title: Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

status: Public on Feb 28 2013

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

summary: For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. Despite low quality RNA, archival phenobarbital samples exhibited strong induction of the positive control genes CYP2b9 and CYP2b10 by RT-PCR. We hybridized Universal Linkage System–labelled cDNA libraries to 8x60K Agilent gene expression arrays. We compared one- and two-colour microarray experiments and tested the effects of increasing the amount of cDNA loaded. Canonical gene responders to phenobarbital treatment were measurably induced under each experimental condition (however increasing cDNA input also increased the array background signal). Individual genes were validated by RT-PCR and literature searches, and pathway analysis demonstrated that 9/10 top canonical pathways were consistent across experiments. These analyses suggested that future experiments should be done in duplicate to identify and eliminate false positive genes. We conclude that FFPE samples can be used for meaningful and reproducible gene expression and pathway analyses using microarrays.

overall_design: Phenobarbital-exposed mice (n=3) versus Control mice (n= 3)

middle: F

first: Andrew

last: Williams

first: Ivy

last: Moffat

first: Leslie

last: Recio

first: Mike

last: Waters

first: Suzanne

last: Phillips

first: Iain

middle: B

last: Lambert

first: Carole

middle: L

last: Yauk


title: Mapping of Three Genetic Determinants of Susceptibility to Estrogen-Induced Mammary Cancer within the Emca8 Locus on Rat Chromosome 5

status: Public on Feb 08 2013

city: Madison

first: James

last: Shull

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

country: USA

institute: University of Wisconsin-Madison

summary: We are using the ACI rat model of 17beta-estradiol induced mammary cancer to define the mechanisms through which estrogens contribute to breast cancer development; identify and functionally characterize the genetic variants that determine susceptibility; and define the hormone-gene-environment interactions that influence development of mammary cancer in this physiologically relevant rat model. Female ACI rats are uniquely susceptible to development of mammary cancer when treated continuously with physiologic levels of 17beta-estradiol. Induction of mammary cancer in female ACI rats occurs through a mechanism that is largely dependent upon estrogen receptor-alpha. Interval mapping analyses of progeny generated in intercrosses between susceptible ACI rats and resistant Brown Norway (BN) rats revealed seven quantitative trait loci (QTL), designated Emca3 (Estrogen-induced mammary cancer) through Emca9, each of which harbors one or more genetic determinants of mammary cancer susceptibility. Genes that reside within Emca8 on RNO5 and were differentially expressed between 17beta-estradiol treated ACI and ACI.BN-Emca8 congenic rats were identified as Emca8 candidates.

overall_design: Two groups of 17beta-estradiol treated female rats were compared. Five ACI and five BN.ACI-Emca8 rats were treated with 17beta-estradiol for 12 weeks. Total RNA was isolated from the mammary glands of these animals, labeled, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays (Affymetrix Inc.). Significantly differentially expressed genes were found between these groups.

first: Beverly

middle: S

last: Schaffer

first: John

middle: A

last: Colletti

first: Christopher

last: Warren

middle: D


title: Comparison of Gene Expression between Peri-implant Soft Tissue and Oral Mucosal Tissue

status: Public on Jan 24 2013

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

country: Japan

institute: Tokyo Dental College

summary: The mucosal penetration area formed by implant placement is critical problems of dental implant treatment, because epithelial barrier is broken and it can become a source of inflammation. To clarify the influence and risk caused by dental implant treatment in peri-implant soft tissue, we compared to gene expression profile of peri-implant soft tissue and oral mucosal tissue with microarray analysis.

overall_design: Both side upper first molars of 4 week-old rat were extracted, and titanium alloy implants were placed only in the left extraction socket. Four weeks after surgery, samples were harvested from left side of peri-implant soft tissue and right side of oral mucosal tissue.

first: Yasushi

last: Makabe

first: Gentaro

last: Mori

first: Masao

last: Yoshinari

first: Yasutomo

last: Yajima


title: Excessive leukotriene B4 in nucleus tractus solitarii is pro-hypertensive in spontaneously hypertensive rats.

status: Public on Mar 01 2013

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

summary:
We have used Affymetrix microarray-driven  gene profiling to comprehensively describe the expression of mRNAs in  the nucleus tractus solitarii (NTS) in the adult male spontaneously hypertensive rat (SHR) as compared to  its normotensive parental Wistar-Kyoto (WKY) strain.
Keywords: Gene expression

overall_design: NTS was dissected from  hypertensive (SHR) and normotensive (WKY) strains of rat. For each structure, 10 independent Affymetrix Genechip 230 2.0 experiments were performed (5 SHR, 5 WKY), with each chip representing an independent biological replication (n=5).

first: Charles

middle: C

last: Hindmarch

first: Hidefumi

last: Waki

first: Emma

last: Hendy

first: Sabine

last: Gouraud

first: Marie

last: Toward

first: Sergey

last: Kasparov

first: Julian

last: Paton

first: David

last: Murphy


title: The RNA-binding protein FXR1P regulates cell-cycle progression by modulating the expression of p21/cdkn1a/Cip1/Waf in myoblasts

status: Public on Feb 01 2013

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The Fragile X Mental Retardation-Related 1 gene (FXR1) belongs to the Fragile X Related gene family, together with FMR1 and FXR2. While inactivation of FMR1 causes Fragile X syndrome, the most common form of inherited mental retardation, inactivation of FXR1 in various animal models suggest a critical role for the RNA-binding protein FXR1P during myogenesis. Seven alternatively spliced FXR1 transcripts have been identified, three of them being muscle-specific. We previously reported a reduction of these isoforms in myoblasts from Fascio Scapulo Humeral Distrophy (FSHD) myopathic patients. However, so far, no mRNA target of FXR1P has been linked to the drastic muscular phenotypes caused by its absence and the exact molecular role of FXR1P in muscular development remains unknown. In the present study, gene expression profiling of C2C12 myoblasts reveals that transcripts involved in cell cycle and muscular development pathways are modulated by Fxr1-depletion. In addition, Fxr1-depletion translates physiologically into a premature cell cycle exit of myoblasts, accompanied by a robust up-regulation of the cyclin-dependant kinase inhibitor p21/Cdkn1a/Waf/Cip1 mRNA. Importantly, we also observe this P21 increase in FSHD human myoblasts depleted in FXR1P muscular isoforms. Our data further indicate that FXR1P muscle-specific isoforms are involved in the post-transcriptional control of p21 mRNA levels via direct interaction with a conserved G-quadruplex structure located in its 3’ untranslated region. This study has crucial implications for the understanding of FXR1P role during myogenesis and the pathophysiology of FSHD.

overall_design: 2 independent experiments performed in a one color design, corresponding to 2 conditions: si-control and si-fxr1, for a total of 4 samples.

first: B

last: Bardoni

first: P

last: Barbry

first: K

last: Mari

first: L

last: Davidovic


title: mRNA reponse to bleomycin instillation

summary: Gene expression analysis of C57BL/6 mice challenged by intratracheal bleomycin instillation: mRNA expression profiles were established from lungs following a 14-days PBS or bleomycin administration.

overall_design: One color -experiment with 1 strain of mice (C57BL/6) following a 14-days PBS or bleomycin administration (n=5), corresponding to a total of 10 samples.

first: Nicolas

last: Pottier


title: Gene expression study of macrophages during early foreign body reaction

status: Public on Jan 23 2013

city: Leuven

first: Lindsay

last: Mesure

address: Minderbroedersstraat 17

department: Cardiovascular Diseases

country: Belgium

institute: KULeuven

summary:
Foreign body reaction (FBR), initiated by adherence of macrophages to biomaterials, is associated with several complications.
Searching for mechanisms potentially useful to overcome these complications, we have established the signaling role of macrophages in the development of FBR. This study profiles gene expression of in vitro fibrinogen activated macrophages as well as that of freshly isolated macrophages from 3-days implants, against a background of unactivated macrophages/monocytes.

overall_design:
Total RNA was isolated from fibrinogen activated macrophages, FBR macrophages and macrophages from blood (control). Samples were processed in triplicate on Rat Genome 230 2.0 Array GeneChips, adding up to 9 arrays in total. Microarray processing was performed at DNAVision (Charleroi, Belgium).

The RMA comparisons between macrophases are linked below.

first: Geofrey

last: De Visscher

first: Willem

last: Flameng


title: Expression data from the telencephalon of wild-type and rSey2/rSey2 rats

status: Public on Jan 11 2013

city: Sendai

first: Takako

last: Kikkawa

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku

institute: Tohoku University Graduate School of Medicine

summary:
Pax6 is one of the important transcription factors involved in regional specification and neurogenesis in the developing cortex.
To identify candidate target genes of Pax6, we performed transcriptome analyses of wild-type (WT) and Pax6 homozygous mutant rats (rSey2/rSey2) telencephalons at E11.5 within a day of onset of Pax6 expression. In our transcriptome analyses, down-regulated genes in the rSey2/rSey2 rat exhibited larger fold changes, whereas up-regulated genes had relatively small fold changes.

overall_design: Total RNA was prepared using  from 13 telencephalon dissected from E11.5 WT or rSey2/rSey2 rats embryos. Experiments using 13 telencephaon were repeated twice in each genotype.

first: Urara

last: Fukuzaki

first: Keiko

last: Numayama-Tsuruta

first: Noriko

last: Osumi


title: Gene expression changes under cyclic mechanical stretch in rat retinal Muller cells

status: Public on Jan 16 2013

city: Shanghai

first: Xin

last: Wang

address: Fenyang road

country: China

institute: Fudan University

summary:
The retina is often subjected to tractional forces in a variety of conditions, for instance, pathological myopia, proliferative vitreoretinopathy. As the predominant glial element in the sensory retina, Muller cells are responsible for the homeostatic and metabolic support of retinal neurons and active players in virtually all forms of retinal injury and disease. Besides, Muller cells span the entire retinal thickness, extending from the inner to the outer limiting membranes, with cell bodies located in the inner nuclear layer and lateral processes expanding into the plexiform layers of the tissue. Because of this unique morphology, Muller cells can sense even minute changes in the retinal structure because of the mechanical stretching of their long processes or side branches. Thus, it’s reasonable to infer that Muller cells also participate in ocular diseases when the retina is overstretched. In this study, we aim to investigate the whole genome regulation of Muller cells under mechanical stretching, which may help in excluding possible molecular mechanisms that would account for many retinal diseases in which the retina is often subjected to mechanical forces.
We used microarrays to identify patterns of gene expression changes induced by cyclic mechanical stretching in Muller cells.

