title: Eye-Specific Gene Expression following Embryonic Ethanol Exposure in Zebrafish: Roles for Heat Shock Factor 1

status: Public on Jan 01 2014

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

institute: University of Idaho

summary: Ethanol is a well-known teratogen. While this teratogenic potential is well-characterized clinically, the mechanisms through which ethanol exposure results in developmental defects remain unclear. Here we use the zebrafish model to elucidate eye-specific mechanisms that may underlie ethanol-mediated microphthalmia (reduced eye size), using time-series microarray analysis of gene expression of eye tissues of embryos exposed to 1.5% ethanol vs. untreated embryos. We identified 62 genes differentially expressed in ethanol-treated as compared to control zebrafish eyes from all sampling times over the period of retinal neurogenesis (24-48 hours post-fertilization). Application of the EDGE (extraction of differential gene expression) algorithm identified over 3000 genes differentially expressed over developmental time in ethanol-treated embryo eyes as compared to untreated embryo eyes. These lists included several genes indicating a mis-regulated cellular stress response (heat shock response) due to ethanol exposure.  Combined treatment with sub-threshold levels of ethanol and a morpholino (MO) targeting heat shock factor 1 (hsf-1) mRNA resulted in a microphthalmic phenotype, suggesting convergent molecular pathways.  Manipulation of the heat shock response by thermal preconditioning partially prevented ethanol-mediated microphthalmia while maintaining Hsf-1 expression. Together these data are consistent with roles for reduced Hsf-1 in mediating microphthalmic effects of embryonic ethanol exposure in zebrafish.

overall_design: time series, 9 samples, no replicates

first: Bhavanim

last: Kashyap


title: Transcriptomic characterization of the novel avian-origin influenza A (H7N9) virus: specific and intermediate host-response between avian (H5N1 and H7N7) and human (H3N2) viruses.

status: Public on Jan 16 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

summary: A novel avian-origin H7N9 influenza A virus (IAV) emerged in China in early 2013 causing mild to lethal human respiratory infections. H7N9 originated from multiple reassortment events between avian viruses and carries genetic markers of human adaptation. Determining whether H7N9 induces a host-response closer to human or avian IAV is important to better characterize this emerging virus. Here we compared the human lung epithelial cell response to infection with A/Anhui/01/13 (H7N9) or highly pathogenic avian-origin H5N1, H7N7, or human seasonal H3N2 IAV.

overall_design: Here, polarized confluent monolayers of Calu-3 cells were infected apically with the avian-origin IAVs A/Anhui/01/2013 (H7N9) [Anhui01], A/Netherland/219/2003 (H7N7) [NL219], A/Vietnam/1203/2004 (H5N1) [VN1203], or a human seasonal virus A/Panama/2007/1999 (H3N2) [Pan99] at an MOI of 1.  Time-matched mocks were also included using the same cell stock as the rest of the samples.  Culture medium (same as what the virus stock is in) was used for the mock infections.  Quadruplicate wells were infected for each virus/timepoint.  Measured timepoints were 3, 7, 12 and 24 hours post-inoculation and the RNA was used for transcriptional analysis via microarray.

first: Terry

last: Tumpey

first: Laurence

last: Josset

first: Hui

last: Zeng

first: Sara

last: Kelly


title: Human HAK-1A hepatocellular carcinoma (HCC) cells: TCF-4J-overexpressing clone (under normoxia) vs. TCF-4K-overexpressing clone (under normoxia)

status: Public on Nov 01 2013

city: Providence

first: Miran

last: Kim

state: RI

address: 55 Claverick St

institute: Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University

summary:
The microarray gene expression analysis revealed that TCF-4 isoforms activate different downstream target genes in HCC.
TCF-4J upregulated genes associated with Wnt/beta-catenin, Notch, and insulin/IGF-1/IRS1 signal transduction pathway.

overall_design: 1 HAK-1A HCC clone overexpressing TCF-4J, 1 HAK-1A HCC clone overexpressing TCF-4K

first: Hironori

last: Koga

first: Yoshito

last: Tomimaru


title: Expression data from early zebrafish embryos either untreated or treated with retinoic acid

status: Public on Dec 09 2013

city: Worcester

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

institute: UMass Medical School

summary: Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation.  Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites.  This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers.  However, little is understood about how the nascent embryonic genome positions nucleosomes during development.  This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte.  Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes.  We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages.  We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements.  Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development.

overall_design: Expression of embronic transcripts were used to determine expressed and non-expressed gene groups for further chromatin studies.

middle: E

first: Charles

middle: G

last: Sagerstrom


title: Gene expression signatures for ELF4

status: Public on Dec 04 2013

city: Bunkyo-ku

first: Mizuo

last: Ando

state: Tokyo

address: 7-3-1 Hongo

department: Otolaryngology-Head and Neck Surgery

country: Japan

institute: The University of Tokyo

summary: To elucidate how ELF4 confers anti-growth activity, gene expression profiles were compared between wildtype-  and mutant-expressing T3M-1 Cl-10 cells with the use of DNA microarrays.

overall_design: T3M-1 Cl-10 cells were infected with a mock retrovirus or virus generated from pMXS-ires-EGFP expressing ELF4 or ELF4(L211M), and EGFP?positive fractions were purified with a cell sorter. Thus gene expression profiling of purely mock/ELF4/ELF4(L211M)-expressing cells was performed with SurePrint G3 Human Gene Expression 8×60K v2 Microarray.


title: Differentially expressed genes associated with hepatic steatosis in zebrafish

status: Public on Oct 01 2013

city: Philadelphia

first: Randolph

last: Matthews

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/GI

institute: The Children's Hospital of Philadelphia Research Institute

summary:
Expression microarray of livers from adult zebrafish: control, overfed, and ahcy+/-
Comparison of expression from livers obtained from ahcy+/+, overfed ahcy+/+, ahcy+/- control and ahcy+/- overfed.

overall_design: Adult zebrafish, ahcy+/+ and +/-, were given a regular diet or were overfed for a month. Livers were removed, RNA isolated, and expression microarray was performed.

middle: P


title: Inhibition of proliferation and induction of autophagy by atorvastatin in PC3 prostate cancer cells correlate with downregulation of Bcl2 and upregulation of miR-182 and p21 [Gene expression]

status: Public on Sep 30 2013

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The epidemiologic association between statin use and decreased risk of advanced prostate cancer suggests that statins may inhibit prostate cancer development and/or progression.  Studies were performed to determine the effects of a model statin, atorvastatin (ATO), on the proliferation and differentiation of prostate cancer cells, and to identify possible mechanisms of ATO action.  ATO inhibited the in vitro proliferation of both LNCaP and PC3 human prostate cancer cells in dose-dependent fashion.  The greater inhibitory activity of ATO in PC3 cells was associated with induction of autophagy in that cell line, as demonstrated by increased expression of LC3-II.  miR-182 was consistently upregulated by ATO in PC3 cells, but not in LNCaP cells.  ATO upregulation of miR-182 in PC3 cells was p53-independent and was reversed by geranylgeraniol.  Transfection of miR-182 inhibitors decreased expression of miR-182 by >98% and attenuated the antiproliferative activity of ATO.  miR-182 expression in PC3 cells was also increased in response to stress induced by serum withdrawal, suggesting that miR-182 upregulation can occur due to nutritional stress.  Bcl2 and p21 were identified to be potential target genes of miR-182 in PC3 cells. Bcl2 was downregulated and p21 was upregulated in PC3 cells exposed to ATO.  These data suggest that miR-182 may be a stress-responsive miRNA that mediates ATO action in prostate cancer cells.

overall_design: Gene and miRNA expression in two prostate cancer cell lines treated with Atorvastatin vs. untreated control.

first: Xinjian

last: Peng

first: Wenping

last: Li

first: Liang

last: Yuan

first: Rajendra

last: Mehta

first: Levy

last: Kopelovich

first: David

middle: L

last: McCormick


title: Effect of light on gene expression in the zebrafish pineal gland

status: Public on Dec 14 2013

city: Tel Aviv

first: Shahar

last: Alon

address: Tel Aviv University

department: Department of Neurobiology, The George S. Wise Faculty of Life Sciences

country: Israel

institute: Tel Aviv University

summary: Microarray data allowed detection of genes that are induced by light in the zebrafish pineal gland

overall_design: Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room. Fish were transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Pools of 12 pineal glands were prepared at each condition and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions.

first: Yoav

last: Gothilf


title: CCAAT/enhancer-binding protein alpha is epigenetically silenced by histone acetylation in endometriosis and promotes the pathogenesis of endometriosis: a novel therapeutic target

status: Public on Oct 21 2013

city: Yufu city

first: Yukie

last: Kawano

state: Oita

address: idaigaoka 1-1

department: Obstetrics and Gynecology

institute: Oita University

summary: Accumulating evidences suggest that various epigenetic aberrations play definite roles in the pathogenesis of endometriosis. The aim of this study is to identify 1) the panel of aberrantly expressed genes that are epigenetically suppressed by histone acetylation in endometriosis; 2) the roles of CCAAT/enhancer-binding protein (C/EBP) alpha, one of the candidate molecules whose expression was epigenetically repressed in endometriotic cyst stromal cells (ECSCs), in the pathogenesis of endometriosis; and 3) the efficacy of the histone deacetylase inhibitors for the treatment of endometriosis.

overall_design: Subconfluent ECSCs cultured in 10-cm dish were further incubated for 72 h with or without VPA (8 mM) and/or 5aza. Total RNA from untreated ECSCs (n=4), VPA-treated ECSCs (n=4), 5aza-treated ECSCs (n=4), and VPA- and 5aza-treated ECSCs (n=4) was extracted and subjected to gene expression microarray analysis.

first: Kaei

last: Nasu


title: PLK1 signaling coopereates with estrogen receptor-dependent gene transcription.

city: Barcelona

first: Michael

last: Wierer

address: c/ Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Analysis of MCF7 breast cancer cells treated with estadiol for 6 h in presence or absence of the specific PLK1 inhibitor BI2536. Together with CHIP and global phosphoproteome data, the results demonstrate a key role of PLK1 in the estrogen receptor-mediated gene response.

overall_design: Hormone-deprived MCF7 cells were pretreated with BI2536 or vehicle (DMSO) followed by induction with estradiol (E2) or vehicle (ethanol). RNA of each condition was analysed in triplicate on an Agilent Human genome 4x44k v2 microarray [note: MCF7_DMSO_E2_rep3 sample was a clear technical outlier (poor hybridization), and was therefore excluded from the further analysis/this record].

