ATP. Both developmental forms showed improved activity when incubated under microaerobic conditions.  Incorporation of isotopically-labeled amino acids into proteins from both developmental forms indicated unique expression profiles which were confirmed by genome-wide transcriptional analysis.  The described axenic culture system will greatly enhance  biochemical and physiological analyses of chlamydiae.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Chlamydia axenic metabolic activity

first: Anders

last: Omsland

first: Janet

last: Sager

first: Vinod

last: Nair

first: Daniel

middle: E

first: Ted

last: Hackstadt


title: Poly(A) RNA profiling upon Gld2 knockdown in cultured hippocampal neurons

status: Public on Sep 01 2012

city: Worcester

first: Timothy

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

overall_design: Neurons transduced with scrambled and Gld2 knowdown shRNA

first: Joel

last: Richter


title: Formaldehyde and Epigenetic Alterations: MicroRNA Changes in the Nasal Epithelium of Nonhuman Primates

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: We set out to test the hypothesis that formaldehyde inhalation exposure significantly alters miRNA expression profiles within the nasal epithelium of nonhuman primates. Here, cynomolgus macaques were exposed to 0, 2, and 6 ppm formaldehyde for 6 hours/day across two consecutive days. RNA was extracted from the nasal maxilloturbinate region, a direct target of formaldehyde inhalation exposure. Genome-wide miRNA expression levels were assessed using microarrays.

overall_design: Cynomolgus macaques (Macaca fascicularis) were exposed to 0, 2 and 6 ppm formaldehyde for 6 hours/day across two consecutive days using whole body exposure chambers. RNA was extracted from the nasal maxilloturbinate region, a direct target of formaldehyde inhalation exposure. Genome-wide miRNA expression levels were assessed using microarrays.

last: Rager

first: Benjamin

last: Moeller

first: Dean

last: Kracko

first: Melanie

last: Doyle-Eisele

first: James

middle: A

last: Swenberg


title: Effect of Nocturnal Hemodialysis (NHD) on Cardiomyocyte Gene Expression

status: Public on Aug 03 2012

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

summary: Frequent hemodialysis is associated with improvement in myocardial mechanics and cardiac gene expression profile

overall_design: Uremic plasma (10%) before and after NHD was added to cultures of Neonatal Sprague-Dawley rat ventricular myocytes

first: Christopher

last: Chan


title: Gene expression profile of cancer cells growing as a co-culture with carcinoma-associated fibroblasts (CAF)

status: Public on May 31 2012

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: Molecular mechanisms of the cancer cells-carcinoma associated fibroblasts (CAF) interactions growing in vitro conditions as a co-culture. The five canine mammary cancer cell lines were cultured with CAF (isolated from canine mammary cancer) for 72hrs. Then, the cancer cells and CAFs were sorted and the gene expression analysis was conducted. The control for each co-cultured cell line was the same cell line growing as a single culture.

overall_design: Dye-swap experiment, each cell line growing in the co-culture conditions was compared to the same cell line growing as a single culture.

first: Karol

middle: M

last: Pawłowski

first: Alicja

last: Majewska

first: Izabella

last: Dolka

first: Tomasz

last: Motyl


title: Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat

city: Providence

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

summary: Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1) identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD) using microarrays; 2) expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3) test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ). Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q < 0.05). All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p < 0.05). In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p < 0.05). The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions.  Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat.

overall_design: Rats were exposed to sub-chronic low doses of the Sertoli cell toxicant 2,5-hexanedione (HD) or water (control for HD) for 3 months. Some rats in each group underwent 3 months of post-exposure recovery.

first: Kim

last: Boekelheide


title: Transcriptomic profiling permits the identification of pollutant sources and effects in ambient water samples

status: Public on Sep 20 2012

city: Davis

first: Richard

middle: Edward

last: Connon

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

summary: The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.

overall_design: Microarray assessments were conducted on larvae exposed for 7-days to Sacramento River water collected at Hood and pooled laboratory controls. Assessments were carried out in quadruplicate, using 3 fish per treatment. RNA was extracted from frozen whole, individual organisms, using Trizol Reagent (Invitrogen) as per manufacturer's guidelines. Total RNA from 5 fish was pooled per treatment and cDNA was synthesized from a total of 2ug total RNA, amplified using a SuperScripttm Indirect RNA Amplification System (Invitrogen). Resulting aRNA was labeled with Alexa fluor dyes (Invitrogen) as per manufacturer’s instructions. Two color microarray assessments were carried out on quadruplicate treatments, using 5µg of aRNA for pooled controls vs exposed sample, (total 4 samples). Microarray hybridizations were performed manually, and incubated in a waterbath at 42C for 16 hours. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment.