overall_design: Rat Muller cells were seeded onto flexible bottom culture plates and subjected to a cyclic stretching regimen of 15% equibiaxial stretching for 1 and 24 h.Muller cells cultured under the same conditions but with no applied mechanical strain were considered as the unstretched control. At each time points (1 and 24 h), three totally independent experiments (3 stretched samples and 3 control samples) were conducted. Muller cells were selected for RNA extraction and hybridization on Affymetrix microarrays. Stretch (S); Control (C)

first: Gezhi

last: Xu

first: Jiawen

last: Fan


title: Comparison of gene expression between MEFs and induced embryonic Sertoli-like cells

status: Public on Dec 20 2012

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: To compare the the genomic profile of MEFs and induced embryonic Sertoli-like cells following 2 weeks of dox withdrawal.

overall_design: ieSCs (from MEFs and from TTFs) and MEF control were grown in F12/DMEM medium without dox for two weeks.

first: Yosef

last: Buganim


title: Effect of IL-1b treatment on cultured rat aortic smooth muscle cells

status: Public on Dec 31 2012

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road

department: Molecular Physiology and Biological Physics

institute: University of Virginia

summary: IL-1 plays an important role in atherosclerosis, and alters expression of a number of genes involved in atherosclerotic plaque development and progression.  Smooth muscle cells play important roles in atherosclerotic plaque formation and stability, so this study was undertaken to determine the global effects of IL-1b on gene expression in smooth muscle cells in vitro.

overall_design: Cultured rat aortic smooth muscle cells were treated with IL-1b (2.5 ng/mL) or vehicle (0.1% BSA) for 24 hours prior to harvest.

middle: K

first: Matthew

middle: R

last: Alexander


title: Gene expression comparison between different stages of endogenous Sertoli cells and induced embryonic Sertoli cells derived from MEFs and TTFs

summary:
To compare the transcriptional profile of endogenous Sertoli cells from different Stage of Sertoli cell development (embryonic, immature, mature) to the transcriptionla profile of induced embryonic Sertoli cells derived from MEFs or TTFs we employed the agilent whole genome microarray

Keywords: Expression profiling by array

overall_design: The following samples were analyzed in duplicates (MEFs, TTFs, ieSCs (derived from MEFs), ieSCs (derived from TTFs), 14.5 dpc male gonad, immature Sertoli (19 dpc embryo testis) and mature (8 week-old mouse testis))


title: Comparison of gene expression between MEFs, MEFs (NWD), immature Sertoli cells and mature Sertoli cells

summary: To compare the the genomic profile of MEFs, immature Sertoli, mature Sertoli cells, and MEFs (NWD) after infection of Nr5a1, Wt1 and Dmrt1 after 1 month of dox exposure.

overall_design: MEFs (NWD) were infected with Nr5a1, Wt1 and Dmrt1 and were exposed to dox for 1 month. MEFs, immature Sertoli and mature Sertoli cells were cultured for 3 days and collected


title: Comparative study of sesame lignans affecting gene expression profile and fatty acid oxidation in rat liver

status: Public on Dec 04 2012

city: Niiza

first: Takashi

last: Ide

address: 2-1-28 Sugasawa

institute: Jumonji University

summary: The impact of sesamin, episesamin and sesamolin (sesame lignans) on hepatic gene expression profiles was compared with a DNA microarray. Male Sprague-Dawley rats were fed experimental diets containing 0.2% sesamin, episesamin or sesamolin, and a control diet free of lignans for 15 d. Compared to a lignan-free diet, a diet containing sesamin, episesamin and sesamolin caused 1.5- and 2-fold changes in the expression of 128 and 40, 526 and 152, and 516 and 140 genes, respectively. The lignans modified not only the mRNA levels of many enzymes involved in hepatic fatty acid oxidation, but also those of proteins involved in the transportation of fatty acids into hepatocytes and their organelles, and regulate hepatic concentrations of carnitine, CoA and malonyl-CoA. It is apparent that sesame lignans stimulate hepatic fatty acid oxidation by affecting the gene expression of various proteins regulating hepatic fatty acid metabolism. We also observed that lignans modified the gene expression of various proteins involved in hepatic lipogenesis, cholesterogenesis and glucose metabolism. The changes were generally greater with episesamin and sesamolin than with sesamin. In terms of the amounts accumulated in serum and the liver, the lignans ranked in the order sesamolin, episesamin and sesamin. The differences in bio-availability among these lignans appear to be important to their divergent physiological activities.

overall_design: Male Sprague-Dawley rats were divided into 4 groups with equal mean body weights consisting of 7 animals each and fed either a diet free of lignan or diets containing 0.2% lignan (sesamin, episesamin or sesamolin) for 15 d. RNA extracted from the livers of 5 rats from each group was subjected to microarray analyses. Rats with the highest and lowest body weights in each group at the time of killing were eliminated from microarray analyses.


title: Expression data from rat INS-1E cells

status: Public on Dec 14 2012

city: CAMBRIDGE

first: Danny

last: Chou

state: Massachusetts

address: 500 Main St

institute: MIT

summary:
Cytokine-induced beta-cell apoptosis is a key event for the death of pancreatic beta cells in the development of type-1 diabetes. We identified BRD0476 as a novel suppressor of cytokine-induced beta-cell apoptosis.
We used microarrays to look for gene set(s) that are regulated by BRD0476.

overall_design: Rat INS-1E cells were treated with cytokine cocktails (IL-1b, IFN-g and TNF-a) and/or BRD0476 for 6 or 12 hours. Total RNAs were isolated using the RNEasy kit from Qiagen.

first: Briddget

last: Wagner


title: Juvenile postnatally overfed mice heart microarray anaylsis

status: Public on Jan 07 2013

city: Angers

first: Celine

last: Fassot-Lucht

address: Rue Haute de Reculée

department: BNMI

institute: INSERM U1083

summary: C57BL/6 mice underwent early postnatal overfeeding by litter size reduction (3 pups/dam, instead of 10 pups/dam, in postatally normally fed mice). These overfeeding conditions lead to early and permanent modifications of body weight and to an increase in body fat mass in the adulthood. When these postnatally overfed mice become adult, they develop several cardio-metabolic alterations (mild hypertension, impairment of heart contractility, remodeling, fibrosis, hyperinsulinemia and hyperleptinemia) but also increases in markers of cardiac and plasma oxidative stress. Moreover, we observed a higher sensitivity of the heart to injuries induced by ischemia reperfusion, such as an increase in necrosis. We now aim to establish if these late-coming modifications might be induced in a very early state of postnatal development, such as a postnatal programming situation. To achieve this objective, we are now comparing heart gene expression between 24 days old postnatally overfed and normally fed mice.

overall_design: Comparison of heart gene expression between 24 days old postnatally overfed and normally fed mice.

first: Catherine

last: Vergely

last: Fassot


title: Gene expression in the wildtype and top2b-deleted cardiomyocytes with or without doxorubicin treatment

status: Public on Oct 28 2012

city: Houston

first: Sui

last: Zhang

state: TX

address: 1400 Pressler St.

department: Cardiology

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

summary:
To compare expression profiles in the cardiomyocytes with wild type top2b and those with top2b deletion after in vivo treatment of mice with doxorubicin or drug vehicle

Doxorubicin is widely used in modern cancer treatments, despite the advent of targeted therapy.  However, a dose-dependent cardiotoxicity often limits its clinical use.  The prevailing theory hypothesizes that doxorubicin-induced cardiotoxicity is the result of reactive oxygen species (ROS) generation due to redox-cycling of doxorubicin.  Here we showed that cardiomyocyte-specific deletion of Topoisomerase II beta (Top2b) markedly reduced DNA double-strand breaks, apoptosis, and functional damages in doxorubicin-treated hearts.  To investigate transcriptomic changes after doxorubicin treatment in wild type mouse and mouse with cardiac specific deletion of Top2b, we examined the expression profiles in 4 groups of mice (3/group), ie. wildtype mice with or without doxorubicin treatment and mice with Top2b deletion in the cardiomyocytes with or without doxorubicin treatment. Mice were treated with doxorubicin (25mg/kg, i.p.) or PBS (drug vehicle) for 16 hr or 72 hr. The heart was removed and cardiomyocytes were isolated by using a Langendorff apparatus. After purification, total RNA was extracted from the cardiomyocytes, purified, and used for gene expression analysis. Compared with that in control cardiomyocytes or cardiomyocytes with Top2b deletion, doxorubicin caused a significant expression change in the genome of cardiomyocytes from the wildtype mice. Among the changes, multiple genes encoding mitochondrial structural protein and components of the respiratory chain complexes were down-regulated 72 hr  after treatment while multiple genes in the p53 pathway were up-regulated 16 hr after treatment in the wildtype cardiomyocytes.

overall_design: Expression changes were examined in 2 groups of mice (wild type and conditional knockout of top2b in the cardiomyocytes) treated with doxorubicin or PBS for 16 or 72 hours

first: Xiaobing

last: Liu

first: Edward

middle: T

last: Yeh


title: Murine Testes: Germ Cell-Specific Sin3a Knockout vs. Hemizygous vs. Wild Type at Postnatal Day 0

status: Public on Oct 01 2012

city: Chicago

first: Christopher

middle: J.

last: Payne

address: 2430 N. Halsted St.

institute: Northwestern University Feinberg School of Medicine

summary: Chromatin modifier Swi-independent 3a (SIN3A), together with associated histone deacetylases, influences gene expression during development and differentiation through multiple transcription factors in a cell-specific manner. Sin3a is essential for the maintenance of inner cell mass cells of mouse blastocysts, embryonic fibroblasts, and myoblasts, but is not required for the survival of trophectoderm or Sertoli cells. To better understand how this transcriptional regulator modulates cells at different developmental stages within a single lineage, we used conditional gene targeting in mice to ablate Sin3a from perinatal quiescent male gonocytes and from postnatal differentiating spermatogonia.