first: Miguel

last: Beato


title: Overexpression of NEK6 Associated with Poor Prognosis of Esophageal Squamous Cell Carcinoma

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: Esophageal squamous cell carcinoma (SCC) is frequently diagnosed at advanced stage and associated with poor prognosis. This study aimed to identify differentially expressed genes for further evaluated as biomarkers for predicting survival of the patients. Five paired of cancerous and normal tissues from esophageal SCC patients were subjected to cDNA microarray analysis and one of these differentially expressed genes, NEK6, was further verified in esophageal SCC tissues. The data showed 444 up-regulated genes and 918 down-regulated genes in tumor tissues (2 folds as a cut-off value). qRT-PCR data showed that 20 of 30 (66.7%) increased levels of NEK6 mRNA in cancerous tissues compared to that of distant normal tissues, while immunohistochemical data showed that 49/94 (52.13%) of the archived esophageal SCC tissues expressed higher levels of NEK6 than that of normal tissues. NEK6 expression was associated with depth of tumor invasion (P=0.005), lymph node metastasis (P=0.018), and advanced clinical tumor stages (P=0.004) of these 94 patients. Kaplan Meier curve showed that the overall survival of NEK6-positive patients was much lower than those of NEK6-negative patients (P<0.001). The median survival of NEK6-positive patients was 23 months, whereas the median survival of NEK6-negative patients was 64 months. The cumulative 5-year survival rate of NEK6-positive patients was 14.3% (7/49), whereas the rate of NEK6-negative patients was 64.4% (29/45). Multivariate analysis showed that N classification (P=0.002) and NEK6 expression (P<0.001) were independent predictors for esophageal SCC patients. These data demonstrated that NEK6 expression may serve as an independent prognostic indicator for patients with esophageal SCC.

overall_design: Gene expression in five paired of cancerous and normal tissues from esophageal SCC patients were measured using Human Genome 4x44K v2 Microarray.

first: Lihuan

last: Zhu

first: Jixue

last: Zhang

first: Long

last: Chen

first: Qiaojia

last: Huang

first: Xuegang

last: Feng

first: Meimian

last: Hua

first: Dehua

last: Zeng

first: Zaizeng

last: Wu

first: Weisheng


title: The effect of MPO inhibitor on the gene expression profiles in HL-60 cell lines exposed to 1, 2, 4,-benzenetriol

status: Public on Dec 01 2013

city: Kagoshima

first: Takuro

last: Nishikawa

address: Sakuragaoka 8-35-1

department: Pediatrics

institute: Kagoshima University

summary: To reveal the gene expression profile changes after exposure to BT, one of benzene metabolites, with or without ABAH, a myeloperoxidase (MPO) inhibitor, and to elucidate how MPO is involved in myelotoxicity of BT, we performed microarray analysis. HL-60 cells suspended in RPMI 1640 containing with 10% of heat-inactivated FBS at 4×10^5/ mL were incubated with or without BT (50 μM) at 37℃ for one or 4 hours. For MPO inhibition experiment, HL-60 (4×10^5 cells/ mL) were pretreatment with 100 μM of ABAH in RPMI 1640/10% of heat-inactivated FBS at 37℃ for 24 hours. Media was then replaced with new media containing the regent plus BT (50 μM) and incubate at 37℃ for one or 4 hours. Unexposed HL-60 cells were used as controls. To validate the microarray results, we selected 22 genes and conducted a real-time PCR.

overall_design: Gene expression alteration induced by 50 μM of BT in HL-60 cells, with or without ABAH, was measured at 1 and 4 hours after exposure to it. Three independent experiments were performed at each time (1 or 4 hours).

first: Emiko

last: Miyahara


title: Circadian adaptive signaling to critical ROS stress for cell survival

status: Public on Nov 09 2013

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

country: France

institute: IRSN

summary: Disruption of circadian clocks exacerbates various diseases, in part likely due to impaired stress resistance. It is unclear how nearly lethal stresses affect circadian clocks. We found that near-lethal doses of reactive oxygen species (ROS)-induced critical oxidative stress (cOS) at the branch point of life and death resets circadian clocks, synergistically evoking protective responses for cell survival. The cOS-triggered clock resetting and pro-survival responses are mediated by transcription factor, central clock-regulatory BMAL1 and heat shock stress-responsive (HSR) HSF1. Casein kinase II (CK2) –mediated phosphorylation regulates dimerization and function of BMAL1 and HSF1 to control the cOS-evoked responses. The core cOS-responsive transcriptome includes CK2-orchestrated crosstalk between the circadian, HSR, NFκB-mediated anti-apoptotic, and Nrf2-mediated anti-oxidant pathways. This novel circadian-adaptive signaling system likely plays fundamental protective roles in ROS-inducible disorders, various diseases, and death.

overall_design: Gene expression was measured 4h, 20h and 32h after treatment with 5 mM H2O2 for 10 min.

first: Teruya

last: Tamaru

first: Mitsuru

last: Hattori

first: Yasuharu

last: Ninomiya

first: Genki

last: Kawamura

first: Kousuke

last: Honda

first: Durga

last: Mishra

first: Bing

last: Wang

first: Ivor

last: Benjamin

first: Paolo

last: Sassone-Corsi

first: Takeaki

last: Ozawa

first: Ken

last: Takamatsu


title: Kidney from controls and SDHD-ESR mice

status: Public on Nov 15 2013

city: Seville

first: Jose

middle: I

last: Piruat

address: Hospital Virgen del Rocio-Edif IBiS. Av. Manuel Siurot sn

department: Hematology

institute: Institute of Biomedicine of Seville (IBIS)

summary:
Several mechanisms have been proposed to account for Sdh-mutation-induced tumorigenesis, the most accepted of which is based on the constitutive expression of the hypoxia-inducible factor 1alpha (Hif1alpha) at normal oxygen tension, a theory referred to as pseudo-hypoxic drive. Other molecular processes, such as oxidative stress, apoptosis or chromatin remodeling have been also proposed to play a causative role. Nevertheless, the actual contribution of each of these mechanisms has not been definitively established. Moreover, the biological factors that determine the tissue-specificity of these tumors have not been identified. In this work, we made use of the inducible SDHD-ESR mouse, a conditional mutant in the SdhD gene, which encodes the small subunit of MCII, and that acts as a tumor suppressor gene in humans.
We performed microarray analysis of  kidney in order to identify other early gene expression changes elicited by SdhD deletion.

overall_design: 8 samples from heterozygous (+/-) and 8 samples from null mutants (SDHD-ESR), paired by two and hybrydized against a pool of 8 samples from homozygous wt (+/+) animals.


title: Gene expression in adrenal medulla and kidney of a conditional mutant mouse in the SdhD gene

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

overall_design: Refer to individual Series


title: Adrenal medulla (AM) from controls and SDHD-ESR mice

summary:
Several mechanisms have been proposed to account for Sdh-mutation-induced tumorigenesis, the most accepted of which is based on the constitutive expression of the hypoxia-inducible factor 1alpha (Hif1alpha) at normal oxygen tension, a theory referred to as pseudo-hypoxic drive. Other molecular processes, such as oxidative stress, apoptosis or chromatin remodeling have been also proposed to play a causative role. Nevertheless, the actual contribution of each of these mechanisms has not been definitively established. Moreover, the biological factors that determine the tissue-specificity of these tumors have not been identified. In this work, we made use of the inducible SDHD-ESR mouse, a conditional mutant in the SdhD gene, which encodes the small subunit of MCII, and that acts as a tumor suppressor gene in humans.
We performed microarray analysis of adrenal medulla (AM) in order to identify other early gene expression changes elicited by SdhD deletion.


title: Gene expression profile of Tet1 knockout cortex and hippocampus

status: Public on Sep 01 2013

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Global gene expression profile of Tet1 knocout cortex or hippocampus is compared to wild-type cortex or hippocampus. All mice used are naïve and of mixed 129 C57BL6 backgound.

overall_design: Tet1 KO in brain cortex and hippocampus

first: Andrii

last: Rudenko

first: Meelad

last: Dawlaty

first: Rudolf

last: Jaenisch

first: Li-Huei

last: Tsai


title: Gene expression in INA6 multiple myeloma cells in an acidic condition

status: Public on Nov 22 2013

city: Tokushima-shi Kuramoto-cho

first: Ryota

last: Amachi

institute: Tokushima University

summary: We found the epigenetic regulation of gene expression in MM cells in acidic conditions. We further looked into gene expression in MM cells in acidic conditions using a cDNA microarray.

overall_design: INA6 cells were cultured for 12 hours, at pH7.4 or pH6.8 in the absence or presence of valproiate at 100 ug/mL. The total RNA was isolated using RNeasy Mini kit.

first: Hideaki

last: Horikawa


title: Microarray data from zebrafish embryos (ZFE) exposed (for 48-96 hr periods and assessed 8 days post-fertilization) to oil emulsions collected from GoM shoreline sites following the Deepwater Horizon blowout.

status: Public on Dec 03 2013

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

summary: Zebrafish embryos/larvae are a choice model system for studying early stages of vertebrate development and how these stages can be perturbed by environmental stressors. Petrochemical combustion products elicit developmental toxicity that is associated with transcriptome changes in zebrafish embryos (ZFE). We used microarrays to characterize transcriptome changes in ZFE that had been exposed in the laboratory to oil emulsions collected from the GoM shoreline, ~9 weeks after the Deepwater Horizon blowout.

overall_design: ZFE were exposed to oil emulsions collected (July 1-4, 2010) at the GoM shoreline. ZFE were exposed to emulsions, consisting of varying amounts of alkanes, polynuclear aromatic hydrocarbons (PAHs), sand and seawater that had been “buttered” on the bottom of cups, in which ZFE were suspended in zebrafish medium. ZFE development was monitored by light microscopy.  Control ZFE were suspended in zebrafish medium without emulsions. Gross developmental abnormalities, including axial changes, altered swimming patterns and yolk sac and pericardial sac swelling were noted and photographed.   ZFE/larvae were collected after exposures ended, and placed in clean medium until 192 hr post-fertilization, when larvae were collected for RNA extraction and hybridization on Affymetrix zebrafish microarrays.