first: Matthias

last: Hasenbein

first: Inge

last: Werner

first: Juergen

last: Geist

first: Erika

middle: B

last: Fritsch

first: Alireza

last: Javidmehr

first: Linda

last: Deanovic

first: Sebastian

last: Beggel

last: Davies

first: Nann

last: Fangue


title: Expression data from EMRSA-15 treated with and without manuka honey

status: Public on Apr 04 2012

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary:
Manuka honey has been shown to inhibit growth in EMRSA-15 by inhibiting cell division, the mode of actin is currently unclear.
We used microarrays to detail the difference in global gene expresson following treatment of cells with honey. We identified distinct classes of up and down regulated genes

overall_design: EMRSA-15 were harvested 4 hours after exposure to treatment for RNA extraction and hybridization on Affymetrix microarrays. Control and honey treated cells were investigates, three biological replicates were used for each sample.

first: Rowena

last: Jenkins

first: Rose

last: Cooper


title: Nanomolar treatment with epigenetic drug combination induces genome-wide methylation and expression alterations in neuro-ectodermal cell lines [DNA methylation]

status: Public on Jul 01 2012

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

institute: Erasmus MC

summary: Epigenetic alterations are a fundamental aspect of cancer cells, and epigenetic drugs are currently used in clinical practice for hematological malignancies. Pediatric neuro-ectodermal tumors originate from neural crest cells and show epigenetic defects of apoptotic pathways, which points to sensitivity towards epigenetic drugs in this patient group. The young age of these patients is accompanied by However, ongoing developmental processes regulated by epigenetic mechanisms may be deregulated by epigenetic drugs in this patient group that is characterized by young age. This prompted us to study molecular effects and side-effects of low dosage epigenetic drugs in neuro-ectodermal tumor cell lines of pediatric origin.   Short term combination treatment of 5-aza-2`-deoxicytidine (DAC) and Trichostatin A (TSA) at nanomolar dosages reduced proliferation, induced wide-spread demethylating effects in 17 NBL and 5 PNET cell lines, and was accompanied  by large effects on gene-expression profiles. Approximately half of the genes that were significantly upregulated upon treatment demonstrated significant demethylating effects in their promoter regions. In NBL cell lines, almost every cellular pathway (193/200) investigated demonstrated altered expression upon treatment, and resulted in upregulation of known epigenetically regulated genes such as X-chromosomal, tissue-specific, and a limited number of imprinted genes, but also known tumor suppressor genes and oncogenes.   In conclusion, genome-wide methylation and gene expression changes are induced DAC and TSA treatment at nanomolar dosages. This treatment affected more than 97% of cellular pathways investigated and further studies towards the effectiveness and side-effects of epigenetic drugs are desirable in pediatric tumors.   Epigenetic alterations are a fundamental aspect of cancer cells, and epigenetic drugs are currently used in clinical practice for hematological malignancies. Pediatric neuro-ectodermal tumors originate from neural crest cells and show epigenetic defects of apoptotic pathways, which points to sensitivity towards epigenetic drugs in this patient group. The young age of these patients is accompanied by However, ongoing developmental processes regulated by epigenetic mechanisms may be deregulated by epigenetic drugs in this patient group that is characterized by young age. This prompted us to study molecular effects and side-effects of low dosage epigenetic drugs in neuro-ectodermal tumor cell lines of pediatric origin.   Short term combination treatment of 5-aza-2`-deoxicytidine (DAC) and Trichostatin A (TSA) at nanomolar dosages reduced proliferation, induced wide-spread demethylating effects in 17 NBL and 5 PNET cell lines, and was accompanied  by large effects on gene-expression profiles. Approximately half of the genes that were significantly upregulated upon treatment demonstrated significant demethylating effects in their promoter regions. In NBL cell lines, almost every cellular pathway (193/200) investigated demonstrated altered expression upon treatment, and resulted in upregulation of known epigenetically regulated genes such as X-chromosomal, tissue-specific, and a limited number of imprinted genes, but also known tumor suppressor genes and oncogenes.   In conclusion, genome-wide methylation and gene expression changes are induced DAC and TSA treatment at nanomolar dosages. This treatment affected more than 97% of cellular pathways investigated and further studies towards the effectiveness and side-effects of epigenetic drugs are desirable in pediatric tumors.

overall_design: DNA methylation analysis of neuro-ectodermal cell lines with and without DAC and TSA

first: F


title: Expression data from Angiotensin II (Ang II)-treated Rat Vascular Smooth Muscle Cells (RVSMC)

status: Public on Mar 23 2012

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary:
Angiotensin II (Ang II)-mediated vascular smooth muscle cells (VSMC) dysfunction plays a critical role in cardiovascular diseases. However, the gene expression in this process is unclear.
We used Rat Affymetrix gene array to profile Ang II-regulated gene in RVSMC and evaluated their role in VSMC dysfunction.

overall_design: Examined 4 samples of Rat VSMC in triplicate. Control (without Ang II treatment) and 3 samples treated with Ang II for 6h, 12h, and 24h. Compared the changes in gene expression in Ang II treated samples relative to control samples.