overall_design: Gene expression in the whole testes of age-matched Ddx4(Vasa/Mvh)-cre mediated conditional Sin3a gene-targeted(VSKO) mice, germ cell-specific Sin3a hemizygous (HEMI) mice, and wild type (WT) mice was measured at postnatal day 0. Two biological replicate animals were used for each condition.

middle: J

first: Shannon

last: Gallagher

first: Amber

middle: E

last: Kofman

first: Jan-Hermen

last: Dannenberg

first: Ronald

last: DePinho

first: Robert

last: Braun


title: A comparative analysis of genistein and daidzein in affecting lipid metabolism in rat liver

status: Public on Oct 10 2012

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary:
Effects of soy isoflavones, genistein and daidzein, on the hepatic gene expression profile and indices for lipid metabolism were compared in rats.
The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.

overall_design: Three groups of rats were fed with an experimental diet containing 2 g/kg of either genistein or daidzein, or a control diet free of isoflavone for 14 days.  The basal composition of the experimental diet was (in g/kg): casein, 200; palm oil, 100; corn starch, 150; cellulose, 20; mineral mixture (AIN-93G), 35; vitamin mixture (AIN-93), 10; L-cystine, 3.0; choline bitartrate, 2.0 and sucrose to 1 kg.

first: Yoko

last: Takahashi

first: Tseye-Oidov

last: Odbayar

first: Tahashi


title: Direct reprogramming of fibroblasts into embryonic Sertoli-like cells by defined factors

first: Albert

last: Cheng

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

overall_design: Refer to individual Series

first: Yosef

last: Buganim


title: Pdx1 overexpression sensitizes to IL-1b-induced apoptosis

status: Public on Sep 20 2012

city: Gentofte

first: Morten

last: Tonnesen

address: Niels Steensensvej 1

country: Denmark

institute: Hagedorn Research Institute

summary: Cytokines have been shown to play a key role in the destruction of beta cells. In the rat insulinoma cell line (INS-1ab) overexpressing pancreatic duodenum homeobox 1 (Pdx1) increases sensitivity to Interleukin 1b (IL-1b). To elucidate mechanisms of action underlying Pdx1 driven potentiation of beta-cell sensitivity to IL-1β, we performed a microarray analysis of INS-1ab cells with and without Pdx1 overexpression exposed to IL-1β between 2h and 24h.

overall_design: INS-1ab cells were cultured with or without 500 ng/ml doxycycline (+/- DOX). After 24 h, 40 ng/ml IL-1b was either added or not (+/- IL-1b). Cells were harvested either 2h, 4h, 6h, 12h or 24h after addition of IL-1b. Four biological replicates for each of the eight groups.


title: Mapping of cohesion factor association sites in S. cerevisiae - Meiosis I chromosome segregation is established through regulation of microtubule-kinetochore interactions.

status: Public on Oct 05 2012

first: Elcin

last: Unal

address: 500 Main Street 76-561

department: Koch Institute

institute: Massachusetts Institute of Technology HHMI

type: Genome variation profiling by genome tiling array

summary: During meiosis, a single round of DNA replication is followed by two consecutive rounds of nuclear divisions called meiosis I and meiosis II. In meiosis I, homologous chromosomes segregate, while sister chromatids remain together. Determining how this unusual chromosome segregation behavior is established is central to understanding germ cell development. Here we show that preventing microtubule-kinetochore interactions during premeiotic S phase and prophase I is essential for establishing the meiosis I chromosome segregation pattern. Premature interactions of kinetochores with microtubules transform meiosis I into a mitosis-like division by disrupting two key meiosis I events: coorientation of sister kinetochores and protection of centromeric cohesin removal from chromosomes. Furthermore we find that restricting outer kinetochore assembly contributes to preventing premature engagement of microtubules with kinetochores. We propose that inhibition of microtubule-kinetochore interactions during premeiotic S phase and prophase I is central to establishing the unique meiosis I chromosome segregation pattern.

overall_design: The association of the cohesion factors Rec8, Pds5, and Sgo1 were measured by ChIP-chip analysis in wild-type and CUP-CLB3 strains.

first: Matthew

middle: P

last: Miller

first: Elçin

last: Ünal

first: Gloria

last: Brar

first: Angelika

last: Amon


title: Mammary Gland Morphology and Gene Expression Signature of Prepubertal Male and Female Rats Following Exposure to Exogenous Estradiol

status: Public on Sep 10 2012

city: Little Rock

first: Isabelle

last: Racine Miousse

address: 15 Children's Way

institute: UAMS

summary: In order to properly understand whether xenoestrogens act as estrogens, it is essential to possess a solid portrait of the physiological effects of exogenous estradiol. Because the estrogen-dependent gene expression is one of the primary biomarkers of estrogenic action, we have assessed effects of three doses of exogenous estradiol (0.1, 1.0 and 10 µg/kg of body weight/day) on the mammary gland morphology and gene expression profiles by microarray analysis of prepubertal male and female rats of both sexes compared to untreated controls.  Estradiol was administered subcutaneously with minipumps from weaning at PND21 to the end of the experiment at PND33. The data suggest that the male mammary is a sensitive tissue for estrogenicity assessment.

overall_design: Groups of male and female rats were infused subcutaneously with mini-osmotic pumps with 17β-estradiol from weaning on post-natal day (PND) 21 until PND 33.  Pumps delivered doses of 0, 0.1, 1.0 and 10 µg/kg/d. At sacrifice (PND 33) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen.

first: I

last: Miousse

first: N

last: Sharma

first: J

last: Badeaux

first: L

last: Hennings

first: K

last: Shankar

first: H

last: Gomez-Acevedo

first: M

last: Cleves

first: T

middle: M

last: Badger

last: Ronis


title: Short-term exposure to effluent from bulk drug industries

status: Public on Sep 01 2012

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

summary: The Patancheru area near Hyderabad in India is recognized as a key link in the global supply chain for many bulk drugs. A central treatment plant receives wastewater from about 90 different manufacturers and the resulting complex effluent has contaminated surface, ground and drinking water in the region. Ecotoxicological testing of the effluent has shown adverse effects for several organisms, including aquatic vertebrates. In an attempt to start investigating how exposure to effluent-contaminated water may affect humans and other terrestrial vertebrates, rats were tube-fed effluent. Results from microarray and quantitative polymerase chain reaction assays indicated, however, no marked effects on hepatic gene expression after five days exposure. Neither did a clinical analysis of blood serum constituents used as biomarkers for human disease reveal any significant changes, nor were there any effects on weight gain. Taken together, we could not find evidence for any acute toxicity in the rat; however, we cannot rule out that higher doses of effluent or a longer exposure time may still be associated with risks for terrestrial vertebrates.

overall_design: 10 rats (5 controls and 5 exposed to effluent) were subjected to microarray analysis. Further information is available in Rutgersson et al., 2010.


title: Gene expression profiles of EpiSCs under epiblastic and neural plate developmental conditions

status: Public on Dec 07 2012

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

institute: Biohistory Research Hall

summary: Epiblast stem cells (EpiSCs) were placed in the epiblastic cell maintenance condition (EpiSC) or in a neural plate developmental condition (Iwafuchi-Doi et al. Dev Biol 352, 354-366, 2011) for one (NPC1) or two (NPC2) days, and expression profiles of total mRNAs were compared.

overall_design: Duplicate EpiSC cultures (A and B) originating from the same seed culture and made in the above conditions were processed for total RNA extraction using TRI Reagent (Sigma-Aldrich), and analyzed

first: Makiko

last: Iwafuchi-Doi

first: Kazunari

last: Matsuda


title: Osteoarthritis-related changes in gene expression in knee articular chondrocytes in a rat model of osteoarthritis.

status: Public on Nov 15 2012

city: London

first: Tom

last: Appleton

state: ON

address: Rm 0061 DSB The University of Western Ontario

department: Physiology & Pharmacology

country: Canada

institute: The University of Western Ontario

summary: Cartilage destruction in osteoarthritis (OA) results from disturbed chondrocyte metabolism. Here, we used microarrays to show that TGF alpha and CCL2 are simultaneously upregulated in a rat model of OA and cooperate to drive cartilage degradation. The goals of the experiments included here were to a) characterize gene expression in knee joint articular chondrocytes at various stages of development of OA (2 and 8 weeks after surgical induction of OA), and b) to establish trends in gene expression among groups of genes related to the TGF alpha-EGFR axis, over time, in OA. The model chosen to study these results has been previously validated (Appleton, CT et al, 2007, Arthritis Rheum) and used to describe similar gene expression results at a different time point (4 weeks) after induction of OA. The rat model of OA involves surgical destabilization of the knee joint, followed by forced low-intensity mobilization over several weeks; a sham surgery is used as the control (representing a healthy non-OA knee joint) wherein a surgical incision is made but not structural (i.e. ligamentous) modification is made to the joint. Altogether, our data indicate that TGF and CCL2 cooperate to drive cartilage degradation in osteoarthritis.

overall_design: A total of 12 samples were analyzed. 3 replicates were used per condition: OA surgery at 2 weeks, OA surgery at 8 weeks, Sham (control) surgery at 2 weeks and Sham surgery at 8 weeks. Expression of OA samples was assessed relaitve to Sham (control) expression levels.

first: Thomas

middle: G

first: Shirine

last: Usmani

first: Michael

last: Pest

first: Vasek

last: Pitelka

first: Veronica

last: Ulici

first: Ian

last: Welch

first: Tracy

last: Hill

first: John

last: Mort

first: Frank

last: Beier


title: Life-long caloric restriction-associated remodeling of rat white adipose tissue

status: Public on Sep 27 2012

first: Tomokazu

last: Konishi

summary: This study explored the role of the growth hormone (GH) / insulin-like growth factor 1 (IGF-1) axis on the life-long caloric restriction (CR)-associated remodeling of white adipose tissue (WAT). Adipocyte size and gene expression profiles, using high-density oligonucleotide microarrays, were analyzed in WAT of six- to seven-month old wild Wistar rats fed ad libitum (AL) or subjected to a 30% caloric restriction (CR), and heterozygous transgenic dwarf rats bearing an anti-sense GH transgene fed ad libitum (Tg). While not significant in Tg rats, adipocyte size was significantly reduced in CR rats compared with AL rats. The microarray data based on the principal component analysis demonstrated that the gene expression profile of CR rats markedly differed from the AL rats, while Tg hardly differed, suggesting that CR-associated WAT remodeling was predominantly regulated in a GH/IGF-1-independent manner. The gene cluster with the largest change induced by CR included several genes involved in lipid biosynthesis and inflammation. Moreover, many of the genes transcriptionally regulated by sterol regulatory element binding proteins (SREBPs) were found in the cluster related to lipid biosynthesis. Real-time reverse transcription polymerase chain reaction analysis confirmed that the expression of SREBP-1 and its down-stream targets was particularly up-regulated in CR rats compared with SREBP-2 and its down-stream targets. Our findings suggest that SREBP-1 is a major transcription factor in CR-associated remodeling of WAT, and might be one of the key regulators of the anti-aging and pro-longevity effects of CR.

