title: affy_med_2011_14-Transcriptomic analysis of roots of WT (A17) Medicago truncatula plants and of a hypermycorrhizal mutant (B9) grown on limiting (P/10) or non-limiting phosphate (P2).

status: Public on Jul 01 2013

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_med_2011_14 - affy_med_2011_14 - -In natural ecosystems most terrestrial plants form arbuscular mycorrhiza (AM), mutualistic symbioses with soil fungi belonging to the order Glomeromycota. This symbiosis takes place when phosphate is limiting and enables the plant to acquire nutrients (in particular phosphate) in exchange of carbon provided to the fungus A hypermycorrhizal mutant B9 was identified (Morandi et al. Mycorrhiza (2009) 19: 435) which displayed higher root colonization by Glomus intraradices. This phenotype could be linked to a defect in phosphate sensing or transport. We have undertaken the analysis of the root transcriptome of both WT and mutant plants grown on limiting or non-limiting phosphate to determine which processes are affected in the hypermycorrhizal mutant.-- Roots were harvested from 4 week-old WT and B9 mutant plants grown in a culture chamber with limiting (P/10, 130 µM phosphate) or non limiting (P2, 2.6 mM phosphate) phosphate under long days (16 hrs day at 22°C with 380 µE.m-2.s-1 light and 8hrs night at 19°C). RNAs were then extracted for transcriptomic analysis. We will compare WT (or mutant) root transcriptome on P/10 versus WT (or mutant) root transcriptome on P2 as well as mutant versus WT transcriptome on either P/10 or P2.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 12 arrays - Medicago; dose response,gene knock out

first: Hoai-Nam

last: Truong

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and mutants in regulator proteins grown in minimal media

status: Public on Aug 03 2013

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

country: USA

institute: Lawrence Berkeley National Laboratory

summary:
Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase.
We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants.

overall_design: 8 samples were collected: 7 regulator mutants and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.

first: Morgan

last: Price

first: Adam

middle: M

last: Deutschbauer

middle: P

last: Arkin

first: Pavel

last: Novichkov

first: Dmitry

last: Rodionov


title: Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20

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

overall_design: Refer to individual Series


title: Transcriptional co-factor TBLR1 controls lipid mobilization in white adipose tissue

status: Public on Apr 01 2013

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Lipid mobilization (lipolysis) in white adipose tissue (WAT) critically controls lipid turnover and adiposity in humans. While the acute regulation of lipolysis has been studied in detail, the transcriptional determinants of WAT lipolytic activity remain still largely unexplored.  Here we show that the genetic inactivation of transcriptional co-factor transducin beta-like-related (TBLR) 1 blunts the lipolytic response of white adipocytes through the impairment of cAMP-dependent signal transduction. Indeed, mice lacking TBLR1 in adipocytes are defective in fasting-induced lipid mobilization and when placed on a high fat diet show aggravated adiposity, glucose intolerance and insulin resistance. TBLR1 levels are found to increase under lipolytic conditions in WAT of both human patients and mice, correlating with serum free fatty acids (FFA). As a critical regulator of WAT cAMP signaling and lipid mobilization, proper activity of TBLR1 in adipocytes may thus represent a critical molecular checkpoint for the prevention of metabolic dysfunction in subjects with obesity-related disorders.
We used microarrays to identify global gene expression in 3T3-L1 adipocytes lacking TBLR1 and compared gene expression to control shRNA treated cells in both basal and isoproterenol stimulated states.

overall_design: We analyzed 12 RNA samples extracted from 3T3-L1 adipocytes that were treated with either control or TBLR1 specific shRNAs and with or without 10 µM isoproterenol for 3 hrs. Three replicates of each condition.

first: Maria

last: Rohm

first: Anke

last: Sommerfeld

first: Daniela

last: Strzoda

first: Allan

last: Jones

first: Tjeerd

last: Sijmonsma

first: Gottfried

last: Rudofsky

first: Christian

last: Wolfrum

first: Norbert

last: Gretz

first: Maximilian

last: Zeyda

first: Lukas

last: Leitner

first: Peter

last: Nawroth

first: Thomas

last: Stulnig

first: Mauricio

last: Berriel Diaz

first: Alexandros

last: Vegiopoulos

first: Stephan

last: Herzig


title: Expression data from exosomes

status: Public on Jul 24 2013

city: Boston

first: Aldo

last: Roccaro

state: MA

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

summary: Bone marrow (BM) niches provide an optimal substrate for multiple myeloma (MM) cell lodgement and growth. Nevertheless, little is known about the putative mechanisms by which the BM microenvironment can lead to initiation or progression of oncogenesis in this disease. We have demonstrated  that BM mesenchymal stromal cell-derived exosomes transfer their miRNA and protein content to clonal plasma cells, thus acting as synaptic vesicles responsible for molding the microenvironment surrounding multiple myeloma (MM) cells, leading to MM growth, dissemination and, therefore, disease progression.  We used microarray to detail the changes in microRNA expression in MM-BM mesenchymal stromal cell (MSC)-derived exosomes, compared to normal- and monoclonal gammopathy of undetermined significance- BM-MSC-derived exosomes.

overall_design: Exosomes have been isolated from cell culture supernatant of BM-MSCs (MM=7; MGUS=2; Normal=4), and subsequently evaluated at ultrastructural level by using electron microscopy and immunogolf labeling. RNA was extracted; and miRNA profiling has been assessed by using TaqMan human miRNA profiling. Mean miRNA expression value has been used for miRNA RT-qPCR data normalization, as described (Mestdagh et al., 2009).