first: Kevin

last: Kleinow

first: Allen

last: Bui

first: Arthur

last: Penn

first: Zakia

last: Perveen

first: Paula

last: Polk


title: Hdac6 regulates Tip60-p400 function in stem cells (gene expression)

status: Public on Nov 20 2013

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

summary: To identify the functional role of Hdac6 in embryonic stem cells, we examined gene expression changes in mouse ES cells upon Tip60, Hdac6 and double knockdown.

overall_design: Two biological replicates each for control (GFP), Tip60, Hdac6 and double KD in E14 mouse ESCs. Lentiviral-based shRNA was used and gene expression changes were determined 3 days after KD. The global gene expression profiles of Tip60, Hdac6 and double KD were compared to control KD cells.

first: Poshen

middle: B

first: Jui-Hung

last: Hung

first: Taylor

last: Hickman

first: Andrew

middle: H

last: Coles

first: James

middle: F

last: Carey

first: Zhiping

last: Weng

first: Feixia

last: Chu

first: Thomas

last: Fazzio


title: Expression data from zebrafish (Danio rerio) embryos exposed to methyl tert-butyl ether

city: Corvallis

first: Josephine

middle: Ann

last: Bonventre

state: OR

address: 1011 Agriculture & Life Sciences Building

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary:
Methyl tert-butyl ether (MTBE) has been shown to target developing vasculature in piscine and mammalian model systems. In the zebrafish, MTBE induces vascular lesions throughout development. These lesions result from exposure to MTBE at an early stage in development (6-somites to Prim-5 stages). During this time period, transcript levels of vegfa, vegfc, and vegfr1 were significantly decreased in embryos exposed to 5 mM MTBE.
We performed global gene analysis as an unbiased approach to discover possible modes of action of MTBE vascular toxicity.

overall_design: Embryos were exposed at 3 hours post fertilization (hpf) in triplicate to one of three concentrations of MTBE: 5mM (induces vascular lesions and significantly decreases vegfa), 0.625mM (NOAEL; no observed adverse effect level), and 0.00625mM (100-fold below NOAEL), or to embryo media  (control). Samples were collected at 6-somites (~15hpf), 21-somites (~24 hpf), and Prim-5 (~30 hpf) stages of development. Embryos were meticulously staged at exposure and at the time of collection to maintain a homogeneous population. Our experimental design sought to explore the effect of three concentrations MTBE on three different stages of zebrafish embryonic development during the critical period established for the chemical. This time period also corresponds to an important time in the cardiovascular system develop of our model vertebrate.

middle: A

first: Tiffany

middle: S

last: Kung

first: Lori

last: White

first: Keith

middle: R

last: Cooper


title: Genome-wide Expression Profiles of Subchondral Bone in Osteoarthritis

status: Public on Oct 24 2013

city: Durham

first: Ching-Heng

last: Chou

state: NC

address: 904 S LaSalle street

department: pathology

institute: Duke university

summary: To date, all of the prior osteoarthritic microarray studies in human tissue have focused on the overlying articular cartilage, meniscus, or synovium but not the underlying subchondral bone. In our previous study, our group developed a methodology for high quality RNA isolation from site-matched cartilage and bone from human knee joints, which allowed us to perform candidate gene expression analysis on the subchohndral bone (published on Osteoarthritis and Cartilage on Dec/5/2012 (doi: 10.1016/j.joca.2012.11.016). To the best of our knowledge, the current study is the first to successfully perform whole-genome microarray profiling analyses of human osteoarthritic subchondral bone. We believe our comprehensive microarray results can improve the understanding of the pathogenesis of osteoarthritis and could further contribute to the development of new biomarker and therapeutic strategies in osteoarthritis.

overall_design: Following histological assessment of the integrity of overlying cartilage and the severity of bone abnormality by microcomputed tomography, we isolated total RNA from regions of interest from human OA (n=20) and non-OA (n=5) knee lateral and medial tibial plateaus (LT and MT). A whole-genome profiling study was performed on an Agilent microarray platform and analyzed using Agilent GeneSpring GX11.5. Confirmatory quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis was performed on samples from nine OA individuals to confirm differential expression of 85 genes identified by microarray. Ingenuity Pathway Analysis (IPA) was used to investigate canonical pathways and immunohistochemical staining was performed to validate protein expression levels in samples.

first: C

last: Lee

first: L

last: Lu

first: I

last: Song

first: H

last: Chuang

first: J

last: Chang

first: S

middle: Y

last: Kuo

last: Wu

first: Y

middle: T

first: V

last: Kraus

middle: C

first: M


title: The effect of miR196a of overall gene expression in oral keratinocytes

status: Public on Nov 28 2013

city: Sheffield

middle: David

last: Hunter

state: South Yorkshire

address: Claremont Crescent

department: School of Clinical Dentistry

country: United Kingdom

institute: University of Sheffield

summary: We wished to assess the effect of miR196a on overall gene expression in reducing it in high expressing epithelial cells (D19 and B16) using antimiR196a and over expressing it in low-expressing cells (OKF4) using pre-miR196a.  We transfected anti miR196a in to D19 and B16 oral keratinocytes which express high levels of miR196a in triplicate cultures, harvesting 24h after transfection.  We transfected pre-miR196 in okf4 immorualised normal oral keratinocytes in duplicate culture. Successful transfection was ensured by qPCR.

overall_design: 16 Samples in total. 2 high expressing cells: control and anti-miR transfected, in triplicate. 1 low expressing cell: control and premiR transfected, in duplicate

middle: D

first: Daniel

last: Lambert


title: Identification of nucleosome positions at hox TSSs during zebrafish early embryonic development

city: Worcester

first: Steven

last: Weicksel

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

middle: E

first: Charles

middle: G

last: Sagerstrom


title: Profiling gene expression of ETV2-induced vascular endothelial cells (ETVECs)

status: Public on Jul 19 2013

city: Tokyo

first: Rimpei

last: Morita

address: 35 Shinanomachi, Shinjyuku-ku

institute: Keio University School of Medicine

summary:
ETV2 induces expression of endothelial-specific genes in primary human adult skin fibroblasts (HAFs)
Human unbillical vein endothelial cells (HUVECs) are used as a control

overall_design: 32 days after ETV2 induction into HAFs, cells are recognized as ETVECs. ETVECs were created from three independent skin donor. Each number of ETVEC is correspond to the number of HAF.

first: Akihiko

last: Yoshimura


title: Effect of progerin on p53-deficient vascular smooth muscle cells

status: Public on Sep 22 2013

city: Chiba

first: Daisuke

last: Kinoshita

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba University

summary: Analysis of p53-deficient (E6-expressing) human vascular smooth muscle cells (VSMCs) that express progerin, a mutated form of lamin A resposible for Hutchinson- Gilford progeria syndrome (HGPS). p53 pathway is associated with HGPS. Results provide insight into molecular mechanisms underlying vascular dysfunction of HGPS caused by other than p53 pathway.

overall_design: The gene expression of VSMCs induced to express E6 and either lamin A or progerin by retroviral vectors.

first: Masakatsu

last: Yamashita

first: Kazuhiro

last: Sato


title: Marinobufagenin regulates gene expression in human brain microvascular endothelial cells in vitro.

status: Public on Nov 01 2013

city: College Station

first: Nancy

last: Ing

state: TX

department: Animal Science

institute: Texas A&M University

summary:
To understand the mechanism by which MBG increases permeability of human brain microvascular endothelial cell (HBMEC) monolayers, the primary cultures were treated with 10nM MBG for 12 h.
RNA was isolated and analysed for gene expression on Agilent one color microarrays.

overall_design: Triplicate wells of HBMEC were treated with 10 nM MBG in DMSO or with just the drug vehicle for 12 h. RNA was isolated from each well and used to reverse transcribe and generate Cy3-labelled cRNA. Microarrays were hybridized, washed and scanned. Data were normalized and assessed for differential gene expression between MBG treated and control HBMEC.

first: Jules

last: Puschett


title: Non-neuronal acetylcholine as an endogenous regulator of proliferation and differentiation of Lgr5-positive stem cells in mice

status: Public on Aug 15 2013

city: Osaka

first: Toshio

last: Takahashi

address: 1-1-1 Wakayamadai

institute: Suntory Foundation for Life Sciences

summary: Acetylcholine (ACh) has been considered a neurotransmitter residing in central, parasympathetic and neuromuscular synapses of mammals. Here, experiments using crypt-villus organoids that lack nerve and immune cells in culture led us to suggest that endogenous ACh is synthesized in the intestinal epithelium to evoke growth and differentiation of the organoids through activation of muscarinic ACh receptors (mAChRs). The extracts of the cultured organoids exhibit a noticeable capacity for ACh synthesis that is sensitive to a potent inhibitor of choline acetyltransferase (ChAT). Imaging mass spectrometry reveals distribution of endogenous ACh that is localized in intestinal epithelial layer in the cultured organoids as well as in mouse small intestinal epithelium in vivo, suggesting non-neural resources of ACh. Treatment of organoids with carbachol down-regulates growth of organoids and expression of marker gene for each epithelial cell. On the other hand, antagonists for mAChRs enhances growth and differentiation of organoids, indicating involvement of mAChRs in regulating proliferation and differentiation of Lgr5-positive stem cells. Collectively, our data provide evidence that endogenous ACh released from intestinal epithelium maintains homeostasis of intestinal epithelial cell growth and differentiation via mAChRs in mice.

overall_design: Gene expression patters of gut, crypt, y-organoid and o-organoid, respectively

first: Hiroe

last: Ohnishi

first: Yuki

last: Sugiura

first: Kurara

last: Honda

first: Makoto

last: Suematsu

first: Takashi

last: Kawakami

first: Tomonori

last: Deguchi

first: Takeshi

last: Fujii

first: Tohru

last: Yamagaki

first: Shunsuke

last: Yuba


title: Vascularised and functional human liver from an iPSC-derived organ bud transplant

status: Public on Jul 01 2013

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

summary: Critical shortage of donor organs for treating end-stage organ failure highlights the urgent need for generating organs from induced pluripotent stem cells (hiPSCs). Despite many reports describing functional cell differentiation, no studies have succeeded in generating a three-dimensional vascularised organ such as liver. Here, we show the generation of vascularised and functional human liver from hiPSCs by transplantation of liver buds created in vitro (hiPSC-LBs). Specified hepatic cells self-organised into three-dimensional hiPSC-LBs by recapitulating organogenetic interactions between endothelial and mesenchymal cells. Immunostaining and gene expression analyses revealed resemblance between in vitro grown hiPSC-LBs and in vivo liver buds. Human vasculatures in hiPSC-LB transplants became functional by connecting to the host vessels within 48 hours. The formation of functional vasculatures stimulated the maturation of hiPSC-LBs into tissue resembling the adult liver. Highly metabolic hiPSC-derived tissue performed liver-specific functions such as protein production and human-specific drug metabolism without recipient liver replacement.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparison of liver developmental gene signatures among hiPSC-LB, hFLC-LB, human adult (30 years old) liver tissues (hALT) and mouse liver tissue (mLT) of various developmental stages (E9.5~P8weeks).