first: Jin

last: Wen

first: Marpadga

last: Reddy


title: Maternal immune activation by LPS selectively alters specific gene expression profiles of interneuron migration and oxidative stress in the fetus without triggering a fetal immune response.

status: Public on Jul 26 2012

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Maternal immune activation is a risk factor for the development of schizophrenia and autism. Infections during pregnancy activate the mother's immune system and alter the fetal environment with sub-sequence effects of CNS function and behavior in the offspring, but the cellular and molecular links between infection-induced altered fetal development and risk for neuropsychiatric disorders are unknown. We investigated the immunological, molecular, and behavioral effects of MIA in the offspring of pregnant Sprague-Dawley rats given an intraperitoneal (0.25 mg/kg) injection of lipopolysaccharide (LPS) on embryonic day 15.  LPS significantly elevated pro-inflammatory cytokines in maternal serum, amniotic fluid, and fetal brain at 4 h, and levels decreased but remained elevated at 24 h. Offspring born to LPS-dams exhibited reduced social and exploration behaviors as juveniles and young adults. Whole genome microarray analysis of the fetal brain at 4 h post maternal LPS was performed to elucidate possible molecular mechanisms by which MIA effects the fetal brain.  We observed dysregulation of 3,285 genes in restricted functional categories, with increased mRNA expression of cellular stress and cell death genes and reduced expression of developmentally-regulated and brain-specific genes, specifically those that regulate neuronal migration of GABAergic interneurons.

overall_design: 19 Fetal Rat Brain Samples: 10 (-) LPS, 9 (+) LPS.

first: Devon

last: Oskvig

first: Abdel

last: Elkahoun

first: Terry

last: Phillips

first: Miles

last: Herkenham


title: Effects of Developmental Lead Exposure on the Hippocampal Transcriptome.

city: Philadelphia

first: Keyur

last: Talsania

state: PA

address: 1020 Locust St

department: Pathology

institute: Thomas Jefferson University

summary: In this study we analyzed the effects of lead-exposure up hippocampal gene expression in males and females exposed to 0ppm, 250ppm and 750ppm lead during two different developmental periods, perinatal (in utero through to weaning at PND21) and postnatal (PND0-PND45).  All tissue was taken at PND 55.  We used affymetrix Rat Gene 1.0ST arrays to obtain global gene expression data from each animal, with a group size of 4 for all conditions (Total number of Arrays = 40)

overall_design: Gene expression was profiled in hippocampus at  no lead exposure (0ppm), 250ppm and 750 ppm lead exposure level at peinatal and postnaltal developmental period.

first: Jay

last: Schneider

first: David

last: Anderson


title: Molecular classification of human cholangiocarcinoma

status: Public on Feb 25 2012

city: Copenhagen

first: Jesper

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

summary:
Transcriptomic profiling
Background  Cholangiocarcinoma accounts for 5-10% of primary hepatic cancers. The etiology is unclear and patients are often diagnosed without risk factors. Resection is the only curative treatment although patients frequently remain undiagnosed until advanced stage of disease.     Methods  To construct molecular classification of cholangiocarcinoma, we profiled the transcriptomes of 104 freshly-frozen tumors and 59 matched non-cancerous livers obtained from Australia, Europe and the United States. We also performed mutational analysis of KRAS, EGFR and BRAF, and used laser-capture microdissection to obtain independent gene expression profiles for epithelial and stromal compartments in a subset of tumors. The selected target genes were validated by western blotting and immunohistochemistry.     Results  Transcriptomic profiling classified cholangiocarcinoma into two distinct subclasses defined by survival (P<0.0007) and early recurrence (P<0.001). Applying leave-one-out cross-validation, we optimized the prognostic classifier to 238 genes which were positively enriched in the epithelial tumor compartment.  A deregulated HER2 network was associated with the epithelial compartment which also showed a frequent overexpression of Ki67, EGFR, MET and pRPS6 whereas inflammatory cytokines were enriched in tumor stroma specifically in patients with poor prognosis. KRAS mutations were found in 24.6% of patients with poor disease outcome.     Conclusion  Our study presents new insights into pathogenesis of cholangiocarcinoma and stratification of the patients according to survival and recurrence. Identification of a subgroup of patients among the poor prognostic cohort characterized by KRAS mutations and oncogenic-addiction may provide a novel therapeutic opportunity for this treatment-refractory malignancy.