first: A

first: I

last: Ghobrial


title: Expression data from growth restricted fetal rat pancreatic islets

status: Public on Jul 10 2013

city: Philadelphia

first: Lane

middle: Johanna

last: Jaeckle Santos

state: PA

address: 421 Curie Blvd, BRB II/III 1341

department: CRRWH

institute: University of Pennsylvania School of Medicine

summary:
Intrauterine growth restriction is a common complication of pregnancy. We induce IUGR in rats by bilateral uterine artery ligation at e18 of a 23 day gestation.
This mimics placental insufficiency. This array experiment compares gene expression changes in isolated pancreatic islets from e19, 24 hours post-surgery , or sham operated animals.

overall_design: RNA from isolated pancreatic islets from e19 fetuses, pooled from an entire litter. There are 4 control (sham) operated litters and 4 IUGR litters.

middle: J

first: Rebecca

middle: A

last: Simmons


title: Expression change in materal and fetal part of Cxcl14-/- placenta

status: Public on Jun 19 2013

city: Beijing

first: Qichen

last: Cao

state: Select one

address: Datun Road, Chaoyang District

department: Qichen Cao

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the maternal part and fetal part of Cxcl14-/- and Cxcl14+/+ placentas were dissect out to extract total RNA respectively (n = 3). Total RNA was extracted using PureYield™ RNA Midiprep System (Promega).The maternal part of placenta that contained mesometrial lymphoid aggregate of pregnancy (MLAp) and decidua basalis (DB); the fetal part ofplacenta consisted of spongiotrophoblast and labyrinthin layer.Microarray hybridization was performed using a Mouse NimbleGen cDNA Microarray Kit (Roche), at CapitalBio Co., Ltd.(Beijing,China). Primary data were scaned using NimbleGen MS200 (Roche), and then extracted using NimbleScan system (Roche).

first: Enkui

last: Duan


title: Expression Profiles of HepG2 cells treated with following oxidants: 100µM menadione, 200µM TBH or 50µM H2O2

status: Public on May 31 2013

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

country: Netherlands

institute: Maastricht University

summary: The transcriptomic changes induced in the human liver cell line HepG2 by 100µM menadione, 200µM TBH or 50µM H2O2 after treatment for 0.5, 1, 2, 4, 6, 8 and 24h.

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 0.5, 1, 2, 4, 6, 8 and 24h hours of exposure to 100µM menadione, 200µM TBH or 50µM H2O2 and medium without compound. Three biological replicates per compound/solvent. In total 126 arrays.


title: Genome-wide analysis of gene expression in LIF and LIF plus 2I in C57BL/6 mouse embryonic stem cells (B6 mESCs)

status: Public on Apr 26 2013

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary:
Analysis of genes induced by 2I condition
2i contains glycogen synthase kinase 3 (GSK3) and mitogen-activated protein kinase kinase (MEK) inhibitors: 3uM Chir99021 and 1uM PD0325901

overall_design: Total RNA obtained from B6 mESCs treated with LIF or LIF/2I for 12 hours.

first: Shoudong

last: Ye

first: Qilong

last: Ying


title: Molecular responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: We have investigated both the response to prolonged darkness and the re-acclimation to “moderate intensity” white irradiance (E = 100 µmol m-2 s-1) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance.

overall_design: The cultures were incubated at 15C under cool white fluorescent light at a scalar irradiance (EPAR) of ~100 µmol m-2 s-1 under continuous white light (CWL) conditions. The cultures were dark-treated for 48 h (DT) before re-exposure to the previous light conditions for 0.5 h, 6 h or 24 h (WL 0.5, 6 and 24 h). Sampling of CWL cultures and DT cultures were performed in addition to the sampling at the WL incubation times of 0.5 h, 6 h, and 24 h. Three biological replicas for each of the five treatments were harvested.

first: Marianne

last: Nymark

first: Tore

last: Brembu

first: Kristin

middle: C

last: Valle

first: Atle

last: Bones

first: Torfinn

last: Sparstad


title: Gene regulation of carbon fixation, storage and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles

status: Public on Mar 01 2013

summary: Regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at cell, metabolite and gene expression level in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time-points provide a comprehensive data set on carbon incorporation, fate and regulation. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light responding genes in e.g. fatty acid biosynthesis were identified. Transcripts and cell chemistry data reflect the link between light energy availability and light energy consuming metabolic processes. Our data confirm spatial localization of processes in carbon metabolism to e.g. either plastids or mitochondria, or glycolysis/gluconeogenesis which are localized to the cytosol, chloroplast and to mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes, and mining of genes involved in light responses and circadian rhythms.

overall_design: Gene regulation in Phaeodactylum tricornutum was examined in cultures acclimatized to growth cycles of 16/8 hour photoperiods (16 hour light, 8 hour dark). Two biological replicas were harvested at each of the eight time points, spaning a 27 hour period. 5 of the time points (0.5 h, 3 h, 6 h, 10.5 h and 15.5 h) were harvested in the light phase, while 3 time points were harvested during the dark phase (0.5 h, 4 h and 7.5 h darkness).

first: Matilde

middle: S

last: Chauton

first: Olav

last: Vadstein


title: The Refilin/Filamin complex regulates filipodia dynamics in oligodendrocyte progenitor cells.