overall_design: The three groups: GH antisense, caloric restriction, and the control were compared by using PCA.

first: Yoshikazu

last: Chujo

first: Naoyuki

last: Okita

first: Namiki

last: Fujii

first: Atsushi

last: Yamada

first: Yuji

last: Haruyama

first: Kosuke

last: Tashiro

first: Takuya

last: Chiba

first: Isao

last: Shimokawa

last: Higami


title: Effect of Methapyrilene on Rat Primary Hepatocytes.

status: Public on Aug 28 2012

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

summary:
This study provides an evaluation of changes in gene expression associated with methapyrilene treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (3 uM and 100 uM) of methaphyriline and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.

overall_design:
This series is part of a SuperSeries in which primary rat hepatocytes were treated with two doses of ten chemical compounds (and corresponding vehicle controls) for 24 and 48 hours.  Each compound/vehicle treatment group was an individual study performed at different times. Each study was analyzed separately and themes common between studies were reported.
Time Course/Dose Response


title: Expression data from HSCs

first: Qin

last: Pan

address: 1665 Kongjiang Rd.

institute: Xin Hua hospital

summary: Hepatic stellate cells (HSCs) experience phenotypic transformation, from the quiescent phenotype to the activated one, after different etiologies of liver injury. Liver fibrosis is then occurred upon the activation of HSCs. miR-16 deficiency is identified to be an important characteristic of HSCs activation. We used Affymetrix rat 230 2.0 arrays (Affymetrix, Santa Clara, U.S.A.) to uncover the global alternations of transcriptome under miR-16 restoration.

overall_design: We isolated quiescent hepatic stellate cells (HSCs) from adult male SD rats (normal control group) by in situ perfusion and density-gradient centrifugation. Activated HSCs were separated from rats of fibrosis model group, which were treated by 40% carbon tetrachloride (CCl4) for 8 weeks, by means of liver section, digestion and sequential centrifugation. Quiescent and activated HSCs were then divided into 4 groups at random, namely quiescent HSCs, activated HSCs, pLV-miR-16-treated HSCs and pLV-GFP-treated HSCs. The pLV-miR-16-treated group, pLV-GFP-treated group were infected with pLV-miR-16 and pLV-GFP, respectively.

first: JIanFeng

last: Huang


title: Effect of WY-14643 on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with WY-14643 treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses 8 uM and 200 uM) of WY-14643 and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Diisononyl Phthalate on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with diisononyl phthalate treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (25 mM and 100 mM) of diisononyl phthalate and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Clofibrate on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with clofibrate treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (60 uM and 1 mM) of clobibrate and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Whole blood microRNA expression in human lung cancer

status: Public on Sep 11 2012

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: Seventh generation Exiqon locked nucleic acid miRCURY LNA microarrays were used to profile the expression of microRNAs in whole blood of patients with lung cancer and of clinically relevant controls without the disease (individuals with non-cancerous lung nodule, at high risk for cancer because of heavy smoking, or with lung cancer treated by surgical resection). The goal was to examine if whole blood microRNAs can be used for developing a non-invasive assay to diagnose lung cancer.

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

overall_design:
Using the PAXgene Blood miRNA kit (Qiagen, Valencia, CA, USA), total RNA was isolated from whole blood stabilized and stored in PAXgene Blood RNA tubes for 85 individuals with lung cancer, 59 individuals without the disease but at a high risk for the disease because of smoking, and 17 individuals with a non-cancerous pulmonary nodule. RNA was also isolated from 13 samples of blood of 12 of the lung cancer cases following surgery; blood samples were collected on two different days post-operatively for one of the cases (Sample names 157 and 160). The data-set here includes data (sample name 171) from a post-operative blood sample of an individual (who had the lung cancer removed by operation) for whom good array data was not obtained for RNA from a pre-operative blood sample. Two RNA samples were used to test technical duplicability of the microarray platform (pairs of sample names 59 & 192, and 175 & 182). Thus, a total of 162 unique individuals and 175 unique RNA samples are covered by this data-set.
Isolated RNA was provided to Exiqon (Denmark) for microRNA quantification using microarrays. Quality and concentration of RNA in the samples was assessed by Nanodrop 2000 (Thermo Scientific, Wilmington, DE, USA) and Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) instruments. Sample RNA (500 ng) was labeled with the Cy3-like Hy3 dye, mixed with 500 ng of a human universal reference RNA (product number AM6000, Ambion, Austin, TX, USA) that was labeled with the Cy5-like Hy5 dye, and hybridized to 7th generation miRCURY locked nucleic acid oligonucleotide microarrays. Sixty-two artificial small RNAs were spiked-in each RNA sample before labeling.
disease state: Lung cancer (before surgical resection of lung cancer): 1, 2, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 61, 63, 64, 65, 67, 68, 69, 70, 81, 82, 85, 86, 87, 88, 89, 90, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 121, 122, 123, 124, 125, 126, 127, 149, 151, 153, 154, 156, 158, 165, 167, 174, 175, 176, 177, 179, 180, 181, 183, 184, 186, 187, 188, 189, 193
disease state: Non-cancerous lung nodule: 128, 129, 130, 131, 133, 134, 135, 136, 137, 140, 141, 142, 144, 145, 146, 148, 182, 190
disease state: None (after surgical resection of lung cancer): 155, 157, 159, 160, 161, 162, 163, 164, 166, 169, 170, 171, 172, 173
disease state: None (no current or past lung cancer or non-cancerous nodule): 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 113, 114, 115, 116, 117, 118, 119, 120, 192
individual: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162

first: Sai

last: Yendamuri

first: Eric

last: Kannisto

first: Anil

last: Vachani


title: Effect of Chlorpromazine HCl on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with chlorpromazine HCl treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (0.8 uM and 20 uM) of chlorpromazine HCl and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Beta-Naphthoflavone on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with beta-naphthaflavone treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses 1 uM and 100 mM) of beta-naphthaflavone and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Sodium Valproate on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with sodium valproate treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (500 uM and 10 mM) of sodium valproate and water vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Hepatotoxicity

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


title: Effect of Phenobarbital on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with phenobarbital treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (300 uM and 3 mM) of phenobarbital and water vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Dioctyl Phthalate on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with dioctyl phthalate treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (250 uM and 1 mM) of dioctyl phthalate and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Effect of Acetominophen on Rat Primary Hepatocytes.

summary:
This study provides an evaluation of changes in gene expression associated with acetominophen treatment of rat hepatocytes in vitro.
Primary rat hepatocytes were treated for 24 and 48 hours with two doses (500 uM and 5 mM) of acetominophen and 1% DMSO vehicle control.  Five replicates of each treatment were performed.  Cells were then extracted and RNA processed for microarray analysis.


title: Expression data from cultured rat astrocytes

status: Public on Aug 09 2012

city: Tokyo

first: Kazunori

last: Kanemaru

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Pharmacology

institute: Graduate School of Medicine, The University of Tokyo

summary: The objective of this study is to search for calcium signal-dependent expression changes.

overall_design: 2 samples comparing active calcium signaling (control) to no signaling (5ppase)

first: Jun

last: Kubota

first: Hiroshi

last: Sekiya

first: Kenzo

last: Hirose

first: Yohei

last: Okubo

first: Masamitsu

last: Iino


title: Adrenal gene expression profiles of male and female Kcnk3 null mice in basal conditions or after hormonal treatment.

status: Public on Aug 20 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Primary aldosteronism (PA) is a common form of endocrine hypertension suspected in the presence of arterial hypertension (HT), hypokalemia and low plasma renin levels. While for a long time the genetic causes of PA have remained mysterious, recent findings have revealed an important role for an altered function of potassium channels in the pathogenesis of this disease. The basis for the unique sensitivity of adrenal zona glomerulosa (ZG) cells for plasma potassium concentration is a very high background potassium conductance, which is dependent on expression at high levels of two 2-pore domain (K2P) potassium channels, Task1 (KCNK3) and Task3 (KCNK9. Recent studies have shown that mice lacking Kcnk3 (Task1) or both Kcnk3 and Kcnk9 have PA. In Kcnk3 null mice, hyperaldosteronism is present in young animals of either sex, but is corrected in males after puberty. Strikingly, in these animals hyperaldosteronism associates with abnormal adrenal cortex functional zonation, since Cyp11b2, the rate-limiting enzyme for aldosterone production, is expressed in the inner region of the adrenal cortex and not in the glomerulosa. Additionally, this phenotype is under the control of sex hormones, as shown by the fact that castration of male Kcnk3 -/- animals prevents normal Cyp11b2 distribution, while testosterone injection in female Kcnk3 null mice restores expression of Cyp11b2 in ZG cells. We took advantage of the unique characteristics of the Kcnk3 null mouse model to search for genes that can modify their phenotype of PA and adrenocortical functional zonation. Using gene expression profiling in the adrenal glands of Kcnk3 null mice and exploiting the possibility of modulation of their phenotype by sexual hormones, we identified a cluster of genes closely associated with hyperaldosteronism in a sex- and hormone-dependent dynamic fashion. Among these genes, we focused our attention on Dkk3 (dickkopf3), encoding a peculiar member of the dickkopf family of Wnt signalling modulators because of its close association with aldosterone-producing cells in humans (11). Inactivation of Dkk3 in the Kcnk3 null background causes extension of the hyperaldosteronemic phenotype and increased expression of Cyp11b2 in the adrenal gland to the male sex, without affecting functional zonation. These data indicate that Dkk3 is a component of the genetic circuitry regulating expression of Cyp11b2 and suggest that it may be implicated in the pathogenesis of low-renin hyperaldosteronism in humans.