overall_design: Profiling of individual cholangiocarcinomas and non-cancerous matched surrounding livers using normal bile ducts as reference

first: Snorri

middle: S

last: Thorgeirsson


title: Sparing of muscle mass and function by passive loading in an experimental intensive care unit model

status: Public on May 12 2012

city: Uppsala

first: Monica

last: Llano-Diez

address: Akademiska sjukhuset, Ing.85, 3tr

department: Neuroscience

country: Sweden

institute: Uppsala university

summary: Critically ill intensive care unit (ICU) patients commonly develop severe muscle wasting and impaired muscle function, leading to delayed recovery, with subsequent increased morbidity and financial costs, and decrease quality of life of survivors. Acute Quadriplegic Myopathy (AQM) is one of the most common neuromuscular disorders associated with ICU-acquired muscle weakness. Although there are no available treatments for the ICU-acquired muscle weakness, it has been demonstrated that early mobilization can improve its prognosis and functional outcomes. This study aims at improving our understanding of the effects of passive mechanical loading on skeletal muscle structure and function by using a unique experimental rat ICU model allowing analyses of the temporal sequence of changes in mechanically ventilated and pharmacologically paralyzed animals at durations varying from 6 h to 14 days.  Results show that passive mechanical loading alleviated the muscle wasting and the loss of force-generation associated with the ICU intervention, resulting in a doubling of the functional capacity of the loaded vs. unloaded muscles after a 2-week ICU intervention. We demonstrated that the improved maintenance of muscle structure and function is likely a consequence of a reduced oxidative stress,  and a reduced loss of the molecular motor protein myosin. A complex temporal gene expression pattern, delineated by microarray analysis, was observed with loading-induced changes in transcript levels of sarcomeric proteins, muscle developmental processes, stress response, ECM/cell adhesion proteins and metabolism. Thus, the results from this study show that passive mechanical loading alleviates the severe negative consequences on muscle structure and function associated with mechanical silencing in ICU patients, strongly supporting early and intense physical therapy in immobilized ICU patients.

overall_design:
This study aims to unravel the effects of passive mechanical loading on skeletal muscle structure and function in an experimental rat ICU model at duration varying between 6h and 14 days.
A total of 23 experimental female Sprague-Dawley rats were included in this study. The experimental rats were anaesthetized, treated with the neuromuscular blocking agent (NMBA) α-cobrotoxin, mechanically ventilated and monitored for durations varying from 6h to 4 days (n=13), from 5 to 8 days (n=4), and from 9 to 14 days (n=6). The left leg of the animal was activated for 6 hours at the shortest duration and 12 hours per day at durations 12 hours and longer throughout the experiment, using a mechanical lever arm that produced a continuous passive maximal ankle joint flexions-extensions at a speed of 13.3 cycles per minute. Muscle biopsies were obtained from gastrocnemius muscle (proximal part) immediately after euthanasia, were quickly frozen in liquid propane cooled by liquid nitrogen, and stored at -80°C. RNA was extracted.

first: Guillaume

last: Renaud

first: Barbara

last: Ravara

first: Luisa

last: Gorza

first: Lars

last: Larsson

first: Han

middle: Z

last: Feng

first: J

middle: P

last: Jin

first: Nicola

last: Cachiani

first: Ann

last: Gustafsson

first: Meishan

last: Li

first: Yvette

last: Hedström

first: G

middle: C

last: Ford

first: K

last: Nair


status: Public on Mar 10 2012

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

summary: Methylation profiling in colorectal cancer : adjacent normal tissue vs colon tumor tissue

overall_design: indirect comparison experiment : CRD(common reference DNA) vs tumor-adjacent normal, CRD vs Colon tumor

first: Nayoung

first: Taejeong

last: Oh


title: Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR).

status: Public on Feb 24 2012

city: Adelaide

first: Melinda

middle: N

last: Tea

state: South Australia

address: Flinders Medical Centre, Carpark Building

department: Ophthalmology

institute: Flinders University

summary: Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time points of day 5 (in response to hyperoxia) and day 6 (in response to relative hypoxia) to identify gene pathways related to the underlying genetic cause of the phenotypic differences observed between strains.

overall_design: To examine gene expression changes in rat strains which are resistant and susceptible to OIR, four different experimental conditions were analysed: F344 cyclic hyperoxia (O2) exposed, F344 room air (RA) exposed, SD O2 exposed and SD RA exposed. Two samples of pooled RNA, comprising of 3 individual rats from 2 separate litters, was used for each experimental condition, for each time point of interest. Pooled RNA from age-matched room air-exposed rats were used as controls.