first: Takanori

last: Takebe

first: Hideki

last: Taniguchi


title: Differentially expressed genes after inhibition of methylation

status: Public on Jul 11 2013

city: Philadelphia

first: Randolph

last: Matthews

address: 3615 Civic Center Blvd

institute: The Children's Hospital of Philadelphia Research Institute

summary:
Expression microarray of livers from 4 dpf control zebrafish larvae, larvae treated with azacytidine, and ahcy mutant larvae
Comparison of expression from livers obtained from ahcy+/+ treated with vehicle, ahcy+/+ treated with azacytidine, and ahcy-/- treated with vehicle.

overall_design: We treated larvae starting at 2 dpf with 1 mM azacytidine or vehicle control. Livers were removed at 4 dpf, RNA isolated, and double amplified.

middle: P


title: TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression

status: Public on Aug 22 2013

city: Kgs. Lyngby

first: Kirstine

last: Belling

address: Kemitorvet, bldg 208

department: Department of Systems Biology

country: Denmark

institute: Center for Biological Sequence Analysis

summary: High levels of Tissue Inhibitor of Metalloproteinases-1 (TIMP1) are associated with poor prognosis, reduced response to chemotherapy, and, potentially, also poor response to endocrine therapy in breast cancer patients. Our objective was to further investigate the hypothesis that TIMP1 is associated with endocrine sensitivity. We established a panel of 11 MCF-7 subclones with a wide range of TIMP1 mRNA and protein expression levels. Cells with high expression of TIMP1 versus low TIMP1 displayed significantly reduced sensitivity to the antiestrogen fulvestrant (ICI 182,780, Faslodex®), while TIMP1 levels did not influence the sensitivity to 4-hydroxytamoxifen. An inverse correlation between expression of the progesterone receptor and TIMP1 was found, but TIMP1 levels did not correlate with estrogen receptor levels or growth-promoting effects of estrogen (estradiol, E2). Additionally, the effects of fulvestrant, 4-hydroxytamoxifen, or estrogen on estrogen receptor expression were not associated with TIMP1 levels. Gene expression analyses revealed associations between expression of TIMP1 and genes involved in metabolic pathways, epidermal growth factor receptor 1/cancer signaling pathways, and cell cycle. Gene and protein expression analyses showed no general defects in estrogen receptor signaling except from lack of progesterone receptor expression and estrogen inducibility in clones with high TIMP1. The present study suggests a relation between high expression level of TIMP1 and loss of progesterone receptor expression combined with fulvestrant resistance. Our findings in vitro may have clinical implications as the data suggest that high tumor levels of TIMP1 may be a predictive biomarker for reduced response to fulvestrant.

overall_design: Microarray analysis of total RNA from 10 subclones of MCF-7 breast cancer cells with various expression levels of TIMP1.

first: Christina

last: Bjerre

first: Lena

last: Vinther

first: Sidse

middle: O

last: Würtz

first: Rachita

last: Yadav

first: Ulrik

last: Lademann

first: Olga

last: Rigina

first: Khoa

middle: N

last: Do

first: Henrik

middle: J

last: Ditzel

first: Anne

last: Lykkesfeldt

first: Jun

last: Wang

last: Nielsen

first: Nils

last: Brünner

first: Ramneek

last: Gupta

last: Schrohl

first: Jan

last: Stenvang


title: Global microarray analysis of changes of gene expression in the epidermis of Brg1(i)ep-/- mice at E16.5

city: Bradford

first: Michael Y

last: Fessing

address: Richmond Road

institute: University of Bradford

summary: Changes in global gene expression in the epidermis of the Brg1(i)ep-/- mice in comparison to the wild type at E16.5 were analyzed using micro-array technology.

overall_design: The RNA was purified from the mouse epidermal tissue after laser capture microdisection (LCM) followed by two rounds of linear amplification. The amplified RNA from two Brg1(i)ep-/- animals were pooled together and the amplified RNA from two control animals was also were pooled together.

first: Andrei

last: Mardaryev

first: Joanne

middle: L

last: Yarker

first: Krzysztof

last: Poterlowicz

first: Andrey

last: Sharov

first: Vladimir

last: Botchkarev

first: Michael


title: Inhibition of proliferation and induction of autophagy by atorvastatin in PC3 prostate cancer cells correlate with downregulation of Bcl2 and upregulation of miR-182 and p21

status: Public on Sep 30 2013

city: Northbrook

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

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

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


title: Identification of Nkx6.1 regulated genes in mature pancreatic islets.

status: Public on Sep 12 2013

city: La Jolla

first: Brandon

last: Taylor

state: CA

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego

summary: Nkx6.1 target genes were identified in mature pancreatic islets by comparing gene expression in conditional Nkx6.1-ablated islets versus control islets using microarray analysis.

overall_design: Nkx6.1 was conditionally ablated in mature pancreatic islets by recombination of a Nkx6.1-flox allele using the tamoxifen-inducible Pdx1-CreERTM allele (Gu et al 2002). Mice were injected with 2 mg/25 g tamoxifen in corn oil four times between 4 and 6 weeks of age. Islets were isolated after the final tamoxifen injection. Total RNA was isolated and pooled from pancreata of 6 week old Nkx6.1fl/-;Pdx1-CreERTM (mutant) versus Nkx6.1fl/+;Pdx1-CreERTM (control) littermates for 3 biological replicates.

first: Maike

last: Sander


title: Expression arrays of KRASG12D rhabdomyosarcoma models in zebrafish

status: Public on Jul 17 2013

first: Richard

middle: Mark

last: White

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Rhabdomyosarcoma is a pediatric malignancy thought to arise from the uncontrolled proliferation of myogenic cells.  Here, we have generated models of rhabdomyosarcoma in the zebrafish by inducing oncogenic KRASG12D expression at different stages during muscle development.  Several zebrafish promoters were used including the cdh15 and rag2 promoters that drive gene expression in early muscle progenitors, and the mylz2 promoter that expresses in differentiating myoblasts.  The tumors that developed differed in their ability to recapitulate normal myogenesis.  cdh15:KRASG12D and rag2:KRASG12D fish developed tumors that displayed an inability to fully undergo muscle differentiation by histologic appearance and gene expression analyses.  In contrast, mylz2:KRASG12D tumors more closely resembled mature skeletal muscle and were most similar to well-differentiated human rhabdomyosarcoma by gene expression.  mylz2:KRASG12D fish showed significantly improved survival compared to cdh15:KRASG12D and rag2:KRASG12D fish.  Tumor-propagating activity was enriched in  myf5-expressing cell populations within all of the tumor types.  Our results demonstrate that oncogene expression at different stages during muscle development has profound effects on the ability of tumor cells to recapitulate normal myogenesis, altering the tumorigenic capability of these cells.

overall_design: 32 samples total: 7 WT muscle, 9 mylz2-KRAS, 9 cdh15-KRAS, and 7 rag2-KRAS tumors

first: Leonard

last: Zon

first: Narie

last: Storer


title: Short-term, high fat-feeding-induced changes in white adipose tissue gene expression are highly predictive for long-term changes

status: Public on Aug 27 2013

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Using standardized, semipurified diets is a crucial factor for reproducibility of experimental nutritional studies. For the purpose of comparability and integration of research, two European consortia, Mitofood and BIOCLAIMS, proposed an AIN-93-based standard reference diet, the standardized BIOCLAIMS low-fat diet (LFD) as well as a high-fat diet (HFD). In order to evaluate the BIOCLAIMS LFD and HFD, we performed short-term (5 days) and long-term (12 weeks) feeding experiments using male C57BL/6 mice. The HFD has the same composition as the LFD except the fat content is increased to 40% energy in exchange for carbohydrates. Both diets were accepted by the animals and proof of principle was given that the BIOCLAIMS HFD increases body weight and body fat and affects glucose homeostasis. Short-term feeding trials (5 days) were performed in order to identify metabolic and molecular parameters which can serve as acute predictors for metabolic disorders due to high-fat diet-induced obesity. We analyzed gene expression in gonadal white adipose tissue of short- and long-term fed animals with whole genome microarrays. The BIOCLAIMS HFD strongly influenced gene expression in white adipose tissue after short- and long-term intervention. A total number of 973 and 4678 transcripts were significantly different between both diets after 5 days feeding and 12 weeks feeding, respectively. A total number of 764 transcripts encoding 549 genes were significantly differentially regulated between LF and HF animals after 12 weeks feeding as well as after 5 days feeding. Of these 549 overlapping genes, a substantial number (434 genes) were expressed at a lower level and 115 genes were expressed at a higher level in the HF mice compared to the LF mice. Without exception, all genes were regulated equally. Pathway analysis revealed a prominent role for genes involved in lipid metabolism, carbohydrate metabolism and oxidative phosphorylation. This was confirmed by quantitative real-time reverse transcription PCR. The high predictive value of gene expression changes in our short-term study compared to long-term high fat feeding is a promising step to get well-defined, early biomarkers that could shorten animal trials considerably and allow a more rapid and efficient screening of different compounds.

overall_design: C57BL/6J wildtype male mice, aged 12 weeks, received a low-fat diet or a high-fat diet for 5 days or 12 weeks. After sacrification, white adipose tissue depots were dissected, and immediately snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 4x44K microarrays.