overall_design: One color -experiment with 2 strains of mice: C57BL/6 WT or Kcnk3 null (KO): male and female in basal conditions or following hormonal treatment (castration for males and testosterone injection for females), corresponding to 8 groups of animals. Total of 24 samples (n=3).

first: E

last: Lalli

first: B

last: Mari

first: P

last: Barbry

first: K


title: 5 Day Oral Study of A-998679 in Male Sprague Dawley Rats (Jejunum)

status: Public on Aug 04 2012

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

summary: Male Sprague-Dawley rats [Crl:CD®(SD)IGS BR], weighing ~250 g at study initiation were obtained from Charles River Laboratories, Inc. (Wilmington, MA).  Rats were housed singly in ventilated, stainless steel, wire-bottom hanging cages and fed non-certified Rodent Chow (Harlan Labs, Madison, WI) and water ad libitum and acclimated for at least 5 days after arrival.  Rats were randomly assigned to various treatment groups (3 rats/group) and were dosed once daily by oral gavage with vehicle (0.2% hydroxypropylmethylcellulose at a dose volume of 10 ml/kg) or with 30, 100, or 200 mg/kg of A-998679.  All rats were fasted overnight after their last dose, weighed and sacrificed under isoflurane anesthesia. Liver and small intestine (jejunum) were flash frozen in liquid nitrogen and stored at −80°C until processing for gene expression profiling on the Affymetrix platform.

overall_design: total of 11 samples, 3 biological replicates (rats) from each of 3 treatments groups 1. vehicle control  2. 30mg/kg A-998679 3. 100mg/kg A-998679  and 2 biological replicates from treatment group 4.  200mg/kg A-998679

first: Michael

last: Liguori


title: Genome-wide transcriptional effects of Pregnancy-Induced Non-coding RNA (PINC)

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Pregnancy-Induced Non-Coding RNA (PINC) is upregulated in alveolar cells of the mammary gland during pregnancy and persist in alveolar cells that remain in the regressed lobules following involution.  Here, we show that in the post-pubertal mouse mammary gland, mPINC expression increases throughout pregnancy and then declines in early lactation, when alveolar cells undergo terminal differentiation.  Accordingly, mPINC expression is significantly decreased when HC11 mammary epithelial cells are induced to differentiate and produce milk proteins.  This natural reduction in mPINC levels may be necessary for lactation, as overexpression of mPINC in HC11 cells blocks lactogenic differentiation, while knockdown of mPINC enhances differentiation.

overall_design: HC11 mammary epithelial cells, with or without knockdown or over-expression of PINC, and with or without treatment by differentiation-inducing agents, were profiled for gene expression.

first: Amy

last: Shore

first: Jeff

last: Rosen


title: 5 Day Oral Study of A-998679 in Male Sprague Dawley Rats


status: Public on Aug 01 2012

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary: The objective of this study was to determine common innate differences in gene expression in the nucleus accumbens shell among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats.

overall_design: Comparison of Differences in Gene Expression in the Nucleus Accumbens Shell of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption.

first: William

last: McBride

first: Jeanette

middle: N

last: McClintick

first: Zheng-Ming

last: Ding

first: Richard

middle: L

last: Bell

first: Petri

last: Hyytia

first: Giancarla

last: Colomobo

first: Howard

last: Edenberg


title: Gene expression profile of HCCs developed in miR-122 knockout mice compared to age-matched wild type mice

status: Public on Aug 07 2012

city: Columbus

first: kalpana

last: ghoshal

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

institute: The Ohio State University

summary: Gene expression profiling of HCCs developed in miR-122 knockout mice compared to age-matched wild type mice. The significance of our study is that miR-122 knockout mice spontaneously develop liver tumors and the gene expression profile demonstrated dysregulation of several pathways involved in liver disease and HCC.

overall_design: Two-condition experiment, liver tumor vs. normal liver. 8 biological replicates.

first: Kalpana

last: Ghoshal

first: Huban

last: Kutay

first: David

last: Newsom

first: Peter

last: White

first: Lianbo

last: Yu


title: Gene expression profiling of myelin-phagocytosing macrophages

city: Diepenbeek

first: Jeroen

middle: Felix Jacobus

last: Bogie

address: Agoralaan Building C

department: Biomedical Research Institute

institute: Hasselt University

summary:
Multiple sclerosis is a chronic, inflammatory, demyelinating disease of the central nervous system in which macrophages and microglia play a central role. During active multiple sclerosis foamy macrophages and microglia, containing degenerated myelin, are abundantly found in demyelinated areas. Recent studies have described an altered macrophage phenotype after myelin internalization. However, by which mechanisms myelin affects the phenotype of macrophages and how this phenotype can influence lesion progression is unclear.
Here we demonstrate, by using genome wide gene expression analysis, that myelin-phagocytosing macrophages have an enhanced expression of genes in pathways involved in migration, phagocytosis and inflammation. More interestingly, we show that myelin internalization induces the expression of genes involved in liver X receptor signaling and cholesterol efflux. In vitro validation shows that myelin-phagocytosing macrophages indeed have an increased capacity to dispose intracellular cholesterol. Additionally, myelin suppresses the production of pro-inflammatory mediators, like nitric oxide and IL-6, by macrophages in a similar manner as a liver X receptor agonist. Our data show that myelin modulates the phenotype of macrophages by nuclear receptor activation, which may subsequently affect lesion progression in multiple sclerosis.

overall_design: Rat peritoneal macrophages were left untreated (n=5) or treated with isolated myelin (n=5) for 3 days. Both untreated and myelin-treated macrophages were subsequently stimulated with IFNү and IL1-β for 9 hours.

middle: F

first: Silke

last: Timmermans


summary: The objective of this study was to determine common innate differences in gene expression in the Central Nucleus of the Amygdala (CeA) among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats.

overall_design: Comparison of Differences in Gene Expression in the Central Nucleus of the Amygdala (CeA) of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption.

middle: W


title: Comparison of Differences in Gene Expression in brain of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption

overall_design: Refer to individual Series


title: 5 Day Oral Study of A-998679 in Male Sprague Dawley Rats (liver)

status: Public on Jul 24 2012

first: Rita

last: Ciurlionis

overall_design: total of 12 samples, 3 biological replicates (rats) from each of 4 treatments groups 1. vehicle control  2. 30mg/kg A-998679 3. 100mg/kg A-998679 4.  200mg/kg A-998679

first: Liguori

last: Michael

first: Ciurlionis

last: Rita


first: Mark

last: Kimpel

summary: The objective of this study was to determine common innate differences in gene expression in the ventral tegmental area (VTA) among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats. There were between 350 and 1400 unique named genes that were significantly different between the individual line-pairs. Gene Ontology (GO) and Ingenuity Pathways analyses indicated significant categories and networks in common for up to 3 line-pairs, but not for all 5 line-pairs; there were few genes in common between any of the line-pairs in these categories and networks. The overall ANOVAs of the combined data for the 5 line-pairs indicated over 1300 significant differences in expression of named genes. Ingenuity analysis revealed (a) several significant networks with clusters of genes associated with App, Egfr, Ccnd1, Itga2b, Rxra and Vcl; and (b) changes in genes within networks associated with dopamine, the glutamate synapse, Nfkb signaling, IL pathways and integrin. There were 22 genes that were significantly different in the overall ANOVA and were significantly different (in the direction) in at least 3 line-pairs, e.g., Crebl2, Gsta4, Itga9 & Itg2. In conclusion, the findings suggest that (a) different innate mechanisms may be contributing to vulnerability to high alcohol drinking behavior among the selectively bred lines, and (b) small contributions in expression of multiple genes within certain transmitter systems and intracellular signaling pathways may contribute to the disparate alcohol drinking characteristics of the 5 line-pairs.

overall_design: Comparison of Differences in Gene Expression in the Ventral Tegmental Area of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption.

first: William

last: McBride

first: Jeanette

last: McClintick


title: Comparison of the gene expression profiles between iPS-OSH, iPS-J, ESC and MEF.

city: Taichung

first: Shih-Ping

last: Liu

address: No.6, Hsueh-Shih Road

country: Taiwan

institute: China medical university

summary: iPS-OSH was the novel iPS cells generated from our lab, the microarray analysis was used for determining the gene expression profiles of iPS-OSH. iPS-J was provided from Dr. Yamanaka (Riken, APS0001). Microarray analysis was used to compare the difference of gene expression profiles in iPS-OSH, iPS-J, ESC and MEF.

overall_design: The total RNA extracted from iPS-OSH, iPS-J, ESC and MEF was used for the microarray analysis to compare the gene expression profiles.


title: Differential gene expression profiling of cultured neu-transformed versus spontaneously-transformed rat cholangiocytes and of corresponding cholangiocarcinomas

status: Public on Jun 21 2012

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary: Characterization of preclinical models of intrahepatic cholangiocarcinoma progression that reliably recapitulate altered molecular features of the human disease. Here, we performed comprehensive gene expression profiling of cholangiocarcinoma tumors arising from bile duct inoculation of different grade malignant rat cholangiocytes.

overall_design: Tumors arising from bile duct inoculation of spontaneously-transformed low grade malignant rat BDE1 cholangiocytes (BDEsp cells) compared to tumors arising from the inoculation of high grade malignant erbB-2/neu- transformed BDE1 cholangiocytes (BDEneu cells) into the livers of syngeneic rats.

first: Alphonse

last: Sirica

middle: I

first: Deanna

last: Campbell

first: Regina

last: Oyesanya


title: A novel 3-D organotypic culture model by co-culturing alpha-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix

status: Public on Jun 23 2012

summary:
The increased α-smooth muscle-actin positive cancer-associated fibroblastic cells (CAF) in the desmoplastic stroma may relate to a more aggressive cancer and worse survival outcomes for intrahepatic cholangiocarcinoma (ICC) patients
We developed a novel 3-D organotypic culture model by co-culturing α-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix.