first: Rhys

last: Fogarty

first: Helen

last: Brereton

first: Michael

last: Michael

first: Rosalie

last: Kenyon

first: Mark

last: Van der Hoek

first: Anna

last: Tsykin

first: Douglas

middle: J

last: Coster

first: Keryn

last: Williams


title: Epigenetic Transgenerational Alterations to Stress Response in Brain Gene Networks and Behaviour

status: Public on Feb 01 2012

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

summary:
Ancestral environmental exposures that promote epigenetic transgenerational inheritance influence all aspects of an individual’s life history.  Stress experienced during adolescence can affect adult physiological and behavioural phenotypes. The current study utilized a systems biology approach to investigate the interactions of these two forms of epigenetic modification, one carried in the germline transgenerationally and the other contained in the context of life history.  A transgenerational epigenetic imprint left by the fungicide vinclozolin promoted regional specific brain gene networks that influenced chronic restraint stress responses to alter adult physiological, brain and behavioural phenotypes.  The environmentally-induced epigenetic transgenerational inheritance was found to interact with early life stress response to impact the adult brain genome activity to bring “the phenotype into being”.
We used microarrays to determine genes expressed differentially in rats' 4 brain areas - basolateral amygdala (BLA),  primary and secondary motor cortex (Crtx),  CA1 of the hippocampus (CA1), and CA3 of the hippocampus (CA3) -  due to Vinclozolin treatments of their grand-grandmothers and/or to stress in adolescence age.

overall_design: For each of 4 brain areas (BLA, CRTX, CA1, and CA3), RNA samples from 4 treatment groups - stressed control (St-Con), non-stressed control (NSt-Con), stressed vinclozolin (St-Vin), and non-stressed vinclozolin (NSt-Vin) - were compared to each other.  Each treatment groups contained 3 biological replica. RNA for each replica was pooled from 4 individual animals forming a certain dyad group.

first: David

last: Crews

first: Ross

last: Gillette

first: Mohan

last: Manikkam

first: Marina

last: Savenkova


title: Gene expression in Plasmodium falciparum NF54 and P. falciparum HOX

status: Public on Mar 01 2012

city: Baltimore

first: Rahul

middle: Prakash

last: Bakshi

address: 303 Hunterian 725 N Wolfe Street

department: Medicine/Clinical Pharmacology

institute: Johns Hopkins University School of Medicine

summary: P. falciparum NF54 proliferates under micro-aerophilic conditions in an environment of 3% O2, 4% CO2, 93% N2. This strain was gradually adapted to proliferate under standard tissue culture conditions of 5% CO2/95% air (~19% O2) to generate P. falciparum HOX. We compared global gene expression profiles of the two strains to identify differences, if any.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Asynchronous cultures of P. falciparum NF54 and HOX propagated in O+ RBCs were processed and gene expression analyzed on Affymetrix microarrays.  All cultures consised of 80% rings + trophozoites.

first: Theresa

last: Shapiro

first: Anne

last: Jedlicka

first: Amanda

last: Dziedzic


title: leaf transcriptome comparison between wt and urt1 (salk_087647) -Transcriptome comparison between WT and a mutant impaired in RNA uridylation.

status: Public on Jul 13 2012

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: rs11-10_urt1 - leaf transcriptome comparison between wt and urt1 (salk_087647)  - Identification of mRNA targets of the terminal uridylyltransferase URT1 (AT2G45620) in Arabidopsis thaliana. - Identification of the RNA targets of the terminal uridylyl transferase URT1 (AT2G45620). Mature rosettte leaf transcriptomes were compared between WT and a urt1 knock-out mutant (SALK_087647).

overall_design: 3 dye-swap - gene knock out

first: Sandrine

last: Balzergue

first: Stéphanie

last: Pateyron

first: Dominique

last: Gagliardi

first: Marie-Laure

last: Martin-Magniette


title: Osmolality as a major regulator of the transcriptome and metabolome in kidney collecting duct cells

status: Public on Feb 09 2012

city: Daegu

first: Hyo-Jung

last: Choi

address: Dongin-dong 101

department: Biochemistry and Cell Biology

institute: Kyungpook National  University

summary: We hypothesized that altered extracellular osmolality per se could affect the transcriptome of the kidney inner medullary collecting duct (IMCD) cells, and hence it might change renal tubular function. The data sets of transcriptomics were incorporated into the "omic" data sets of metabolomics. Primary cultured IMCD cells of rat kidney were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with either reduced (300 mOsm/KgH2O) or the same osmolality for 1 or 2 d more.

overall_design:
Osmolality stress response.
Total RNA from IMCD cells exposed to 300 or 640 mOsm/KgH2O for 24 h (n=3 in each group, 24 h-300 and 24 h-640) or for 48 h (n=3 in each group, 48 h-300 and 48 h-640) after a 4-day-culture in culture media (640 mOsm/KgH2O) were subjected to transcriptome analysis (Affymetrix GeneChip® Rat Gene 1.0 ST array containing 29,215 gene-level probe sets) to profile the gene expression at the mRNA level.

first: Tae-Hwan

last: Kwon


title: Expression data from in utero exposure to genistein, vinclozolin and the mixture of genistein and vinclozolin on the mammary gland

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
Morphogenesis of the mammary gland relies on the precise developmental control of morphological elements including TEBs, ducts and lobules. In the peripubertal mammary gland, rising levels of ovarian hormones control this development through a tightly controlled genetic program where specific sets of genes are up-regulated.
We used microarrays to detail the program of gene expression underlying different classes of up-regulated genes during the peripubertal process after administration of endocrine disruptors during the fetal and neonatal development.