first: Anja

last: Voigt

first: Katrin

last: Agnew

middle: M

first: Jaap

last: Keijer

first: Susanne

last: Klaus


title: Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse pituitary gland

status: Public on Jun 21 2013

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Vitamin D2 (VD) and the VD3 receptor (VDR) are proposed to have multiple important physiological roles that include but are not limited to glucose homeostasis, bone health, immune competency and more recently maintenance of normal reproductive physiology. The prevalence of VD deficiency in the US is reported to be as high as 60% in some populations. Several recent studies suggest that reproductive-aged women and their offspring are at the greatest risk for VD deficiency. The objective of our study was to determine the effect of early life (intrauterine through preweaning) and peripubertal VD deficiency on female reproductive physiology.

overall_design: Profile and compare the hypophysis transcriptomes of 2-month-old C57BL/6J mice that received a normal (OC samples) or a VD-deficient diet only during the early life (OE samples) or peripubertal (OP samples). Each diet group (OC, OE and OP) was composed of 4 females (biological replicas).

first: Genevieve

last: Neal-Perry

first: Joseph

last: Davis

first: Thomas

last: Fisher

first: Cary

last: Dicken

first: Yan

last: Sun

first: Jun

last: Shu

first: Sanda

middle: A


title: Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse ovaries

overall_design: Profile and compare the ovarian transcriptomes of 2-month-old C57BL/6J mice that received a normal (OC samples) or a VD-deficient diet only during the early life (OE samples) or peripubertal (OP samples). Each diet group (OC, OE and OP) was composed of 4 females (biological replicas).


title: Transcriptomic effects of early life and peripubertal dietary vitamin D deficiency on mouse ovaries and pituitary glands

overall_design: Refer to individual Series


title: Expression data from zebrafish pigment cells at adult stage

status: Public on May 30 2013

city: Suita

first: hiroki

last: hamada

state: Osaka

address: 1-3 Yamadaoka

department: Frontier Biosciences

institute: Osaka University

summary:
In zebrafish, there are interactions between black pigment cells (melanophores) and yellow pigment cells (xanthophores) for pigment-pattern formation. However, the detailed molecular mechanism of these interactions remains largely unknown.
We used microarray for identifying the molecular basis of these interactions by comparing gene expression between melanophores and xanthophores.

overall_design:
Zebrafish pigment cells were collected from adult-fish fins by centrifugal separation or using cell sorter.
melanophores vs. xanthophores

first: Masakatsu

last: Wantanabe

first: Shigeru

last: Kondo


title: Transcriptional impact of organophosphate and metal mixtures on olfaction: copper dominates the chlorpyrifos-induced response in adult zebrafish.

status: Public on May 21 2013

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Chemical exposures in fish have been linked to loss of olfaction leading to an inability to detect predators and prey and decreased survival. However, the mechanisms underlying olfactory neurotoxicity are not well characterized, especially in environmental exposures which involve chemical mixtures. We used zebrafish to characterize olfactory transcriptional responses by two model olfactory inhibitors, the pesticide chlorpyrifos (CPF) and mixtures of CPF with the neurotoxic metal copper (Cu).

overall_design: 30 one-year-old adult AB strain zebrafish were exposed, in groups of three, to CPF/Cu concentrations of 0/0, 0.1/0, 0.25/0, 0.6/0, 0/0.1, 0/0.25, 0/0.6, 0.1/0.25, 0.25/0.25, 0.6/0.25.

first: Theodor

middle: K

last: Bammler

first: Richard

last: Beyer

first: Evan

last: Gallagher


title: Expression data of kidney multiciliated cells from zebrafish embryos

status: Public on May 11 2013

city: Shanghai

first: Lei

last: Wang

address: Room 408, Building 1 225 South Chong Qing Road

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Multiciliated cells (MCCs) possess multiple motile cilia on the cell surface and are widely distributed throughout the vertebrate body to perform important physiological functions by regulating fluid movement in the intercellular space. However, neither their function during organ development nor the molecular mechanisms underlying multiciliogenesis are yet well understood. We aim to study the function of miR-34b in multiciliogenesis.
We used microarrays to study the global gene expression change in multiciliated cells after miR-34b knockdown.

overall_design: Multiciliated cells were isolated from 3 dpf control embryos (injected with control morpholino) and miR-34b morphants (injected with miR-34b morpholino) for RNA extraction and hybridization on Affymetrix microarrays. Two independent sets of biological replicates were used.

first: Yong

last: Zhou


title: Network Understanding of SNAIL inhibitor induced perturbations in EMT models

status: Public on May 31 2013

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

summary:
Two engineered HMLE cell lines representing various degrees of EMT were treated with a drug in development to target and inhibit SNAIL interaction with PTP53, called GN-25
total RNA was isolated and analyzed in an Agilent two-color experiment. Four biological replicates of each condition were directly compared, GN25 treated compared to untreated reference

overall_design: The impact of GN-25 on gene expression was investigated using two engineered HMLE cell lines: one stably overexpressing Kras another stably overexpressing Kras and SNAIL

first: Asfar

last: Azmi


title: MiR-376c down-regulation accelerates EGF-dependent migration by targeting GRB2 in the HuCCT1 human intrahepatic cholangiocarcinoma cell line

status: Public on May 23 2013

city: Bunkyo-ku

last: Iwaki

address: 1-1-5 Sendagi

institute: Nippon Medical School

summary: The biological significance of the down-regulation of miR-376c in HuCCT1 cells is unknown. We revealed that miR-376c significantly reduced EGF-dependent cell migration through its target GRB2 in HuCCT1 cells. To elucidate key molecules in EGF-dependent HuCCT1 migration, in which GRB2 upregulation is caused by abnormal suppression of miR-376c, we compared expression profiles of mRNAs affected by pre-miR-376c and siRNA targeting GRB2.

overall_design: We compared expression profiles of mRNAs affected by pre-miR-376c and siRNA targeting GRB2 in EGF-treated HuCCT1 cells.

first: Toshihiro

last: Takizawa


title: Characterization of gene expression profiles at low and very low doses of ionizing radiation

status: Public on Jun 24 2013

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

summary: The aim of the present study is to analyze by microarray techniques how gene expression is modulated after exposure to low and very low doses of ionizing radiation, to evaluate if the pattern of gene expression shows dose dependence, and to search for putative regulatory mechanisms behind the observed gene-expression modifications.For this, whole blood samples from five healthy donors diluted in IMDM (1:10) were exposed at six doses between 5 and 500 mGy. Total RNA extraction from CD4+ lymphocytes was done at four different post-irradiation times (150, 300, 450 and 600 min). After mRNA amplification, aRNAs were hybridized on 4x44k DNA microarrays. The results indicated that up-regulation were twice than down-regulation. Surprisingly, the number of modulated genes doesn’t seem to change drastically with dose, even at the lowest dose of 5 mGy. Clustering analysis revealed seven gene expression clusters with different dose dependence profiles. The functional analysis showed that the genes which increased their expression with the dose were related to p53 pathway and DNA damage response. This could be observed from 25 mGy, but becomes very clear at doses equal or greater than 100 mGy. On the other hand, genes with a constant modulation of their expression in all the tested doses were related to cellular respiration, ATP metabolic process and chromatin organization. These latter molecular mechanisms seem to be triggered at very low doses (5-25 mGy). In-silico promoter analysis seems to confirm the implication of transcription factors related to the pathways mentioned above.

overall_design: Human whole blood samples from 5 healthy donors were diluted in IMDM medium (1:10) and exposed to 500,100,50,25,10 and 5 mGy of Cobalt 60 gamma-rays. Gene expression alterations were measured 150, 300, 450 and 600 min post exposure after negative cell sorting of lymphocytes TCD4+ cells.

first: Ingrid

last: NOSEL

first: Aurélie

last: VAURIJOUX

first: Joan-Francesc

last: BARQUINERO


title: ATM mediates pRB function to control DNMT1 protein stability and DNA methylation

city: Kanazawa

first: Awad

last: Shamma

state: Ishikawa

address: Kakuma-machi

department: Cancer Research Institute

institute: Kanazawa Uiniversity

summary: The retinoblastoma tumor suppressor gene (RB) product has been implicated in epigenetic control of gene expression owing to its ability to physically bind to many of chromatin modifiers. However, the biological and clinical significance of this activity was not well elucidated. To address this, we performed genetic and epigenetic analyses in an Rb-deficient mouse thyroid C cell tumor model.  Here we report that the genetic interaction of Rb and ATM regulates DNMT1 protein stability, and hence controls the DNA methylation status in the promoter of at least Ink4a, Shc2, FoxO6 and Noggin genes. Further, we demonstrate that inactivation of pRB promotes the Tip60 (acetyltransferase)-dependent ATM activation, allows activated ATM to physically bind to DNMT1 forming a complex with Tip60 and UHRF1 (E3 ligase), and consequently accelerates DNMT1 ubiquitination driven by Tip60-dependent acetylation. Our results indicate that inactivation of pRB pathway in coordination with aberration in DNA damage response leads to abnormal DNA methylation pattern by affecting the stability of DNMT1.

overall_design: 163; Rb-/-;ATM-/- MEFs, D4; DNMT1 knockdown from 163 cells and analysed at day 4, WT8S; 163 cells reconstituted with ATM expression vector

first: Takumi

last: Nishiuchi

first: Chiaki

last: Takahashi


title: LGR5 positivity defines stem-like cells in colorectal cancer

status: Public on May 07 2013

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

type: Genome variation profiling by genome tiling array


title: Affect of liver transcriptome by acute acetaminophen exposure [mRNA]

status: Public on May 03 2013

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: To study the global changes of liver transcriptome after acetaminophen overdose.

overall_design: To study the global changes of transcriptome in the liver after acetaminophen overdose.  Eight week old female C57BL/6 mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure; plasma and tissue samples were collected for pathological examination and biochemical analyses.

first: Kai

last: Yuan

first: Hong

last: Li

first: David

last: Huang

first: Li

last: Gray

first: Shizhen

last: Qin

last: Galas


title: Control vs Diabetic mice skeletal muscle miRNA microarray

status: Public on Apr 22 2013

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

summary: To extract the differentially expressed miRNA between control vs diabetic mice skeletal muscle.

overall_design: We used obese diabetic (C57BL/KsJ db/db) and normal control (C57BL/KsJ db+) mice, which were obtained from the Animal House Facility of the Central Drug Research Institute (CSIR), Lucknow, India.