status: Public on May 01 2013

city: Grenoble

first: jacques

last: Baudier

address: 17 Rue des Martyrs

department: iRTSV

country: France

institute: INSERM

summary: Actin assembly and dynamics control the shape, motility and functions of diverse cell types. Programme for controlling theses dynamics is hard-coded into actin binding proteins and regulatory proteins. Refilins (RefilinA and RefilinB) are short lived regulatory proteins that interact with the actin-binding protein Filamin to convert it from an actin branching protein into one that bundles. We here show that different mechanisms converge to increase Refilin level in brain NG2+ precursor cells (polydendrocytes) committed to differentiate into the oligodendrocyte lineage. RefilinA is up-regulated through transcriptional activation during commitment into oligodendrocyte progenitor cells (OPC). RefilinB expression relies on PDGF signalling and is further stabilized by a unique auto-inhibitory domain masking the adjacent conserved PEST degradation signal. In NG2+ precursor cells and OPC, the RefilinB/Filamin complex localizes on filipodia protrusions and filipodial processes. Stable ectopic expression of Refilins in cells stimulates membrane remodelling dynamics linked with filipodia growth. These studies extend the function of the Refilin/FLNA complex to cell membrane remodelling linked with reorganization of underlying actin cytoskeleton.

overall_design: We performed whole transcriptomic analysis on the three cell population derived from OPC cells. Three different cultures were done and for each experiment we compared each cell population (NG2+, NG2+/A2B5 and O4) to the other 2 cell populations.

first: Olivia

last: Gay

first: Benoit

last: Gilquin

first: Anne

last: Wierinckx

first: Catherine

last: Rey

first: Joël

last: Lachuer

first: Jacques

first: Christelle

last: Benaud

first: Alexandre

last: Deshiere

first: Nicole

last: Assard

first: Pascale

last: Stuelsatz

first: Christian

last: Delphin

first: Jérôme

last: Honnorat


title: Control of Autophagic Cell Death by Caspase-10 in Multiple Myeloma

status: Public on Mar 13 2013

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: We performed a loss-of-function, RNA interference screen to define new therapeutic targets in multiple myeloma, a genetically diverse plasma cell malignancy. Unexpectedly, we discovered that all myeloma lines require caspase-10 for survival, irrespective of their genetic abnormalities. The transcription factor IRF4 induces both caspase-10 and its associated protein cFLIPL in myeloma, generating a protease that does not induce apoptosis but rather blocks an autophagy-dependent cell death pathway. Caspase-10 inhibits autophagy by cleaving the BCL2-interacting protein BCLAF1, itself a strong inducer of autophagy that acts by displacing beclin-1 from BCL2. While myeloma cells require a basal level of autophagy for survival, caspase-10 tempers this response to avoid cell death. Drugs that disrupt this vital balance may have therapeutic potential in myeloma.

overall_design: To generate a gene expression signature of caspase 10 signaling in multiple myeloma, cell lines (SKMM1 n=16, KMS12 n=8 and H929 n=12) were transduced with retroviral vectors expressing either shCasp10-2 or shCasp10-3. Similarly, lymphoma cell lines (OCI-Ly7 n=2 and OCI-Ly19 n=2) were transduced and used as a control. Following puromycin selection, shRNA expression was induced for 24 to 120 hours and gene expression was measured, comparing uninduced (Cy3) to induced (Cy5) cells, using lymphochip microarrays. Biological repeats were performed of H929 and SKMM1 samples.


title: Time course of gene expression changes after muscle contraction in spinal cord injured rats

status: Public on Mar 30 2013

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

summary: Purpose: The goal of this study was to determine the gene expression changes that occur over 7 days in parralyzed muscle in response to isometric contraction elicited by electrical stimulation initiated 4 months after spinal cord injury and to compare such changes to those observed in a normal muscle subjected to overload.

overall_design:
Methods:  Electrical stimulation of the soleus and plantaris muscle was stimulated in female rats with complete transection of the spinal cord at the interspace between the 9th and 10th thoracic vertebrae.  Stimulation was begun 16 weeks after spinal cord transection and produced near-isometric contraction of soleus, plantaris and tibialis anterior.  Muscle was analyzed at 1, 2 and 7 days after starting exercise with electrical stimulation. To provide a baseline reference for gene expression at 16 weeks after spinal cord injury, muscle was also analysed from an additional group of spinal cord transected animals.  One additional group of animals with a sham-spinal cord injury was included to provide information about gene expression in neurologically intact animals of similar age.  In parallel studies, rats underwent bilateral gastrocnemius ablation to overload soleus and plantaris, or a sham ablation as a control. Muscle was analyzed at 1, 3 and 7 days after gastrocnemius ablation or sham-ablation.
Gene expression was determined using Affymetrix Rat Exon microarrays. For each group of animals, microarray analysis was performed for soleus muscle for each of 3 separate animals, using one array per animal.  Control sammples for the spinal cord injured groups included a group of animals with a Sham-spinal cord injury, and a group of spinal cord injured animals that did not get electrical stimulation.   The comparator for determining fold-change expression values was the spinal cord injured group that did not receive electrical stimulation.  For each day after gastrocnemius ablation, a control was included that received all procedures needed for this ablation except cutting the distal insertion of the gastrocnemius into the Achilles tendon to control for effects of the surgery on gene expression.