overall_design: Cholangiocarcinoma cell lines were established by isolating α-SMA positive cancer-associated fibroblastic cells (CAF) (BDEsp-TDFE4) and cholangiocarcinoma cells (BDEsp-TDEH10) from tumors arising from bile duct inoculation of spontaneously-transformed low grade malignant rat BDE1 cholangiocytes (BDEsp cells). These tumor-derived cells lines were then grown in a rat tail type I collagen gel matrix, alone or in co-culture, and their gene expression profile were compared.

first: Nadia

last: Lamour


title: DSB formation in replication compromised cells

status: Public on Jun 19 2012

city: Cambridge

first: Stephen

last: Bell

address: 68-630, 77 Massachusetts Ave.

department: Biology

institute: MIT

summary: DSBs were mapped genome-wide by ssDNA enrichment in cdc6-mn replication comprimsied strains.

overall_design:
We mapped DSB sites by detecting DSB-associated ssDNA enrichment on microarrays. To test the role of DNA replication in DSB formation, we mapped ssDNA in a cdc6-mn replication depleted strain. ssDNA was isolated from cells after 5 hours in sporulation medium. As a reference, ssDNA isolated from cells at 0 hrs in sporulation medium prior to DSB formation was differentially labeled and co-hybridized to the same array.
For each experiment, we have submitted biological replicates that were hybridized to separate arrays. For each experiment a dye swap was performed and shown to have no effect on the data observed, although not all experiments in this series include the dye swap sample (we have included only two representative experiments for each strain).

first: Hannah

last: Blitzblau

first: Clara

middle: S

last: Chan

first: Andreas

last: Hochwagen


title: Blueberry Diets during Early Development Only Is Sufficient to Prevent Senescence of Osteoblasts and Bone Loss in Adulthood

status: Public on Jul 01 2012

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

summary: Appropriate nutrition during early development is essential for optimal bone mass accretion; however, linkage between early nutrition, childhood bone mass and prevention of bone loss later in life has not been extensively studied. In this report, we have demonstrated several fundamental issues in the field. 1) A significant prevention of ovariectomy (OVX) -induced bone loss from adult rats can occur with only 14 days consumption of a blueberry-containing diet immediately prior to puberty. 2) The molecular mechanisms underlying these effects involve increased myosin production and preserved a shuttle for transcription factors such as Runx2 from cytoplasm to nucleolus which stimulates osteoblast differentiation and reduces mesenchymal stromal cell senescence. 3) The effects of blueberry diet on preserving fidelity of osteoblast differentiation also overcome reduced osteoblast differentiation and activity due to OVX-induced degradation of collagen matrix.

overall_design: Bone quality was compared among casein control diet sham operated, casein diet ovariectomized, long term BB diet ovariectomized, and short term BB diet ovariectomized female rats

first: Jian

last: Zhang

first: Oxana

last: Lazarenko

first: Michael

last: Blackburn

first: Thomas

last: Badger

first: Martin

last: Ronis

first: Jin-Ran

last: Chen


title: Changes in mammary gene expression and morphology following consumption of soy protein isolate in female Sprague-Dawley rats differs from that produced by 17b-estradiol treatment

status: Public on May 22 2012

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Soy foods have been suggested to have both positive health benefits and potentially adverse effects largely as a result of their content of isoflavone phytoestrogens. Since soy protein isolate (SPI) contains isoflavones, in addition to purported health benefits, safety concerns have been raised regarding the use of SPI and soy formulas, because of potential estrogenic actions during the neonatal period, including the potential for reproductive toxicity, infertility, and the possibility of increased risk for development and recurrence of estrogen sensitive cancers such as breast cancer. In the current study, we used a rat model to compare the effects of SPI with those of 17b-estradiol (E2), on global gene expression profiles and morphology in the female rat mammary gland. Rats were either fed AIN-93G diets containing casein (CAS) or SPI beginning on postnatal day (PND) 30.

overall_design: Rats were ovariectomized (OVX) on PND 50 and treated with E2 or vehicle for 14 days. Microarray analysis was carried out to compare the effects of SPI and E2 alone or in combination on the mammary gene expression. The data suggest a non-estrogenic effect of SPI on the rat mammary even in the absence of endogenous estrogens.

first: Rohit

last: Singhal

first: Leah

last: Hennings


title: Role of miR-125b in B-cell acute lymphoblastic leukemia (B-ALL)

first: Kevin

last: Lebrigand

summary: B-cell acute lymphoblastic leukemia (B-ALL) is often associated with chromosomal translocations leading to the deregulation of proto-oncogenes. MicroRNAs can also be affected by chromosomal alterations and thus contribute to carcinogenesis. The microRNA miR-125b-1 is over-expressed in B-ALL cases with the t(11;14)(q24;q34) translocation, therefore we sought to determine the role of this microRNA in B-cell fate. We used murine pre-BI cells alongside murine and human leukemic B-cell lines to show that miR-125b expression enhances proliferation by targeting Bright/ARID3a, an activator of immunoglobulin heavy-chain transcription. Accordingly, this target gene was down-regulated in B-ALL patients with the t(11;14)(q24;q34) translocation. Repression of Bright/ARID3A blocked differentiation and conferred a survival advantage to Ba/F3 cells under IL3 starvation. In addition, over-expression of miR-125b protected pre-BI and leukemic B-cell lines from apoptosis through blockade of caspase activation via a mechanism that was independent of p53 and BAK1. In summary, miR-125b can act as an oncogene in B-ALL by targeting ARID3a and mediating its repression, thus leading to a blockage in differentiation, increased proliferation and inhibition of apoptosis.

overall_design: To identify specific targets of mir-125b, we overexpressed miR-125b as well as a control miRNA in 70Z/3 and 18-81 pre-B leukaemia cells. Chemically synthesized miRNA duplexes, called pre-miR-125b and miR-Neg, were purchased from Ambion. The cells were transfected with pre-miRNA at a final concentration of 10 nM using Lipofectamin RNAi MAX (Invitrogen) according to the manufacturer’s instructions. The medium was replaced 8 hours after transfection. RNA samples were harvested at 48 hours post-transfection. 2 independent experiments were carried out for a total of 8 samples labeled with Cy3 dye (one color design).

first: Marie-Pierre

last: Puissegur

first: P

last: Barbry

first: K


title: Effect of interleukin-1 and PDGF-DD on SMCs

status: Public on May 03 2012

city: Charlottesville

first: Gary

last: Owens

address: 415 Lane Road

department: Molecular Physiology and Biological Physics

institute: University of Virginia

summary: This experiment tests the hypothesis that interleukin-1 promotes SMC phenotypic modulation to a distinct inflammatory state relative to the growth factor PDGF-DD.

overall_design: Cultured rat aortic smooth muscle cells were treated with IL-1b (2.5 ng/mL) or vehicle (0.1% BSA and 10 mM acetic acid) or PDGF-DD (30 ng/mL) or vehicle (0.01% BSA) for 24 hours prior to harvest (n=1).

middle: K

first: Matthew

middle: R

last: Alexander


title: S phase and HU profiles in wild-type and mutant cells

first: Stephen

last: Bell

summary: Total S phase was measured for wild-type cells undergoing meiS and mitS. Early replication origins were mapped in mitS in wild-type cells, and in meiS for wild-type, sml1 delete, rec8 delete and spo11 delete cells.

overall_design: Comparative genome hybridization was used to measure the kinetics and final extent of DNA replication in wild-type and mutant cells. First, S phase profiles were produced from wild-type cells undergoing pre-mitotic S phase (mitS) and pre-meiotic S phase (meiS) to measure the kinetics of DNA replication in the two S phases. For these experiments, a pool of samples collected throught out all of S phase were labeled and hybridized to a microarray together with a control G1 DNA sample. Second, early replication origins were mapped by exposing cells to levels of HU that strongly reduced DNA replication. Early replication was compared for wild-type cells in mitS to wild-type, sml1, rec8 and spo11 delete strain undergoing meiS. In these experiment, samples were collected after 4 hours exposure to HU. Total genomic DNA was isolated, labeled and hybridized to a microarray together with a control G1 DNA sample. A control G1 vs. G1 sample was prepared to measure the level of noise inherent in the CGH technique.

first: Hannah

last: Blitzblau

first: Clara

last: Chan

first: Andreas


title: Chromatin IP for Mcm2-7, Rec8, Hop1 and Red1

type: Genome binding/occupancy profiling by genome tiling array

summary: Mcm2-7 ChIP in pre-meiotic and pre-mitotic cells, axis factor ChIP in wild-type and replication compromised strains in meiosis

overall_design: Multiple studies of meiotic chromosomes were undertaken. To study DNA replication, the locations of replicative helicase (Mcm2-7) were mapped in pre-meiotic and pre-mitotic cells, and DNA replication profiles were created for pre-meiotic S (meiS) and pre-mitotic S (mitS) phases. Early origins were mapped in hydroxyurea for wild-type cells in mitS + 200mM HU, and meiS +20mM HU for wild-type, sml1, rec8 and spo11 deletion cells. Rec8, Hop1 and Red1 binding to meiotic chromosomes was evaluated using ChIP-chip in wild-type cells with and without 20 mM HU, and in cdc6-mn and clb5 clb6 delete cells. Finally, meiotic DNA double-strand breaks (DSBs) were mapped in cdc6-mn dmc1 delete cells by measuring the ssDNA that accumulates at DSB hotspots.