first: Priyanka

last: Agarwal


title: Identification of genes regulated by glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitor using microarray experiment

status: Public on Jun 14 2013

city: Cambridge

first: Lingbo

last: Zhang

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research and MIT Department of Biology

summary: Early erythroid progenitors were isolated from mouse E14.5 fetal liver, infected with viruses encoding either control shRNA or shRNAs targeting the RNA binding protein (RBP), and cultured in a medium containing stem cell factor, erythropoietin, and insulin-like growth factor 1, in the absence or presence of dexamethasone (DEX). After 3 days of culture, microarray experiments were carried out to profile the gene expression pattern of these cells.

overall_design: Examination of mRNA expression profiles in day3 cultured cells


title: Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver [array]

status: Public on May 01 2013

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Metabolic homeostasis in mammals critically depends on the regulation of fasting-induced genes by CREB in the liver. Previous genome-wide analysis has shown that only a small percentage of CREB target genes are induced in response to fasting-associated signaling pathways. The precise molecular mechanisms by which CREB specifically targets these genes in response to alternating hormonal cues remain to be elucidated. We performed chromatin immunoprecipitation coupled to high-throughput sequencing of CREB in livers from both fasted and re-fed mice. In order to quantitatively compare the extent of CREB-DNA interactions genome-wide between these two physiological conditions we developed a novel, robust analysis method, termed the ‘single sample independence’ (SSI) test that greatly reduced the number of false positive peaks. We found that CREB remains constitutively bound to its target genes in the liver regardless of the metabolic state.  Integration of the CREB cistrome with expression microarrays of fasted and re-fed mouse livers and ChIP-seq data for additional transcription factors revealed that the gene expression switches between the fasted and fed states are associated with co-localization of additional transcription factors at CREB sites. Our results support a model in which CREB is constitutively bound to thousands of potential target genes and combinatorial interactions between DNA-binding factors are necessary to achieve the specific transcriptional response of the liver to fasting. Furthermore, our genome-wide analysis identifies thousands of novel CREB target genes in liver, including a previously unknown role for CREB in regulating ER stress genes in response to nutrient influx.

overall_design: Individual livers were collected from 24hr fasted and re-fed mice, with 4 biological replicates per condition. Extracted RNA was hybridized to Agilent two-color arrays, using randomly paired fasted/re-fed replicates.

first: John

last: Le Lay

first: Sabina

last: Lukovac

first: Diana

last: Bernstein

last: Steger

first: Mitchell

last: Lazar

first: Klaus

middle: H

last: Kaestner


title: Affect of liver transcriptome by acute acetaminophen exposure

last: Cho

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


title: Mouse Hepa1c1c7 cells: TCDD vs. TCDD plus blebbistatin

status: Public on Apr 16 2013

city: Hirosaki

first: Hideaki

last: Kikuchi

address: 3 Bunkyo-cho

department: Faculty of Agriculture and Life Science

institute: Hirossaki University

summary: Transcriptional profiling of mouse Hepa1c1c7 cells comparing control TCDD-treated cells with Hepa1c1c7 cells treated with TCDD plus blebbistatin. The latter causes dysfunction of MYH9. Goal was to determine the effects of blebbistatin on global Hepa1c1c7 gene expression.

overall_design: Two-condition experiment, TCDD treated Hepa1c1c7 vs. TCDD plus blebbistatin. Biological replicates: 1 TCDD sample, 1 TCDD plus blebbistatin sample.


title: Comparison of extravillous trophoblast cells derived from human embryonic stem cells and from first trimester human placentas

status: Public on May 02 2013

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary: The goal of the present study was to  characterize HLA-G-positive cells derived from human embryonic stem cells treated with BMP4 for five days and compare them to HLA-G positive cells derived from human first trimester placentas

overall_design: Human embryonic stem cells were cultured with BMP4 in the absence of FGF2 for 5 days. They were then dispersed and separated into HLA-G+ and HLA-G-, TACSTD2 positive cells by using immunomagnetic bead separation.  First trimester human placental samples from 8-12 weeks gestation were enzymatically separated into single cells, and then also separated into HLA-G+ and HLA-G-/TACSTD2+ cell populations

first: R

last: Roberts

middle: C


title: Direct proteomic quantification of the secretome of activated immune cells

status: Public on Apr 11 2013

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Protein secretion can mediate communication of distant cells in a multicellular organism and can control a broad range of physiological functions. Regulation of this process is crucial, especially for cells of the immune system that sense pathogens through specific receptors and release proteins that initiate and orchestrate the immune response. This secretome is today analyzed using antibody-based assays, but mass spectrometry could provide an unbiased and comprehensive alternative. Here we developed a quantitative, high resolution mass spectrometric workflow to detect and quantify proteins that are released from macrophages upon Toll-like receptor 4 (TLR4) activation by the microbial component lipopolysaccharide (LPS)5. We quantified the time-resolved release of 775 proteins, including 52 annotated cytokines, from only 150.000 primary cells per condition. The dynamic range of the secretory induction was at least 10,000 fold and we achieved sensitivity in the low picogram range. Comparison to the transcriptome revealed high correlation for some protein classes but also anti-correlation resulting from the transcriptionally decoupled release of lysosomal proteins. Using gene knockout (KO) mouse strains as genetic models with intracellular signaling adaptor deficiencies, we defined distinct secretory profiles depending on which arms of the signaling pathways are missing. We show that MyD88 dominates over TRIF in the number and fold-induction of secreted proteins6,7. Interestingly, the sum of the two signaling arms does not equal the wild-type response; instead, protein secretion is tuned by synergistic and predominantly redundant mechanisms. The kinetic data reveals that the release of anti-inflammatory proteins dampens the initial pro-inflammatory response. Our study provides a paradigm for the sensitive and time-resolved identification of receptor activation induced cellular secretomes, including proteins with unexpected extracellular presence, and allows the characterization of the underlying signal transduction pathways.

overall_design: Microarray experiments were performed as dual-color hybridizations.

first: Felix

last: Meissner

first: Richard

last: Scheltema

first: Matthias

last: Mann


title: Left-right transcriptomic differences in adult male mouse heart ventricles

status: Public on Mar 21 2013

first: Dumitru

last: Iacobas

summary: Left and right heart ventricles of adult male mice were profiled to determine the differences in gene expression, control, coordination and signaling fabrics

overall_design: Two-sides (L= left, R = right) gene expression profiling experiment in adult mouse male (M) ventricles (V). 4 biological replicates: MVL1-4, MVR1-4.

first: Sanda


title: Expression data from early Zebrafish embryos after knockdown of mir-34

status: Public on Apr 03 2013

city: NEW DELHI

first: Kartik

last: Soni

address: Mathura Road

department: FGU

institute: INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY

summary:
microRNAs play crucial roles in the early development of an organism.  However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied.
We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization.

overall_design: Zebrafish embryos were selected at specific stages of early embryonic development (1, 7, and 24 hours post fertilization). RNA was extracted and hybridized to Affymetrix microarrays. The embryos were injected with anti-microRNA LNA and were kept for constant monitoring for the indicated time points. A mockLNA was injected as a control. The embryos were visualized for any visible developmental abnormalities.

first: Beena

last: Pillai


title: Comparing gene expression of human cardiac stem cells between automatic cell culture and manual handling culture

status: Public on Mar 31 2013

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary:
BACKGROUND: Cell-based regeneration therapies hold great promise and potential for new area in clinical medicine, although some obstacles still remain to be overcome for a wide range of clinical applications. One of the major impediments in this field is difficulties in large-scale production of cells of interest with reproducibility. Current protocol of cell therapy requires a long-time laborious manual process. To solve this problem, we focused on the robotics of automated and high throughput cell culture system. To date, an automated robotic cultivation of stem or progenitor cells in clinical trials has not been reported.

METHODS: The system, AutoCulture®, used in this study can automatically replace the medium, centrifuge cells, split the cells, and take a photograph for their morphology. We examined the feasibility to use it in the clinical field by comparing the growth rate and the characteristics of cardiac stem cells (CSCs) cultivated by AutoCulture and the manual handling culture, which protocol is the exact same as current performing clinical trial in our institute.

RESULTS: We demonstrated similar characteristics in both culture methods, in terms of growth rates, gene expression profiles, cell surface profiles by FACS, carbon hydrate structures on the cell surface, and genomic DNA stability.

IMPLICATIONS: The results of this study showed that AutoCulture is feasible to cultivate human cells for regenerative medicine. An automated cell-processing machine for cell therapy will play more important role, as it will be widespread from multi-center trials to off-the-shelf cell products.

overall_design: The cells were cultured by manual handling or by the automatic cell culture apparatus. Total RNA was extracted from these cells at day 7 by the RNeasy Plus Mini Kit (QIAGEN). Gene expression analysis was performed using the Agilent Whole Human Genome Microarray chips G4112F (Agilent). Raw data were normalized and analyzed by GeneSpring GX11 software.

first: Daisuke

last: Kami

first: Masashi

last: Toyoda

first: Kahori

last: Minami

first: Hidenori

last: Akutsu

first: Tomoya

last: Kitani

first: Yoko

last: Itakura

first: Satoshi

last: Gojo


title: Expression data from Disulfiram or 5-FU treated EpCAM-negative non-tumor-initiating hepatocellular carcinoma (HCC) cells.

status: Public on Mar 16 2013

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

institute: Graduate School of Medicine, Chiba University

summary: Cancer stem cells (CSCs) or tumor-initiating cells (TICs) organize a cellular hierarchy in a similar fashion to normal stem cell systems and exhibit high tumorigenic activity in xenograft transplantation assay. Disulfiram (DSF) could preferentially eradicate TICs, but the molecular machinery of its effect against TICs still remains largely unknown. We found that DSF but not 5-FU erradicates tumor-initiating HCC cells. To compare the gene expression profiles in EpCAM-positive cells and EpCAM-negative cells, we conducted microarray analyses of EpCAM-negative HCC cells treated with DSF or 5-FU.

overall_design: Purified EpCAM-negative HCC cells treated with Disulfiram or 5-FU were subjected to RNA extraction and hybridization on Agilent microarrays.

first: Atsushi

last: Iwama

first: Osamu

last: Yokosuka


title: Left-right transcriptomic differences in adult male mouse heart atria

status: Public on Mar 20 2013

city: Prairie View

address: Ann Preston St

institute: Prairie View A&M University

summary: Left and right heart atria of adult male mice were profiled to determine the differences in gene expression, control, coordination and signaling fabrics

overall_design:
Two-sides (L= left, R = right) gene expression profiling experiment in adult mouse male (M) atria (A). 4 biological replicates: MAL1-4, MAR1-4.
This experiment used our standard multiple yellow strategy in which Cy3 and Cy5 labeled biological replicates are cohybridized with a two-color array and each channel is processed independently.