first: Yong

last: Wu

first: Lauren

last: Collier

first: Weiping

last: Qin

first: Graham

last: Creasy

first: William

last: Bauman

first: Jonathan

last: Jarvis

first: Christopher

last: Cardozo


title: Bone marrow dendritic cells response to LPS, PAM and poly IC

status: Public on Mar 17 2013

city: Tel-Aviv

first: Irit

last: Gat Viks

address: Department of Cell Research and Immunology

department: Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

summary: Individual genetic variation affects gene expression and cell phenotype by acting within complex molecular circuits, but this relationship is still largely unknown. Here, we combine genomic and meso-scale profiling with novel computational methods to detect genetic variants that affect the responsiveness of gene expression to stimulus (responsiveness QTLs) and position them in circuit diagrams. We apply this approach to study individual variation in transcriptional responsiveness to three different pathogen components in the model response of primary bone marrow dendritic cells (DCs) from recombinant inbred mice strains. We show that reQTLs are common both in cis (affecting a single target gene) and in trans (pleiotropically affecting co-regulated gene modules) and are specific to some stimuli but not others. Leveraging the stimulus-specific activity of reQTLs and the differential responsiveness of their associated targets, we show how to position reQTLs within the context of known pathways in this regulatory circuit. For example, we find that a pleiotropic trans-acting genetic factor in chr1:129-165Mb affects the responsiveness of 35 anti-viral genes only during an anti-viral like stimulus. Using RNAi we uncover RGS16 the likely causal gene in this interval, and an activator of the antiviral response. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in other complex circuits in primary mammalian cells.

overall_design: The transcriptional response of DCs to pathogen components in the context of the mouse BXD recombinant inbred lines. We isolated DCs from individual age-synchronized female mice of different BXD and parental strains. We measured 30 global transcription profiles in resting and stimulated DCs from two parental strains (B6 and D2) and six BXD strains. We used bone marrow derived primary DCs from a panel of recombinant inbred (RI) BXD mice derived from a cross of the parental C57BL/6J (B6) and DBA/2J (D2) strains. We measured transcriptional responses in DCs from each of two parental strains and 6 BXD strains stimulated by three ligands of Toll-like receptors: LPS (TLR4 ligand), Pam3CSK ('PAM', TLR2 ligand) and poly IC (TLR3/RIG-I ligand).

last: Gat-Viks

first: Ido

last: Amit

first: Aviv

last: Regev


title: Microarray analysis of primary melanoma patient cells, melanoma cell lines, and HL cell lines

status: Public on Mar 09 2013

city: Cologne

first: Kerstin

last: Brinkmann

address: Joseph-Stelzmann-Str. 9

department: IMMIH2, Geb. 37

institute: University Hospital Cologne

summary: Gene expression analyses of 1300 genes involved in UPS-signalling in malignant and non-malignant cells

overall_design: Gene ratio of references (non-malignant) were compared to gene ratio of samples (malignant cells) under non-treated conditions

first: K

first: H

last: Kashkar


title: Plasma cells from spleen were FACS sorted using Blmp1 and CD138 expression and gene expression compared to naïve B cells, FACS sorted using B220 and IgD

status: Public on Feb 03 2013

city: Parkville

first: David

last: Tarlinton

state: Vic

address: 1G Royal Pde

country: Australia

institute: WEHI

summary: RNA extracted from plasma cells purified from spleens  were examined by Illumina microarray for gene expression. This was correlated with location and stage of differentiation using Blimp1 expression as a divider. All plasma cell samples were then compared to resting follicular B cells.

overall_design: Two plasma cell populations were sorted from pools of 5 - 10 animals. Arrays used in Peperzak et al., 2013, Figure 3d

first: Cam

last: Wellard


title: Salvelinus Microarray experiment: The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill)

status: Public on Dec 31 2012

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

country: Canada

institute: Laval university

summary: Parental effects represent an important source of variation in offspring phenotypes. Depending on the specific mechanisms involved, parental effects may be caused to different degrees by either the maternal or paternal parent, and these effects may in turn act at different stages of development. In order to detect parental effects acting on gene transcription regulation and length phenotype during ontogeny, the transcriptomic profiles of two reciprocal hybrids from Laval × Rupert and Laval × domestic populations of brook charr were compared at hatching, yolk sac resorption, and 15 weeks after exogenous feeding. Using a salmonid cDNA microarray, our results show that parental effects modulated gene expression among reciprocal hybrids only at the yolk sac resorption stage. In addition, Laval × domestic and Laval × Rupert reciprocal hybrids differed in the magnitude of theses parental effects, with 199 and 630 differentially expressed transcripts, respectively. This corresponds to a maximum of 18.5% of the analyzed transcripts. These transcripts are functionally related to cell cycle, nucleic acid metabolism and intracellular protein traffic, which is consistent with observed differences associated with embryonic development and growth differences in other fish species. Our results thus illustrate how parental effects on patterns of gene transcription seem dependent on the genetic architecture of the parents. In addition, in absence of transcriptomic differences, the non-transcriptomic deposits could also act to highlight the offspring differences in length before the yolk sac resorption.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Pair-wise direct comparisons between 8 reciprocal hybrids (LavalRupert vs RupertLaval and LavalDomestic vs DomesticLaval) were performed at each developmental stage. For each developmental stage, cDNA of 8 samples from each cross were hybridized for a total of 48 microarrays analyzed. The distribution of dyes is equilibrated among each cross (4 samples with cy3 and 4 samples with Al647).