overall_design: Rat mammary glands were selected at two peripubertal periods (days 35 and 50), after administration of genistein and vinclozolin during the fetal and neonatal development,  for RNA extraction and hybridization on Affymetrix microarrays.. We sought to obtain homogeneous populations of mammary gland for each treatment, and at each developmental stage, in order to increase the temporal and specific effect resolution of time course and endocrine disruption.

first: Martine

last: Perrot-Applanat

first: Hanan

last: El Sheikh Saad


title: Activated YAP1 stimulates cardiomyocyte proliferation

status: Public on Jan 12 2012

city: Boston

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

summary:
Postnatal day 4 neonatal rat cardiomyocytes transduced with LacZ or flag-tagged, activated YAP1 (S127A) expressing adenovirus
After transduction, cells were cultured in serum free media and collected 48 hours later.

overall_design: 2 group comparison, n=4 biological replicates per group

first: Zhiqiang

last: Lin

first: Alexander

last: von Gise


title: Gene expression profile changes upon knock-down of Pax8

status: Public on Dec 20 2011

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

country: Italy

institute: Unversity of Naples Federico II

summary:
In order to define the transcriptional network functionally regulated by Pax8 as well as infer its direct targets, we performed RNAi to knock-down Pax8 gene in FRTL-5 thyroid cells. Expression data from three independent silencing experiments were analyzed by microarray technology unraveling 2815 genes differentially expressed between silenced cells and controls. Of these, 1421 genes were down-regulated and 1394 genes were up-regulated 72hrs after Pax8 silencing.
The results obtained suggest that Pax8 regulates numerous pathways, some of which involved in the regulation of cell cycle, thyroid cancer and apoptosis, thus confirming that Pax8 is a master regulatory gene.

overall_design: Rat differentiated thyroid cells from FRTL-5 line were transfected with siGENOME Pax8 siRNA (siPax8, experimental) or siGENOME Non-Targeting siRNA (ntPax8, controls). The trascriptome from three siPax8 biological replicates, 72 hours after transfection, was compared to the trascriptome from 3 control ntPax8 biological replicates. Microarray analysis was performed at gene-level using the AffymetrixGeneChip Rat Gene 1.0 ST array

first: Tina

last: Di Palma

first: Anna

last: Conti

first: Tiziana

last: de Cristofaro

first: Serena

last: Scala

first: Mariastella

last: Zannini


title: rnapaths--3_02/2012-RNAPATHS-3

first: Soubigou-Taconnat

last: Ludivine

summary: blanc-08-01_2012_01_rnapaths_03 - rnapaths--3_02/2012 - Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT. - Identify transcripts that are significantly changed in double mutants (L1 vcs sgs2) (xrn4-5/sgs3-11) versus their respective single mutants (L1 vcs and L1 sgs2) (xrn4-5 and sgs3-11) , and identify transcripts that are changed among the single and double mutants compared to WT (Col) reference or to mutant L1 reference.

overall_design: 20 dye-swap - genotype comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Allison-

last: Mallory


title: Transcriptome Remodeling Associated with Chronological Aging in the Dinoflagellate, Karenia brevis

status: Public on Jan 01 2012

city: Charleston

first: Frances

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

summary: To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2,958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate.

overall_design: Twenty seven 900ml batch cultures of K. brevis were inoculated at a starting concentration of approximately 1000 cells/ml from mid-logarithmic stage starter cultures on day 0. Triplicate cultures were harvested every other day from day 2 to 18 and total RNA was extracted. One color arrays were then run on all biological replicates (n=3 at each timepoint) for days 4, 6, 10, 14 and 18.

first: Jillian

middle: G

last: Johnson


title: Gene expression in response to short and long term cAMP stimulation in the INS-1 insulinoma cell line

status: Public on Nov 22 2011

city: La Jolla

first: Sam

last: Van de Velde

address: 10010 North Torrey Pines Road

department: Peptide Biology Laboratories

institute: Salk Institute

summary:
Long term exposure to incretin hormones is known to have salutory effects on beta cell function and viability. While short-term cAMP induction is known to have a signature CREB-CRTC target gene response, the long-term effects of cAMP on beta cell gene expression are less well understood.
We used rat microarray analysis to compare the genome-wide gene expression response to short-term (2 hours) and long-term (16 hours) stimulations of the cAMP agonist forskolin in INS-1 insulinoma cells.

overall_design: INS-1 cells were exposed to forskolin for 2 or 16 hours in RPMI medium containing 10% serum. Control samples wer incubated for the same time without forskolin. Extracted RNA was used for hybridization on Affymetrix rat 1.0 st gene arrays.