title: Expression profiles of zebrafish transgenic line Tg(fabp10a:def)-I

status: Public on Feb 28 2013

city: Hangzhou

first: Jinrong

last: Peng

address: 866 Yuhangtang Road

institute: Zhejiang University

summary:
We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a.
We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line.

overall_design: Total RNA from the adult livers of three independent batches of 3-month-old Tg(fabp10a:def)-I and wild type (AB strain) male fish was extracted using TRIzol (Invitrogen), each batch with the liver samples from three fish mixed together. The samples were subjected to microarray hybridization and the data were generated for further analysis.

first: Ting

last: Tao

first: Hui

last: Shi


title: Glucose Metabolism impacts the spatio-temporal onset and magnitude of HSC induction in vivo

status: Public on Feb 15 2013

city: Boston

first: Trista

last: North

address: 3 Blackfan Circle

institute: BIDMC

summary: Many pathways regulating blood formation have been elucidated, yet how each coordinates with embryonic biophysiology to modulate the spatio-temporal production of hematopoietic stem cells (HSCs) is currently unresolved. Here, we report that glucose metabolism impacts the onset and magnitude of HSC induction in vivo. In zebrafish, transient elevations in physiological glucose levels elicited dose-dependent effects on HSC development, including enhanced runx1 expression and hematopoietic cluster formation in the Aorta-Gonad-Mesonephros (AGM) region; embryonic-to-adult transplantation studies confirmed glucose increased functional HSCs. Glucose uptake was required to mediate the enhancement in HSC development; likewise, metabolic inhibitors diminished nascent HSC production and reversed glucose-mediated effects on HSCs. Increased glucose metabolism preferentially impacted hematopoietic and vascular targets, as determined by gene expression analysis, through mitochondrial-derived reactive oxygen species (ROS)-mediated stimulation of hypoxia inducible factor 1α (hif1α); epistasis assays demonstrated hif1α regulates HSC formation in vivo and mediates the dose-dependent effects of glucose metabolism on the timing and magnitude of HSC production. We propose this fundamental metabolic-sensing mechanism enables the embryo to respond to changes in environmental energy input and adjust hematopoietic output to maintain embryonic growth and ensure viability.

overall_design: We performed microarray analysis to explore the changes in gene expression that occur in repsonse to altered metabolism during the induction of developmental hematopoeisis. We compared RNA from zebrafish raised in a solution of 1% glucose from 12-36hpf vs controls. Two biological replicates for each condition were performed.

first: J

last: Harris

first: V

last: Esain

first: G

last: Freschette

first: L

first: A

middle: G

last: Cox

first: M

last: Cortes

last: Garnaas

first: K

last: Carroll

first: C

last: Cutting

first: Y

last: Khan

first: P

last: Elks

first: S

last: Renshaw

first: B

last: Dickinson

last: Chang

last: Murphy

last: Paw

last: Vander Heiden

first: W

last: Goessling

first: T

middle: E


title: Gene expression profiles of MAIT cells, MAIT-iPSCs, hiPSCs, hESCs, and reMAIT cells

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

institute: ASUBIO PHARMA CO., LTD.

summary: To show the similarity among MAIT-iPSCs, hiPSCs and hESCs and the gradual change of global gene expression of reMAIT cells along with differentiation, this experiment was designed.

overall_design: MAIT cells, MAIT-iPSCs, hiPSCs, hESCs, MAIT cells, and reMAIT cells at the several differerent stages of differentiation were collected. Then, they were applied in this experiment.


title: Transcriptional responses of the zebrafish (Danio rerio) brain to acute sodium selenite supplementation.

status: Public on Feb 26 2013

city: Moscow

first: Maia

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

summary:
The possible benefits of selenium (Se) supplementation are currently under investigation for prevention of certain cancers and treatment of neurological disorders. Little is known concerning the response of the brain to increased dietary Se under conditions of Se sufficiency, despite the majority of Se supplementation trials occurring in healthy subjects considered Se sufficient. We evaluated the transcriptional response of the zebrafish (Danio rerio) brain to supplementation with nutritionally relevant levels of dietary Se (sodium selenite) during conditions of assumed Se sufficiency.
We used a microarray approach to analyze the global gene expression response of the brain to dietary Se supplementation for 14 days.

overall_design: The experiment used Affymetrix microarrays to compare whole brain RNA from 8 adult zebrafish (Danio rerio) fed a diet with control selenium levels (1.4ppmSe) and 8 fed a diet supplemented with sodium selenite (5.6ppmSe) for 14 days, and with an equal sex ratio within each diet.

first: Barrie

middle: D

last: Robison

first: Matt

last: Settles

first: Gordon

last: Murdoch

first: Ron

middle: W

last: Hardy


title: Influence of the two different cryopreservation methods to inflammation of dental pulp cells

status: Public on Mar 27 2013

city: Seoul

first: Sang Hyuk

last: Park

address: Dongdaemungu, Hoegidong 1

country: South Korea

institute: Kyung Hee University

summary: Dental pulp cells of cryopreserved teeth (slow and rapid speed) were examined with microarray for screening which gene is involve in the inflammation process during the cryopreservation process.

overall_design: Intact caries-free, freshly extracted premolars (n=6) were collected from 3 patients for microarray assay analysis. They were classified as control and cryopreserved groups. Cryopreserved groups were divided into rapid freezing and slow freezing group.

first: Sang

first: Su

middle: J

last: Ahn


title: Hypoxia induces myocardial regeneration in zebrafish

status: Public on Jan 15 2013

city: Montpellier

first: Chris

last: Jopling

address: 141 rue de la Cardonille

department: Physiologie

institute: Institut de Génomique Fonctionnelle

summary: Conditional expression of dominant-negative HIF1a in zebrafish cardiomyocytes severely inhibits heart regeneration. To understand more about the mechanism, we performed microarray analysis of wildtype regenerating zebrafish and dnHIF1a regenerating zebrafish to determine which genes are regulated by hypoxia/HIF1a.

overall_design: We amputated both wildtype and dnHIF1a zebrafish and allowed them to regenerate for 7 days, then compared their transcriptomic profile with unamputated wildtype and dnHIF1a zebrafish, respectively.

first: Juan

last: Ispizua Belmonte


title: Polyphenols protection against fructose overload

status: Public on Feb 04 2013

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: To decipher the beneficial effects of Polyphenols on health, healthy volunteers were randomized into two groups and were submitted to either a red grape polyphenol rich extract supplemented diet (PP) or a placebo diet (PCB) during 8 weeks. Then they were submitted to a fructose load (3g/kg Fat Free Mass/day) during 7 days. Muscle biopsies were taken before the protocol, 8 weeks after PP or PCB diet and after the 7 days fructose load. We have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by fructose and to identify the mechanism of action of Polyphenols.

overall_design: Healthy volunteers were randomized into two groups and were submitted to either a red grape polyphenol rich extract supplemented diet (PP) or a placebo diet (PCB) during 8 weeks. Then they were submitted to a fructose load (3g/kg Fat Free Mass/day) during 7 days. Muscle biopsies were taken before the protocol, 8 weeks after PP or PCB diet and after the 7 days fructose load. We have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by fructose and to identify the mechanism of action of Polyphenols. Ten biological replicates were processed for PP diet, nine for PCB diet.

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

first: Hubert

last: Vidal

first: Emilie

last: Blond

first: Antoine

last: Avignon


title: Estrogen signaling and the Metabolic Syndrome: Targeting the hepatic ERalpha action

status: Public on Dec 01 2012

city: Huddinge

first: Marko

last: Matic

address: Halsovägen 7

country: Sweden

institute: Karolinska Institutet

summary: We have previously shown that total estrogen receptor alpha (ERalpha knockout (KO) mice exhibit hepatic insulin resistance. To investigate the contribution of hepatic ERalpha action for the observed phenotype, we established a liver-selective ERalphaKO mouse model, LERKO. We demonstrate that LERKO mice have efficient reduction of ERalpha selectively within the liver. However, LERKO and wild type control mice do not differ in body weight, and have a comparable hormone profile as well as insulin and glucose response, even when challenged with a high fat diet. Furthermore, LERKO mice display very minor changes in their hepatic transcript profile. Collectively, our findings indicate that hepatic ERalpha action may not be the initiating factor for the previously identified hepatic insulin resistance in ERalphaKO mice.

overall_design: We have previously shown that total estrogen receptor alpha (ERalpha knockout (KO) mice exhibit hepatic insulin resistance. To investigate the contribution of hepatic ERalpha action for the observed phenotype, we established a liver-selective ERalphaKO mouse model, LERKO. Using microarray analysis, we compared the hepatic transcriptional profile of LERKO vs control mice.

first: Hui

last: Gao


title: Zebrafish early eye development

status: Public on Dec 31 2012

city: Dublin

first: Breandan

last: Kennedy

address: Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute, University College Dublin

summary: Gene expression profiling of zebrafish early eye development on 3 to 5 days post fertilization (dpf)

overall_design: Gene expression on 3 to 5 dpf eyes were compared. Each sample contains three replicates.

first: Jun

last: Yin

first: Antonino

last: Glaviano


city: Kumamoto

first: Satomi

middle: S

last: Tanaka

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: To explore the loss of  Dullurd function in mouse embryo development, we have performed the Agilent microarray analysis between a Dullard-heterozygous and a Dullard-homozygous E7.5 embryo. Our findings show that Dullard does not act in concert with BMP4 and Smad1/5/8, whereas loss of Dullard is associated with a reduced level of WNT/β-catenin signaling activity, accompanied by elevated expression of Wnt3 and WNT antagonists including Dkk1, Sfrp1 and Sfrp5 in mouse germ cell formation.

overall_design: E7.5 mouse embryos were collected. One Dullard-heterozygous embryo and one Dullard-homozygous embryo were used for the analysis.


title: Effect of synbindin on the gene expression profile of gastric cancer cells

status: Public on Dec 05 2012

city: Shanghai

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

institute: Shanghai Institute for Digestive Diseases

summary: In order to determine the effect of synbindin on the gene expression profile of gastric cancer cells, MGC-803 cells were infected with adenoviruses carrying either synbindin or GFP. The differentially expressed genes caused by synbindin ectopic expression suggests the underlying mechanism for synbindin-induced cell proliferation.