first: Bérénice

last: Bougas

first: Céline

last: Audet

first: Louis

last: Bernatchez


title: CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

status: Public on Feb 15 2013

first: Ishminder

last: Mann

address: 9000 Rockville pike

institute: National Cancer Institute, NIH

summary: To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer present three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TF, which may be functional in vivo.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 8 mouse B-ZIP homodimers and one hetrodimer transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded and methylated or unmethylated 44K Agilent microarrays, containing a DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

middle: K

first: Raghunath

last: Chatterjee

first: Jianfei

last: Zhao

first: Ximiao

last: He

first: Matthew

middle: T

last: Weirauch

first: Timothy

middle: R

last: Hughes

first: Charles

last: Vinson


title: Clostridium thermocellum Transcriptomic Profiles after Exposure to Furfural or Heat Stress

status: Public on Jan 01 2013

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

summary: Background: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism.   Results: In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate physiological and regulatory responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and selected extracellular metabolite determinations and compared to a published dataset from an ethanol stress study. In total 1,474 genes were differentially expressed significantly in at least a single time point for a given stressor. One hundred and forty three common genes were differentially expressed for heat, furfural and ethanol stressors including up-regulated genes encoding DNA repair enzymes, Hsp20, sulfate transporter subunits and enzymes in the sulfate assimilatory pathway.  Conclusions: This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism’s physiology and regulation.

overall_design: A forty three array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 10, 30, 60, and 120 min post-treatment with 3.95 g.L-1 ethanol, 3 g.L-1 furfural or 68°C treatment compred to that of control without treatment. At least two biological replicates were performed for each treatment and control condition.

first: Shihui

last: Yang

first: Courtney

last: Johnson

first: Miguel

last: Rodriguez Jr

first: Lezlee

last: Dice

first: Steven

middle: D

last: Brown

first: Qin

last: Ma

first: Ying

last: Xu


title: Comparison of S. boulardii cells in H2O vs. S. boulardii cells in H2O+HCl

status: Public on Jan 04 2013

city: Providence

first: David

last: Laprade

state: RI

address: 1 Cunningham Sq.

institute: Providence College

summary: We sought to better understand the mechanism of acid-induced cell death in Saccharomyces boulardii--a probiotic yeast routinely used to prevent and treat gastrointestinal disorders. To do this we generated microarray gene expression profiles of S. boulardii cells cultured in an acidic environment.

overall_design: Two samples were analyzed. One replicate per array.

first: Vincent

last: Cascio

first: Kevin

last: Murphy

first: Racquel

last: Sherwood

first: Richard

last: Bennett

first: Nicanor

last: Austriaco


title: Bmp-regulated cardiac genes in zebrafish

status: Public on Mar 25 2013

city: Berlin

first: Salim

last: Seyfried

address: Robert-Rössle Str. 10

institute: Max Delbrück Center for Molecular Medicine

summary: The aim of this study was to identify genes that are regulated by Bmp signaling with the zebrafish heart at the heart cone stage around 21-23 hours post fertilization.

overall_design: In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of Tg(hsp70l:bmp2b)fr13 transgenic embryos heatshocked at 18 hpf and 2 WT control samples.

last: Abdelilah-Seyfried


title: Transcription profile of the bovine pretransfer endometrium based on pregnancy success after in vivo produced embryos transfer

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: In summary the main goal of this study is to determine the transcriptional profile of bovine endoemtrium at early stage of development in relation to pregnancy success after transfer of in vivo derived blastocysts

overall_design: 12 pool of  bovine endometrium based on out come of pregnancy sucess

first: Siriluck

last: Ponsuksili


title: Whole-transcriptome profiling analysis of first trimester placental villi in Indian women

status: Public on Jan 09 2013

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

country: India

institute: All India Institute of Medical Sciences

summary: Whole-transcriptome profiles of individual human placental villi samples from twenty-five (25) Indian women with normal pregnancies during 6- to 8-weeks of gestation were examined using human whole genome expression arrays (NimbleGen 135K).

overall_design: The present study focused on the whole-transcriptome profiling using NimbleGen135K (070925_HG18_exp__12X135K) human whole genome expression arrays of individual human placental villi samples obtained from twenty-five (25) proven-fertile women bearing normal pregnancies voluntarily terminated between 6- and 8-weeks of gestation. Gestational age was estimated from menstrual history, physical and ultrasonographic evaluation. No case of complicated pregnancy from infection, and other significant fetal and maternal clinical indications was included. These twenty five (25) samples include biological replicates of 6, 7 and 8 weeks placental villi samples.

first: Debabrata

last: Ghosh

first: Jayasree

last: Sengupta


title: Transcription profile of the bovine pretransfer endometrium based on pregnancy success after in vitro produced embryos transfer

summary: In summary the main goal of this study is to determine the transcriptional profile of bovine endoemtrium at early stage of development in relation to pregnancy success after transfer of in vitro derived blastocysts


title: Expression Data from Brucella abortus strain 2308 and isogenic mucR mutant cells

status: Public on Dec 01 2012

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
MucR is one of the few transcriptional regulatory proteins that has been linked to Brucella pathogenesis.
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to copare the gene expression properties of wild type and isogenic mucR mutant cells.

overall_design: B. abortus strain 2308 or mucR mutant cells were grown to stationary phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of MucR.