title: Gene expression profile analysis of non small cell lung cancer in North East India

status: Public on Jan 31 2012

city: New Delhi

first: Rakhshan

last: Ihsan

state: Delhi

address: Safdurjung Hospital Campus

country: India

institute: Institute of Pathology(ICMR)

summary: The objective of this study was to identify the genes differentially expressed in non small cell lung carcinoma associated with prevalent risk factor such as smoking and betel quid chewing in high-risk north eastern Indian population. The tumor biopsies and matched normal tissue from distant site were collected in RNA later, snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical and pathologic report. Institutional human ethics committee approved the study.

overall_design: Total RNA was isolated from tumor biopsies and matched normal of five patients. Total RNA from normal tissue from three patients was pooled in one slide and normal tissue from another two patients was pooled in another slide. Individual slide were used for each tumor samples.   Isolation Kit: RNeasy mini Kit (Qiagen)   Scanner Used: AFFYMETRIX, 428 Array

first: R

first: S

last: Kapur

last: Saxena


title: Segmentation and intensity estimation for microarray images with saturated pixels

status: Public on Nov 23 2011

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

summary: Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels

overall_design: Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image.  These images had several saturated spots at 70PMT and 100% laser power.  The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.

first: Yang

last: Yan

first: Stafford

last: Phillip

first: Kim

last: YoonJoo


title: Global expression analysis identified a preferentially NGF-induced transcriptional program regulated by sustained MEK/ERK and AP-1 activation during PC12 differentiation.

status: Public on Nov 13 2011

first: Steven

last: Mullenbrock

state: MA

address: 24 Cummington St.

department: Biology

institute: Boston University

summary: Neuronal differentiation of PC12 cells in response to NGF is a prototypical model in which signal duration determines a biological response. Sustained ERK activity induced by NGF, as compared to transient activity induced by EGF, is critical to the differentiation of these cells. To characterize the transcriptional program activated preferentially by NGF, we compared global gene expression profiles between cells treated with NGF and EGF for 2-4 hrs, when sustained ERK signaling in response to NGF is most distinct from the transient signal elicited by EGF. This analysis identified 69 genes that were preferentially upregulated in response to NGF.

overall_design: PC12 cells that were starved in low serum media for 24 hrs were treated with NGF (50ng/mL) or EGF (25ng/mL) for 2 or 4 hrs, or left untreated.  Total RNA for 3 independent biological replicates was extracted and subjected to Affymetrix Rat Gene 1.0ST Arrays.  The 69 genes that were preferentially upregulated by NGF compared to EGF met the following criteria: NGF/No treatment log2> 1, FDR p value< 0.01 and NGF/EGF log2> 0.75, FDR p value< 0.01.

first: Janki

last: Shah

first: Geoffrey

last: Cooper


title: Toxicogenomic Study of Pentamethylchromanol (PMCol)

status: Public on Nov 01 2011

city: Menlo Park

first: Hanna

middle: Hongchin

last: Ng

address: 333 Ravenswood Avenue

institute: SRI International

summary:
The objective of this study is to determine the molecular mechanisms of PMCol-induced hapatotoxicity using microarray
The study demonstrated that chronic exposure to high doses of PMCol induces liver damage and dysfunction, probably due to both inhibition of synthesis and depletion of liver glutathione as well as modification of other drug metabolism pathways.

overall_design: PMCol was administered to male Sprague-Dawley rats at at doses of 200 and 2000 mg/kg daily for 7 or 28 days

middle: H

first: Deborah

middle: I

last: Bunin

first: Abraham

last: Wang


title: Gene expression profile of preclinical arthritis and its modulation by antigen-induced tolerance

status: Public on Nov 16 2011

first: Kamal

middle: D.

last: Moudgil

address: 685 W. Baltimore Street

department: Microbiology and Immunology

institute: University of Maryland School of Medicine

summary:
During the course of adjuvant arthritis, maximal changes in gene expression were observed at the incubation phase. A major group of genes affected was related to immune activity. Tolerance induction by mycobacterial heat-shock protein 65 (Bhsp65), the disease-related antigen, caused upregulation of a large number of genes. These included immune activity genes as well as cell proliferation-related genes.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: The draining lymph node cells (LNC) were harvested from arthritic rats at different phases of adjuvant arthritis (incubation,peak and recovery). Also tested were LNC of naïve rats. LNC were tested ex vivo. Total RNA isolated from LNC was used for testing with affymetrix gene chip following manufacturer's instructions. Similarly, LNC of Bhsp65-tolerized rats harvested at incubation phase were tested with or without Bhsp65 restimulation in vitro. LNC of arthritic rats in incubation phase were similarly restimulated with Bhsp65 in vitro as controls, and the results compared with that of the tolerized rats.