overall_design: Total RNA from each sample was amplified and transcribed into fluorescent cRNA using Agilent's Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After washing, the arrays were scanned by the Agilent Scanner G2505C. 3 replicates per treatment (GFP adenovirus, synbindin adenovirus).

first: Xuan

last: Kong

first: Jing

middle: Y

last: Fang


title: Expression profile of colon crypts from WT and GMCSF-/- mice with or without DSS treatment

status: Public on Nov 21 2012

city: La Jolla

first: Laia

last: Egea

address: 9500 Gilman Dr

department: Medicine

institute: UCSD

summary: To discover possible molecular mechanisms mediated by GM-CSF that may be involved in regeneration of the colon epithelium after DSS-induced injury we performed whole-genome wide mRNA microchip analysis of isolated crypt epithelial cells from unchallenged and DSS-challenged WT and GM-CSF-/- mice.

overall_design: Total RNA was prepared from isolated crypts obtained from colons of GM-CSF deficient mice and WT littermates treated or untreated with 1.5%DSS for 6 days. Three biological replicates were performed for each experimental condition.

first: Christopher

last: McAllister

first: Omar

last: Lakhdari

first: Ivelina

last: Minev

first: Steve

last: Shenouda

first: Martin

middle: F

last: Kagnoff


title: Gene expression data from time course of fin regeneration in Danio rerio (part 2)

status: Public on Nov 01 2012

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: Olsen et al (2010) have shown that induced Diabetes mellitus (DM) in adult Zebrafish results in an impairment of tissue regeneration as monitored by caudal fin regeneration. In those studies, streptozocin was used to induce hyperglycemia in adult zebrafish, and then, following streptozocin withdrawal, a recovery phase was allowed to re-establish euglycemia, due to pancreatic b-cell regeneration. DM-associated impaired fin regeneration continued indefinitely in the metabolic memory state (MM);  allowing for subsequent molecular analysis of the underlying mechanisms of MM. This study focuses on elucidating the molecular basis explaining DM-associated impaired fin regeneration and why it persists into the MM state. The analysis of microarray data indicated that of the 14,900 transcripts analyzed, aberrant expression of 71 genes relating to tissue developmental and regeneration processes were identified in DM fish and the aberrant expression of these 71 genes persisted into the MM state.  Key regulatory genes of major signal transduction pathways were identified among this group of 71; and therefore, these findings provide a possible explanation for how hyperglycemia induces impaired fin regeneration and why it continues into the MM state.

overall_design: Total RNA was extracted from caudal fin at 0, 12, 24 and 48 hours post amputation from STZ treated (DM) and untreated controls.

first: Michael

middle: P

last: Sarras

first: Ansgar

last: Olsen

first: Gina

last: Pisano

first: Robert

middle: V

last: Intine


title: Gene expression data from time course of fin regeneration in Danio rerio

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

overall_design: Refer to individual Series


title: Expression profile of zebrafish embryonal rhabdomyosarcoma

city: Charlestown

first: David

middle: M

last: Langenau

state: MA

department: Molecular Pathology

institute: Massachusetts General Hospital

summary:
Fluorescent-labeled zebrafish RAS-induced embryonal rhabdomyosarcoma (ERMS) were created to facilitate in vivo imaging of tumor-propagating cells, regional tumor heterogeneity, and dynamic cell movements in diverse cellular compartments.  Using this strategy, we have identified a molecularly distinct ERMS cell subpopulation that expresses high levels of myf5 and is enriched for ERMS-propagating potential when compared with other tumor-derived cells.
Embryonal rhabdomyosarcoma (ERMS) is an aggressive pediatric sarcoma of muscle. Here, we show that tumor-propagating potential is confined to myf5+ERMS cells and can be visualized in live, fluorescent transgenic zebrafish. During early tumor growth, myf5+ERMS cells reside within an expanded satellite cell compartment, but by late stage ERMS, myf5+cells are dynamically reorganized into distinct regions separated from differentiated tumor cells. Human ERMS also contain distinct areas of differentiated and undifferentiated cells. Time-lapse imaging revealed that myf5+ERMS cells populate newly formed tumor only after seeding by highly migratory myogenin+ ERMS cells. This finding helps explain the clinical observation that Myogenin positivity correlates with poor clinical outcome in human ERMS and suggests that differentiated tumor cells play critical roles in metastasis.

overall_design: One-cell stage myf5-GFP/mylz2-mCherry fluorescent transgenic zebrafish were injected with rag2-kRAS12D.  A subset of animals developed ERMS.  Tumor cells were transplanted into syngeneic recipient animals that lacked fluorescent reporter expression. ERMS cell subfractions were isolated from transplant animals and purified cell populations obtained following two rounds of FACS.  Sorted cells were 1) analyzed by microarray/RT-PCR and 2) transplanted at limiting dilution into syngeneic animals.  These experiments confirm that zebrafish ERMS contain molecularly distinct cell subfractions that express high levels of myf5-GFP and exhibit difference in gene expression when compared to other ERMS cell subtypes.  All four fluorescent-labeled cell populations were analyzed (n=2 tumors total).

first: Myron

last: Ignatius


title: microRNA expression during ovine adult mammary gland development

status: Public on Jan 04 2013

city: JOUY-EN-JOSAS

first: Laurent

last: GALIO

address: Domaine de Vilvert

institute: INRA

summary: The mammary gland undergoes extensive remodeling between the begin- ning of pregnancy and lactation; this involves cellular processes including cell proliferation, differentiation, and apoptosis, all of which are under the control of numerous regulators. To unravel the role played by miRNA, we describe here 47 new ovine miRNA cloned from mammary gland in early pregnancy displaying strong similari- ties with those already identified in the cow, human, or mouse. A microarray study of miRNA variations in the adult ovine mammary gland during pregnancy and lactation showed that 100 miRNA are regulated according to three principal patterns of expression: a de- crease in early pregnancy, a peak at midpregnancy, or an increase throughout late pregnancy and lactation. One miRNA displaying each pattern (miR-21, miR-205, and miR-200b) was analyzed by qRT- PCR. Variations in expression were confirmed for all three miRNA. Using in situ hybridization, we detected both miR-21 and miR-200 in luminal mammary epithelial cells when expressed, whereas miR-205 was expressed in basal cells during the first half of pregnancy and then in luminal cells during the second half. We therefore conclude that miR-21 is strongly expressed in the luminal cells of the normal mammary gland during early pregnancy when extensive cell prolif- eration occurs. In addition, we show that miR-205 and miR-200 are coexpressed in luminal cells, but only during the second half of pregnancy. These two miRNA may cooperate to maintain epithelial status by repressing an EMT-like program, to achieve and preserve the secretory phenotype of mammary epithelial cells.

sample_organism:
Ovis aries
Mus musculus

overall_design: 5 samples for sheep and 5 samples for mouse

last: Galio

first: Stéphanie

last: Droineau

first: Hania

last: Boudiaf

first: Sandrine

last: Truchet

first: Eve

last: Devinoy


title: Danio rerio larvae exposed to SSRIs Fluoxetine and Sertraline

status: Public on Sep 06 2012

city: Knoxville

first: Julia

last: Gouffon

state: TN

address: 1215 West Cumberland Ave, RM 229

department: Nutrition

institute: Univ. of TN

summary: Pharmaceutical chemicals used in human medicine are released into surface waters via municipal effluents and pose a risk for aquatic organisms.  Among these substances are selective serotonin reuptake inhibitors (SSRIs) which can affect aquatic organisms at sub ppb concentrations.  To better understand biochemical pathways influenced by SSRIs, evaluate changes in the transcriptome, and identify gene transcripts with potential for biomarkers of exposure to SSRIs; larval zebrafish Danio rerio were exposed (96 h) to two concentrations (25 and 250 µg/L) of the SSRIs, fluoxetine and sertraline, and changes in global gene expression were evaluated (Affymetrix GeneChip® Zebrafish Array).  Significant changes in gene expression (>=1.7 fold change, p<0.05) were determined with Partek® Genomics Suite Gene Expression Data Analysis System and ontology analysis was conducted using Molecular Annotation System 3.  The number of genes differentially expressed after fluoxetine exposure was 288 at 25 µg/L and 131 at 250 µg/L; and after sertraline exposure was 33 at 25 µg/L and 52 at 250 µg/L.  Five genes were differentially regulated in all treatments relative to control, suggesting that both SSRIs share some similar molecular pathways.  Among them, expression of the gene coding for FK506 binding protein 5 (FKBP5), which is annotated to stress response regulation, was highly down-regulated in all treatments (results confirmed by qRT-PCR).  Gene ontology analysis indicated that regulation of stress response and cholinesterase activity were critical functions influenced by these SSRIs, and suggested that changes in the transcription of FKBP5 or acetylcholinesterase could be useful biomarkers of SSRIs exposure in wild fish.

overall_design:
Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained at the Center for Environmental Biotechnology at the University of Tennessee.  Fish husbandry, spawning, and experimental procedures were conducted with approval from the UT Insititutional Animal Care and Use Committee (Protocol #1690-1007).  Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl. Embroyos were obtained by spawning adult fish with no history of contaminant exposure.  Fertilization of embryos took place at the same time (<15 minutes), such that larvae used in experiments were of similar age at the time of exposure.  All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27 +/- 1 C and 14:10h light:dark photoperiod.
Larval zebrafish (72 hpf) were exposed for 96 h in 200ml fish water containing appropirate amount of SSRI stock (i.e. fluoxetine or sertraline).  There were four SSRIs treatments (25 and 250 ug/L fluoxetine and 25 and 250 ug/L sertraline) and one control (no SSRIs) with triplicate beakers and each beaker contained about 100 larval fish.  During exposure for 96 hours, beakers were kept covered to prevent water evaporation and fish were not fed (i.e., fish consumed their yolk sac).

first: June

last: Park

first: Tze

last: Heah

first: Theodore

last: Henry

first: Gary

last: Sayler


title: Gene expression data from time course of fin regeneration in Danio rerio (part 1)

first: Alexey

last: Leontovich

overall_design: Total RNA was extracted from caudal fin at 0, 12, 24 and 48 hours post amputation from untreated controls and metabolic memory zebrafish.

last: Sarras

middle: A