first: R

last: Roop


title: Evaluation of methods for modeling transcription factor sequence specificity

status: Public on Dec 13 2012

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

summary: Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity by representing sequence motifs, including the gaps and dependencies between binding-site residues, but these methods have not been systematically compared. Here we applied 26 such approaches to in vitro protein binding microarray data for 66 mouse TFs belonging to various families. For 9 TFs, we also scored the resulting motif models on in vivo data, and found that the best in vitro–derived motifs performed similarly to motifs derived from in vivo data.  Our results indicate that simple models based on mononucleotide position weight matrices learned by the best methods perform similarly to more complex models for most TFs examined, but fall short in specific cases. In addition, the best-performing motifs typically have relatively low information content, consistent with widespread degeneracy in eukaryotic TF sequence preferences.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 86 mouse transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

first: Atina

last: Cote

first: Raquel

last: Norel

first: Matti

last: Annala

first: Yue

last: Zhao

first: Todd

last: Riley

first: Julio

last: Saez-Rodriguez

first: Thomas

last: Cokelaer

first: Anastasia

last: Vedenko

first: Shaheynoor

last: Talukder

first: Phaedra

last: Agius

first: Aaron

last: Arvey

first: Philipp

last: Bucher

first: Curtis

middle: G

last: Callan Jr

first: Cheng

middle: W

last: Chang

first: Chien-Yu

last: Chen

first: Yong-Syuan

first: Yu-Wei

last: Chu

first: Jan

last: Grau

first: Ivo

last: Grosse

first: Vidhya

last: Jagannathan

first: Jens

last: Keilwagen

first: Szymon

last: Kiełbasa

first: Justin

middle: B

last: Kinney

first: Holger

last: Klein

first: Miron

last: Kursa

first: Harri

last: Lähdesmäki

first: Kirsti

last: Laurila

first: Chengwei

last: Lei

first: Christina

last: Leslie

first: Chaim

last: Linhart

first: Anand

last: Murugan

first: Alena

last: Myšičková

first: William

last: Noble

last: Nykter

first: Yaron

last: Orenstein

first: Stefan

last: Posch

first: Jianhua

last: Ruan

first: Witold

last: Rudnicki

first: Christoph

last: Schmid

first: Ron


title: Genome-wide analysis of differentiation in murine embryonic stem cells

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Examination of transcriptional responses to Embryonic stem cell differentiation in  the Brca1 (+/+) cell line AB2.2  compared to Brca1 (+/-) cell line PL2F8

overall_design: Total RNA obtained from murine Stem cell lines AB2.2 and PL2F8 at 0,2,4,6,8 days following induction of differentiation via the removal of the Leukemia Inhibitory factor (LIF).


title: Expression analysis of the effect of overexpression of Cebpb shRNA in mouse 4T1 mammary tumor cells

status: Public on Sep 28 2012

city: Stockholm

first: Jonas

last: Fuxe

address: Scheeles v. 2, A3:4

department: Department of Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary:
Investigation of whole genome gene expression level changes in mouse 4T1 mammary tumors expressing Cebpb shRNA, compared to 4T1 tumors expressing control shRNA.
Analysis of mouse 4T1 mammary tumors expressing Cebpb shRNA compared to control shRNA are further described in Johansson & Berg et al 2012.

overall_design: A 10 chip study using total RNA recovered from five separate 4T1 tumors expressing Cebpb shRNA and five separate 4T1 tumors expressing control shRNA. All tumors were surgically removed after subcutaneous implantation in syngeneic BALB/c mice two weeks earlier. Each chip measures the expression level of 44,170 genes from Mus Musculus with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Piotr

last: Religa

first: Ali

last: Moshfegh


title: Influenza-induced inflammation drives pneumococcal otitis media

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

summary: Influenza A virus (IAV) predisposes individuals to secondary infections with the bacterium Streptococcus pneumoniae (the pneumococcus). Infections may manifest as pneumonia, sepsis, meningitis or otitis media (OM). It remains controversial as to whether secondary pneumococcal disease is due to the induction of an aberrant immune response or IAV induced immunosuppression. Moreover, as the majority of studies have been performed in the context of pneumococcal pneumonia, it remains unclear how far these findings can be extrapolated to other pneumococcal disease phenotypes. Here, we demonstrate that the viral hemagglutinin (HA) mediates bacterial OM by inducing a pro-inflammatory response in the middle ear cavity in a replication-dependent manner. Importantly, our findings show that it is the inflammatory response that mediates pneumococcal replication; not viral suppression of the immune system or epithelial damage. This study provide the first evidence that HA induced inflammation drives pneumococcal replication in the middle ear cavity, which has important consequences to the treatment of pneumococcal OM.

overall_design: Five-day old C57BL/6 mice were colonised intranasally (i.n.) with 2×103 colony forming units (CFU) of  S. pneumoniae EF3030Lux in 3 µLs of PBS. Alternatively, mice were mock-infected with an equivalent volume of phosphate buffered saline (PBS). At 14-days of age, infant mice were infected i.n. with 20 plaque forming units (PFU) (PR8/34, Cambridge/34 and WSN/33) or 102.5 PFU (all other virus strains) of egg-grown IAV in 3 µLs of PBS. Viral doses were selected to ensure a reproducible infection with minimum morbidity and no mortality. Six days post-IAV infection, mice were euthanised and organs were collected for analysis. Six independent biological replicates (where both ears from one mouse were pooled to create one sample) were used for each condition and analyzed using the NimbleGen platform (12×135K Mouse Gene Expression Arrays, Roche Nimblegen, USA). Indirect labeling, hybridization and washing was performed according to the manufacturer’s instructions. Array images were acquired with a NimbleGen MS200 scanner, and images were processed with NimbleScan software using the RMA algorithm. Data was processed using Arraystar (DNASTAR, USA) with default settings as described in the manual. Differential expression tests were performed with a moderated T-test implemented in Arraystar, followed by FDR correction of the P values (Q-values) according to the method of Storey and Tibshirani