first: Hua

last: Yu

first: Changwan

last: Lu

first: Ming

last: Tan

middle: D


title: Ischemic Pre- and Post Conditioning has pronounced effects on Gene Expression Profiles in the Rat Liver after Ischemia/Reperfusion

status: Public on Oct 01 2011

city: Aarhus C

first: Anders

middle: Riegels

last: Knudsen

address: Nørrebrogade 44, building 1c, LVN-research

department: Department of Surgery, Section for upper GI surgery

institute: Aarhus University Hospital

summary: Ischemia/reperfusion injuries is a known complication to hepatic surgery. Ischemic pre- (IPC) and postconditioning (IPO) protects the liver against ischemia/reperfusion-injuries. Expression profiling were performed on liver biopsies seeking to identify molecular mediators of the protective properties.

overall_design: 48 rats were divided into 5 groups; sham (n=8), IRI (n=10), IPC (n=10), IPO (n=10) and IPC+IPO (n=10). All rats except sham rats were subjected to 30 min of total liver ischemia and 30 min of reperfusion before liver biopsies were sampled. In the IPC group, liver ischemia was preceded by 10 min of hepatic ischemia, followed by 10 min of reperfusion. IPO were performed by three cycles of 30 sec of reperfusion and 30 sec of ischemia, applied immediately after the 30 min of total liver ischemia. In the IPC+IPO group the two interventions were combined.

first: Anne-Sofie

last: Kannerup

first: Rune

last: Dich

first: Peter

last: Funch-Jensen

first: Henning

last: Grønbæk

first: Mogens

last: Kruhøffer

first: Frank

middle: V

last: Mortensen


title: Expression data from pig BMDM treated with salmonella LPS

status: Public on Sep 01 2011

city: St Lucia

first: ronan

last: kapetanovic

state: QLD

address: The University of Queensland

institute: Institute for Molecular Bioscience

summary:
Mouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig bone marrow cells for 5-7 days in presence of rhCSF-1 generated a pure population of BMDM that expressed the usual macrophage markers (CD14, CD16, CD163, CD172a), are potent phagocytic cells and produced tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS). Bone marrow cells could be stored frozen and thawed, providing a renewable resource.
We profiled gene expression in pig BMDM from outbred animals (Large-White Landrace F1cross) responding to LPS using Affymetrix microarrays. The temporal cascade of inducible and repressible genes more closely-resembled human than mouse macrophages, and included genes involved in tryptophan metabolism (IDO, KYN), lymphoattractant chemokines (CCL20) and the vitamin D3-converting enzyme Cyp27B1. Conversely, pig BMDM, like human macrophages, did not induce genes involved in arginine metabolism, nor did they produce nitric oxide. The data establish pig BMDM as an alternative tractable model for the study of macrophage transcriptional control.

overall_design: RNA for gene expression analysis was collected at time points 0, 2, 7 and 24 hours post LPS stimulation (100ng/ml). Each time point included BMDM from the same three pigs and each cell culture was replicated. The replicate of the pig3_24h was not suitable for RNA analysis. Therefore, a total of 23 microarrays were hybridized.

first: Ronan

last: Kapetanovic

first: Dario

last: Beraldi

first: Lynsey

last: Fairbairn

first: David

last: Sester

first: Chris

last: Tuggle

middle: A

last: Hume


title: mRNA and miRNA expression analysis of developmental ethanol exposure in zebrafish

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary:
During early neurogenesis, multiple whole animal gene expression profiling studies revealed widespread changes in developmental mRNA and miRNA abundance in ethanol-exposed embryos.
Consistent with a role for miRNAs in neurobehavioral development, miRNA target prediction analyses identified multiple miRNAs misexpressed in the ethanol exposed cohorts that were also predicted to target inversely expressed transcripts known to influence brain morphogenesis.

overall_design:
[mRNA] A twelve chip study using total RNA recovered from pools of 75 tropical 5D zebrafish embryos at 24 hours post fertilization (hpf). Embryos were exposed to control embryo medium, 100 mM ethanol, or 300 mM ethanol from 4-24 hpf, with four-fold biological redundancy per condition.  A single 12x135K Nimblegen array was used to measure the expression level of 38,489 genes from Danio rerio using 60-mer probes, with three-fold technical redundancy.

[miRNA] A twelve chip study using miRNA recovered from pools of 75 tropical 5D zebrafish embryos at 12, 24, 36, and 48 hours post fertilization (hpf). Embryos were exposed to control embryo medium or 300 mM ethanol from 4-24 hpf, with two-fold biological redundancy per condition.  Control samples were pooled and hybridized to a single array. 12 miRZebrafish arrays (based on MirBase release 12.0) were used to measure the expression level of 218 mature miRNA from Danio rerio, with 12-fold technical redundancy.

first: Tamara

last: Tal

first: Jill

last: Franzosa

first: Susan

last: Tilton

first: Kenneth

last: Philbrick

first: Urszula

last: Iwaniec

first: Russell

last: Turner

first: Katrin

middle: M

last: Waters