last: Hochwagen


title: Role of IGFBP-3 in the Regulation of β-Cell Mass during Obesity: Adipose Tissue/ β-Cell Cross Talk

status: Public on Mar 30 2012

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: In obesity an increase in β-cell mass occurs to cope with the rise in insulin demand. This β -cell plasticity is essential to avoid the onset of hyperglycemia, although the molecular mechanisms that regulate this process remain unclear. This study analyzed the role of adipose tissue in the control of β -cell replication. Using a diet-induced model of obesity, we obtained conditioned media from three different white adipose tissue depots. Only in the adipose tissue depot surrounding the pancreas did the diet induce changes that led to an increase in INS1E cells and the islet replication rate. To identify the factors responsible for this proliferative effect, adipose tissue gene expression analysis was conducted by microarrays and quantitative RT-PCR. Of all the differentially expressed proteins, only the secreted ones were studied. IGF binding protein 3 (Igfbp3) was identified as the candidate for this effect. Furthermore, in the conditioned media, although the blockage of IGFBP3 led to an increase in the proliferation rate, the blockage of IGF-I receptor decreased it. Taken together, these data show that obesity induces specific changes in the expression profile of the adipose tissue depot surrounding the pancreas, leading to a decrease in IGFBP3 secretion. This decrease acts in a paracrine manner, stimulating the β -cell proliferation rate, probably through an IGF-I-dependent mechanism. This cross talk between the visceral-pancreatic adipose tissue and β -cells is a novel mechanism that participates in the control of β -cell plasticity. (Endocrinology 153: 177–187, 2012)

overall_design: Adult male Wistar rats (Charles River Laboratories, Wilmington, MA), 7 wk old (weighing 225–250 g), were caged individually in a 12-h light, 12-h dark cycle in a temperature- and humidity-controlled environment. Animals were divided into two dietary sets for 30 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 146:4362–4369, 2005). Adipose tissue from the mesenteric surrounding the pancreas (pMES), was excised, weighed, cut, and rapidly frozen in liquid nitrogen for RNA isolation. Ten micrograms of total RNA from pMES adipose tissue were converted into cRNA, biotinylated, fragmented, and hybridized to GeneChip Rat Genome 230 2.0 (Affymetrix, Santa Clara, CA). Five microarrays were hybridized, three with independent samples coming from rats fed with standard chow (lean group) and two with independent samples coming from rats fed with the cafeteria diet (obese group).

first: N

last: Palau

first: S

middle: A

last: Rebuffat

first: J

last: Piquer

first: F

last: Hanzu

first: R

last: Gomis

first: A

last: Barbera


title: Separation of DNA replication from the assembly of break-competent meiotic chromosomes

status: Public on Jun 15 2012

summary:
The meiotic cell division reduces the chromosome number from diploid to haploid to form gametes for sexual reproduction. Although much progress has been made in understanding meiotic recombination and the two meiotic divisions, the processes leading up to recombination, including the prolonged pre-meiotic S phase (meiS) and the assembly of meiotic chromosome axes, remain poorly defined. We have used genome-wide approaches in Saccharomyces cerevisiae to measure the kinetics of pre-meiotic DNA replication, and to investigate the interdependencies between replication and axis formation. We found that replication initiation was delayed for a large number of origins in meiS compared to mitosis, and that meiotic cells were far more sensitive to replication inhibition, most likely due to the starvation conditions required for meiotic induction. Moreover, replication initiation was delayed even in the absence of chromosome axes, indicating replication timing is independent of the process of axis assembly. Finally, we found that cells were able to install axis components and initiate recombination on unreplicated DNA. Thus, although pre-meiotic DNA replication and meiotic chromosome axis formation occur concurrently, they are not directly coupled. The functional separation of these processes reveals a modular method of building meiotic chromosomes, and predicts that any crosstalk between these modules must occur through superimposed regulatory mechanisms.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
Multiple studies of meiotic chromosomes were undertaken. To study DNA replication, the locations of replicative helicase (Mcm2-7) were mapped in pre-meiotic and pre-mitotic cells, and DNA replication profiles were created for pre-meiotic S (meiS) and pre-mitotic S (mitS) phases. Early origins were mapped in hydroxyurea for wild-type cells in mitS + 200mM HU, and meiS +20mM HU for wild-type, sml1, rec8 and spo11 deletion cells. Rec8, Hop1 and Red1 binding to meiotic chromosomes was evaluated using ChIP-chip in wild-type cells with and without 20 mM HU, and in cdc6-mn and clb5 clb6 delete cells. Finally, meiotic DNA double-strand breaks (DSBs) were mapped in cdc6-mn dmc1 delete cells by measuring the ssDNA that accumulates at DSB hotspots.


title: Reproducibility of global gene expression in rat lung

status: Public on Feb 28 2012

city: Sapporo

first: Satoru

last: Tsunemine

institute: Contract Research Laboratory, GeneticLab Co., Ltd.

summary:
We used microarrays to assess the reproducibility of global gene expression in rat lung from experiments performated by 2 individuals.
Expression analyses in 01matsu and 01suzu rat lung. Both prepared under the same conditions, and the comparison is between the reproducibility of the experiment as performed by two different individuals.

overall_design: Affymetrix® GeneChip® Rat Genome 230 2.0 Array was used to analyze total RNA from rat lung.

first: So

last: Matsuzawa

first: Yusuke

last: Suzuki


title: Expression data from an ex vivo ischaemia reperfusion model of renal deceased by cardiac death (DCD) donation in rat

status: Public on Mar 22 2012

city: Sunderland

first: Noel

middle: Mark

last: Carter

state: Tyne and Wear

address: Wharnecliffe St

department: Pharmacy, Health and Wellbeing

institute: University of Sunderland

summary:
In DCD organ donation one of the significant problems for the organ is the inflammatory response due to ischaemia reperfusion injury caused by warm ischaemia prior to retrieval followed by warm reoxygenation upon transplantation. We developed a model where a DCD kidney was retrieved and preserved using hypothermic machine perfusion with cold University of Wisconsin  solution with/without the addition of heparinoids low molecular weight heparin and pentosan polysulfate (PPS) followed by warm oxygenated perfusion with modified Krebs-Henseleit buffer to simulate early ischaemia reperfusion injury (IRI). The donor rats consisted of a control group cold perfusion group compared to warm perfusion and groups treated with either low molecular weight heparin or PPS to assess their activity in ameliorating IRI.
We used equimolar pooled RNA samples from each group to perform an exploratory microarray experiment

overall_design: Donor kidneys were harvested and preserved by hypothermic machine perfusion with University of Wisconsin (UW) Solution for 3 hours followed by warm oxygenated perfusion with modified Krebs-Henseleit buffer for 30 minutes to simulate transplantation and whole blood ischaemia reperfusion injury. The model was then used to test the anti-inflammatory properties of the glycosaminoglycan heparin and PPS when used as supplements into perfusate solutions.  Half of the donor kidney was used to extract RNA using the Tri reagent and stored in RNA Later. The qualitative best three RNAs from each group were quantified by fluorimetry and mixed in an equimolar manner and used for microarray analysis.

first: Aimee

last: Kibondo

first: Hugh

last: Birch

first: Daniel

last: Swan

first: Simon

last: Cockell

first: Liming

last: Wang

first: Heiko

last: Peters

first: Anne

last: Cunningham

first: Vijay

last: Anand

first: Muhammad

last: Khuram

first: David

last: Talbot


title: The effect of GW3965 and dexamethasone on gene expression of rat livers

status: Public on Apr 02 2012

city: Bethesda

first: Tomoshige

last: Kino

state: MD

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

summary: GLUCOCORTICOIDS are steroid hormones that strongly influence intermediary carbohydrate metabolism by increasing the transcription rate of glucose-6-phosphatase (G6Pase) a key enzyme of gluconeogenesis, and suppress the immune system which makes them one of the most important therapeutic agents in the treatment of allergic, autoimmune and inflammatory diseases. The biologic actions of circulating glucocorticoids are transmitted to the cells nucleus by the glucocorticoid receptor (GR). The nuclear liver X receptors (LXRs) bind to cholesterol metabolites, heterodimerize with the retinoid X receptor (RXR), and regulate the cholesterol turnover, the hepatic glucose metabolism by decreasing the expression of G6Pase, and repress a set of inflammatory genes in immune cells. The aim of this study is to evaluate the crosstalk between the GR- and LXR-mediated signaling systems. Transient transfection-based reporter assays and gene silencing methods using siRNAs for LXRs showed that overexpression/ligand (GW3965) activation of LXRs/RXRs repressed GR-stimulated transactivation of certain glucocorticoid response element (GRE)-driven promoters in a gene-specific fashion. Activation of LXRs by GW3965 attenuated dexamethasone-stimulated elevation of circulating glucose in rats and suppressed dexamethasone-induced mRNA expression of hepatic glucose-6-phosphatase (G6Pase) in rats, mice and human hepatoma HepG2 cells. In microarray transcriptomic analysis of rat liver, GW3965 differentially regulated glucocorticoid-induced transcriptional activity of about 15% of endogenous glucocorticoid-responsive genes. Mechanistically, and in vitro chromatin immunoprecipitation assay, we found that LXRα/RXRα bound GREs and inhibited GR binding to these DNA sequences in a gene-specific fashion. These novel results were further confirmed in in vivo binding assays, and in gel mobility shift assays, where recombinant LXRα/RXRα proteins were used to examine their interaction with classic or G6Pase GREs. We propose that administration of LXR agonists may be beneficial in glucocorticoid treatment- or stress-associated dysmetabolic states by directly attenuating the transcriptional activity of the GR on glucose and/or lipid metabolism.

overall_design: 4 Sprague-Dawley rats (180-200g) were orally gavaged for three days with GW3965 prepared in 1% Tween 80, 0.5% hydroxypropyl methylcellulose, 20 mM Na2HPO4 and 20 mM NaH2PO4 (50 mg/kg animal). Another set of animals were also orally gavaged with the same volume of the vehicle control (1% Tween 80, 0.5% hydroxypropyl methylcellulose, 20 mM Na2HPO4 and 20 mM NaH2PO4). On the third day, GW3965 or its vehicle control was administered first to the animals followed by an intra-muscularly injection of dexamethasone (1.5 mg/kg) or physiologic saline in two animals from each group. Twenty-four hours after the injection, levels of blood glucose were measured in these rats using the Freestyle GlucoMeter (Abbott Laboratories, Abbott Park, IL) by sampling blood from their tails. The animals were then euthanized using CO2, and their livers were harvested for extraction and purification of total RNA and proteins. Five μg of total RNA purified from rat livers was used for producing probes with the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix, Inc., Santa Clara, CA). [Rat230_2] Affymetrix Rat Genome 230 2.0 Arrays (Affymetrix Inc.) were then labeled with the prepared probes.