first: Kirsty

last: short

first: Dimitri

last: Diavatopoulous


title: Gene Bionetworks that Regulate Ovarian Primordial Follicle Assembly

status: Public on Jan 15 2013

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
Primordial follicle assembly is the process by which ovarian primordial follicles are formed.  During follicle assembly oocyte nests break down and a layer of pre-granulosa cells surrounds individual oocytes to form primordial follicles.  The pool of primordial follicles formed is the source of oocytes for ovulation during a female’s reproductive life.  Complex networks of cellular signaling and gene expression are essential for any biological process.  A systems biology experimental approach provides a global view of these gene relationships in a particular developmental process.  The current study utilized a systems approach to detect all genes that are differentially expressed in response to seven different growth factor and hormone treatments known to influence primordial follicle assembly in a neonatal rat ovary culture system.  One novel growth factor, basic fibroblast growth factor (FGF2), was experimentally determined to inhibit follicle assembly.  The different growth factor and hormone treatments were all found to affect the same physiological pathways, but each treatment affected a unique set of differentially expressed genes (signature gene set).  A gene bionetwork analysis identified gene modules of coordinately expressed interconnected genes and it was found that different gene modules appear to accomplish distinct tasks during primordial follicle assembly.  Unique gene networks were identified for a number of the modules and signature gene sets. Predictions of physiological pathways important to follicle assembly were validated using ovary culture experiments in which ERK1/2 (MAPK1) activity was increased. A number of the highly interconnected genes in these gene networks have previously been linked to primary ovarian insufficiency (POI) and polycystic ovarian disease syndrome (PCOS). Observations have identified novel factors and gene networks that regulate primordial follicle assembly. This systems approach has helped elucidate the molecular control of primordial follicle assembly and provided potential therapeutic targets for the treatment of ovarian disease.
We used microarrays to determine genes expressed differentially between control and P0 ovaries  treated with 7 growth factors: AMH, CTGF, estradiol (E2), Activin-a, FGF2, progesterone (P4), and TNFa.

overall_design: RNA samples from 7 control samples  are compared to 3 growth factor treated ovary samples  for each AMH (human Anti-Mülerian hormone), CTGF (connective tissue growth factor ),  estradiol (E2), TNF (tumor necrosis factor ), FGF2 (fibroblast growth factor 2), Inhba (inhibin, beta A), and 2 samples for progesterone (P4).

first: Eric

middle: E

last: Nilsson

first: Bin

last: Zhang


title: ChIP-on-chip from KYSE410 cells with CUL4B, EZH2 and BMI

status: Public on Oct 17 2012

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
A total of 619 unique promoters were found to be co-targeted by CUL4B and EZH2, among which only 53 were overlapped with the 891 targets of BMI
EZH2/PRC2 and CUL4B/CRL4B have a predominant cooperation, at least in KYSE410 cells.

overall_design: comparison of CUL4B, EZH2, and BMI target genes


title: High-resolution analysis of RNA expression in Desulfovbrio alaskensis G20

status: Public on Jul 19 2012

city: Berkeley

first: Morgan

middle: N

last: Price

state: CA

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

type: Expression profiling by genome tiling array

summary: High-resolution tiling analysis of the D. alaskensis G20  transcriptome in lactate/sulfate media, both rich (LS) and defined (LS4D)

overall_design: One chip each for rich and media minimal media and one “genomic control” array hybridized to genomic DNA

first: Jennifer

middle: V

last: Kuehl

first: Adam

middle: M

last: Deutschbauer

middle: P

last: Arkin


title: Efficient Generation of Integration-free and Engraftable induced Neural Stem Cells (iNSC) from Epithelial-like Cells in Human Urine

city: Guanghou

first: Guangjin

last: Pan

state: China

address: Kaiyuan Street, Guangzhou Science district

institute: Guangzhou Institute of Biomedicine and Health, CAS

summary: Human neural stem cells (NSCs) hold great promise in reparative therapy for neural diseases and injuries. However, the isolation of NSCs from either fetal or adult tissue and their application remain difficult due to ethical and immune-rejection concerns.  One promising solution is to generate patient specific induced pluripotent stem cells (iPSCs) and subsequently differentiate them into NSCs. Alternatively, induced neurons (iN) can be generated directly from fibroblasts by retroviral delivery of neural specific transcription factors or miroRNAs.  The later two approaches remain inefficient and with safety concerns.  Here, we describe a process to generate, from epithelial-like cells present in human urine, integration free and engraftable NSCs (UiNSC) efficiently.  Using an episomal system to deliver reprogramming factors and microRNAs into human urine cells and subsequently culture them in a chemically defined medium supplemented with a cocktail of small molecules, we generated UiNSCs capable of proliferation and without the transgenes upon prolonged expansion.   These transgene free UiNSCs express typical neural stem cell markers and are able to differentiate into all neuronal subtypes and glial cells in vitro and more importantly could engraft and differentiate in vivo upon transplantation into the brain of new born rat.  Thus, our work provides an efficient and highly practical platform to generate patient specific NSCs for regenerative medicine.

overall_design: This is a general expression microarray design (NimbleGen platform). It includes 6 samples.