first: Nancy

last: Nader

first: Sinnie

last: Sin Man Ng

first: Yonghong

first: Brent

last: Abel

first: George

middle: P

last: Chrousos


title: Function-based discovery of significant transcriptional temporal patterns in insulin-stimulated muscle cells

city: Padova

first: Barbara

last: Di Camillo

address: via Gradenigo 6B

department: Information Engineering Department

country: Italy

institute: University of Padova

summary:
Background: Insulin's effect on protein synthesis (translation of transcripts) and post-translational modifications, especially those involving reversible modifications such as phosphorylation of various signaling proteins, are extensively studied. On the other hand, insulin's effect on the transcription of genes, especially of transcriptional temporal patterns, is not well investigated in the literature.
Methods: To identify significant transcriptional temporal patterns, primary differentiated rat skeletal muscle myotubes were treated with insulin and samples were collected every 10 min for 8 hours. Pooled samples at every hour were analyzed by a gene array approach to measure transcript levels. The pattern of transcript levels were analyzed based on a novel method that integrates selection, clustering, and functional annotation to find the main temporal patterns associated with functional groups of differentially expressed genes.
Conclusion: In response to insulin, 326 genes were selected as differentially expressed in response to in vitro insulin treatment in skeletal muscle myotubes.  Approximately 20% of the genes that were differentially expressed were identified as belonging to the insulin signaling pathway. 12 different clusters of gene expression profiles are identified which shows patterns that includes a slow and gradual decrease in gene expression, a gradual increase in gene expression reaching a peak at about 5 hours and then reaching a plateau or an initial decrease and other different variable patterns of increase in gene expression over time. As far as we know, this is the first systematic study in the literature monitoring transcriptional response to insulin in endothelial cells, in a time series microarray experiment.

overall_design: The purpose of this investigation was to examine the transcriptional response of skeletal muscle cells during acute insulin stimulation. Samples were collected at times 0, 20, 40, 60, . . . , 480 minutes (every 20 minutes, for 8 hours) from both insulin treated and control cultures, for a total of 50 biological samples. Samples (20, 40, 60), (80, 100, 120), (140, 160, 180), (200, 220, 240), (260, 280, 300), (320, 340, 360), (380, 400, 420) and (440, 460, 480) from insulin-treated and control cultures were pooled together, obtaining eight joint samples. Consistently, sample 0’ was harvested and collected in triplicates and pooled together (0a, 0b, 0c) for each culture and two targets for the hybridization were prepared separately. All of the culturing and sampling procedures described above were repeated two additional times on different days, using the same identical cell line, to obtain a complete triplicate of the experiment. Sample 'Insulin_3_rep_a' (pool of 140', 160', 180') was excluded from the analysis since it had quite poor MvA plots compared to the median microarray signal.

first: Brian

last: Irving

first: Jill

last: Schimke

first: Tiziana

last: Sanavia

first: Gianna

last: Toffolo

first: Claudio

last: Cobelli

first: K

last: Nair


title: The effect of mequindox on gene expression in rat liver tissue

city: Wuhan

first: Xiu-Ju

last: ZHAO

state: Hubei

address: No.68 South Xuefu Road, Changqing Garden

department: School of Biology and Pharmaceutical Engineering

institute: Wuhan Polytechnic University

summary:
Veterinary drug mequindox, 3-methyl-2-acethyl-quindoxaline-N-1,4-dioxide, belongs to a class of antibiotic and growth-prompting drug called quinoxalines that are often used in livestock and poultry industry. Previous researches focused on traditional toxicity. However, the effect of mequindox on endogenous metabolic profile remains unknown.
We used microarrays to detail the global programme of gene expression underlying mequindox toxicity.

overall_design: Two groups (control and high-dosed mequindox) were selected for GeneChip analysis based on PCA score of liver aqueous extracts and clinical chemistry changes.

last: Zhao

first: Yulan

last: Wang


title: Comparison of hepatocarcinogen-induced gene expression profiles in conventional primary rat hepatocytes with in vivo rat liver

status: Public on Apr 24 2012

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

institute: VUB

summary: At present, substantial efforts are focused on the development of in vitro assays coupled with ”omics” technologies for the identification of carcinogenic substances as an alternative to the classical 2-year rodent carcinogenicity bioassay. A prerequisite for the eventual regulatory acceptance of such assays, however, is the in vivo relevance of the observed in vitro findings.

overall_design: In the current study, hepatocarcinogen-induced gene expression profiles generated after exposure of conventional cultures of primary rat hepatocytes to three non-genotoxic carcinogens (methapyrilene hydrochloride, piperonyl butoxide and Wy-14643), three genotoxic carcinogens (aflatoxin B1, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and 2-nitrofluorene), and two non-carcinogens (nifedipine and clonidine) are compared with previously obtained in vivo data after oral administration for up to 14 days of the same hepatocarcinogens to rats.

middle: Y

first: Heidrun

last: Ellinger-Ziegelbauer

first: Mathieu

last: Vinken

first: Tamara

last: Vanhaecke

first: Joost

last: van Delft

first: Jos

last: Kleinjans

first: Hans-Juergen

last: Ahr

first: Vera

last: Rogiers


title: Gene expression response to acrylamide in rat pups

status: Public on Feb 08 2012

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

summary: Acrylamide is a type-2 alkene monomer with established human neurotoxic effects.  While the primary source of human exposure to acrylamide is occupational, other exposure sources include food, drinking water, and smoking.  In this study, neurobehavioral assays coupled with transcriptional profiling analysis were conducted to assess both behavioral and gene expression effects induced by acrylamide neurotoxicity in rats when administered during early postnatal life.  Acrylamide administration in rat pups induced significant characteristic neurotoxic symptoms including increased heel splay, decrease in grip strength, and decrease in locomotor activity.   Transcriptome analysis with the Affymetrix Rat Genome 230 2.0 array indicated that acrylamide treatment caused a significant alteration in the expression of genes involved in muscle contraction, pain regulation, and dopaminergic neuronal pathways.  First, in agreement with the observed behavioral effects, expression of the Mylpf gene involved in muscle contraction was downregulated in the spinal cord in response to acrylamide. Second, in sciatic nerves, acrylamide repressed the expression of the opioid receptor gene Oprk1 that is known to play a role in neuropathic pain regulation. Finally, in the cerebellum, acrylamide treatment caused a decrease in the expression of the nuclear receptor gene Nr4a2 that is required for development of dopaminergic neurons.   Thus, our work examining the effect of acrylamide at the whole-genome level on a developmental mammalian model has identified novel genes previously not implicated in acrylamide neurotoxicity that can be further developed into biomarkers for assessing the risk of acrylamide exposure.

overall_design: Three-week-old male Wistar rat pups were treated with either acrylamide or saline daily (30 mg/kg) for 21 days, then tissues (cerebellum, spinal cord, and sciatic nerve) were harvested and frozen.  Two biological replicate samples, each sample consisting of pooled tissue from 2 rats, were analyzed for each treatment.


title: Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system

status: Public on Feb 16 2012

city: Milwaukee

first: Sheng

last: Yang

state: WI

address: 8701 Watertown Plank Road

department: Human and Molecular Genetics Center

institute: Medical College of Wisconsin

summary:
Induced pluripotent stem (IPS) cells have attracted enormous attention due to their vast potential in regenerative medicine, pharmaceutical screening and basic research. The majority of prior established rat IPS cells were generated from somatic cells by retroviral and lentiviral transduction with expression of Oct4, Sox2, Klf4 and c-Myc and using chemical inhibitors of key differentiation pathways. A major difficulty in the application of this technology is the efficient delivery of reprogramming factors and the long-term maintenance of properties of stem cells.

Here, we employed the PiggyBac (PB) transposon carrying four 2A peptide-linked reprogramming factors for generating rat IPS cells. These stable rat IPS cells are similar to embryonic stem (ES) cells in morphology, proliferation, teratoma formation, expression characteristic pluripotency markers, developmental potential, and germline transmission. Transcriptional profiling of the IPS cells revealed both pathways in common with ES cells from rat and unique signaling pathway to our cells, including Wnt, TGF and Notch. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying germline pluripotency and pave the way for exploration of cell-based therapies using the rat.

overall_design: To compare the gene expression profiling between rat IPS cells and ES cells to show if the rat IPS cells had been reprogrammed into pluripotent status like rat ES cells at the gene expression level.

first: Rebecca

last: Schilling

first: Jamie

last: Foeckler

first: Martin

last: Hessner

first: Shuang

last: Jia

first: Alison

last: Zappa

first: Akiko

last: Takizawa

first: Shawn

last: Kalloway

first: Aron

middle: M

last: Geurts

first: Howard

middle: J

last: Jacob


title: Expression data from a model of renal deceased by cardiac death (DCD) donation in rat

status: Public on Feb 06 2012

first: Noel

last: Carter

summary: In DCD organ donation one of the significant problems for the organ is the inflammatory response due to ischaemiua reperfusion injury caused by warm ischaemia prior to retrieval followed by warm reoxygenation upon transplantation. We developed a model where a DCD kidney was retrieved and stoired overnight then the organ was surgically attached to the femoral artery of a recipient rat and blood flow restored for up to six hours to simulate early ischaemia reperfusion injury (IRI). The recipient rats consisted of a control group compared to groups recieveing either low molecular weight heparin or an anti-inflammatory peptide to assess their activity in ameliorating IRI. We used equimolar pooled RNA samples from each group to perform an exploratory microarray experiment.

overall_design: Donor kidneys were harvested and static cold stored in University of Wisconsin (UW) Solution overnight before being surgically connected to the femoral artery of a recipient rat to simulate transplantation and whole blood ischaemia reperfusion injury. The model was then used to test the anti-inflammatory properties of the glycosaminoglycan heparin and a peptide based upon the heparin binding domain of the pro-inflammatory chemokine CCL5. The treatments were delivered as a bolus in normal saline and control recipients were given normal saline as a control. The kidneys underwent perfusion by normal blood flow for a period of up to six hours after which the recipient was euthanased and the donor kidney was removed. Half of the donor kidney was used to extract RNA and half taken for immunohistochemical analysis. The RNA was extracted using the Tri reagent and stored in RNA Later. The qualitative best three RNAs from each group were quantified by fluorimetry and mixed in an equimolar manner and used for microarray analysis.

first: Vijay

last: Anand

first: Hugh

last: Birch

first: Daniel

last: Swan

first: Simon

last: Cockell

first: Liming

last: Wang

first: Heiko

last: Peters

first: Anne

last: Cunningham

first: John

last: Kirby

first: Simi

last: Ali

first: David

last: Talbot