first: Lihui

first: Linli

first: Huanxing

last: Su

first: Yanting

last: Xue

first: Wenhao

last: Huang

first: Dajiang

last: Qin

first: Duanqing

last: Pei


title: Placental Growth Factor/Nrp-1 signaling is required for medulloblstoma growth

status: Public on Oct 01 2012

city: Boston

first: Matija

last: Snuderl

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

type: Genome variation profiling by genome tiling array

summary:
Here we present that growth of medulloblastoma is dependent on PlGF/Nrp-1 signaling. PlGF and Nrp-1 are expressed across different molecular subgroups of medulloblastoma.
Data presented here are part of a combined molecular effort to subclassify our medulloblastoma cohort according to current molecular criteria (Taylor et al., 2011). Furthermore, we include aCGH of two medulloblastoma cell lines that were used as models in our experiments.

overall_design: Analyses were performed on 32 archival specimens of medulloblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital from 1998 to 2009. aCGH data included are for two medulloblastoma cell lines, D283 and D341, and 6 clinical cases for which DNA (good quantity and quality) was available.


title: Oligo array for CNV calling AUTS2 project [Bluegnome]

status: Public on Jul 12 2012

city: Amsterdam

first: Els

last: Voorhoeve

address: De Boelelaan 1117

department: Clinical Genetics

institute: VU medical center

summary: Phenotypic and genotypic description of AUTS2 deletion patients found by Array analysis in an international cohort of intellectual disability (ID) and multiple congenital malformations (MCA).

overall_design: Arrays were hybridized and analysed using manufacturer's  protocols on DNA from patients with ID/MCA

first: Una

last: Maye

first: Gea

last: Beunders


title: SNP array for CNV calling AUTS2 project [Illumina]

first: Anath

last: Lionel


title: Oligo array for calling CNV's for AUTS2 project [NimbleGen]

first: Santosh

last: Girirajan


title: comparison of mRNA expression among rat hepatoma cell lines with different metastatic ability

status: Public on Jun 21 2012

city: Kamiyoga, Setagaya-ku

first: Kumiko

last: Ogawa

state: Tokyo

country: Japan

institute: National Institute of Health Sciences

summary: To reduce cancer mortality, understanding of mechanisms of cancer metastasis is crucial. We have established 6 rat hepatocellular carcinoma (HCC) cell lines, which exhibit differing metastatic potential to the lung after inoculation into the tail veins of nude mice. Micorarray analysis of 4 kinds of HCC cells and rat normal liver tissue was performed to find a potent molecular target for prevention of cancer metastasis.

overall_design: By the microarray analysis, mRNA expression was compared among two low-metastatic rat HCC cell lines (C5F and C6) and two high-metastatic rat HCC cell lines (N1 and L2) as well as non-treated rat liver tissue (as a reference sample).

first: Teera

last: Chewonarin

first: Shugo

last: Suzuki

first: Makoto

last: Asamoto

first: Pornsiri

last: Pitchakarn

first: Tomoyuki

last: Shirai


title: Promoter methylation analysis in rat Pubertal Hypothalamus

status: Public on Jun 06 2012

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

type: Methylation profiling by genome tiling array

summary: Promoter methylation analysis of hypothalamc DNA from female rats at different juvenile developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.

overall_design: SD rats were housed (4/cage) in a controlled environment and euthanized at different ages (Early Juvenile: 21 days, Late Juvenile: 28 days,  Late Proestus (the day of first ovulation): 31 days.  Rats were anesthetized and brains were rapidly removed. The hypothalamus was dissected away from the rest of the brain and flash frozen. Total RNA and DNA was isolated from each sample using AllPrep DNA/RNA Mini Kit-Qiagen (Valencia, CA).

first: Sergio

last: Ojeda


title: Gene expression profile in human hepatoma HepG2 cells induced by gambogic acid and bortezomib

status: Public on Jun 15 2012

city: Guangzhou

first: Jinbao

last: Liu

address: Dongfeng xi road 195#

institute: Guangzhou medical college

summary: This experiment is designed to evaluate gene expression alterations following treatment with gambogic acid and bortezomib in human HepG2 cells. We find gambogic acid yielded a similar gene expression profile as did bortezomib.

overall_design: Total RNA were extracted from human HepG2 cancer cells treated with gambogic acid (0.25μM, 0.5μM, 0.75μM) or bortezomib (50nM) for 9hr. HepG2 cells treated with vehicle alone was used as a control.


title: Expression Profiles of HepG2 cells treated with genotoxic and non-genotoxic agents

status: Public on Aug 02 2012

city: Maastricht

first: Christina

last: Magkoufopoulou

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

institute: Maastricht University

summary: The lack of accurate in vitro assays for predicting in vivo toxicity of chemicals together with new legislations demanding replacement and reduction of animal testing has triggered the development of alternative methods. This study aimed at developing a transcriptomics-based in vitro prediction assay for in vivo genotoxicity. The transcriptomics changes induced in the human liver cell line HepG2 by 34 compounds after treatment for 12h, 24h and 48h were used for the selection of gene-sets that can discriminate between in vivo genotoxins (GTX) and in vivo non-genotoxins (NGTX). By combining publicly available results for these chemicals from standard in vitro genotoxicity studies with transcriptomics, we developed several prediction models. These models were validated by means of an additional set of 28 chemicals.

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 12 hours of exposure to 34 different compounds and their solvents; 24 and 48 hours of exposure to 62 different compounds and their solvents. Three biological replicates per compound/solvent. In total 560 arrays .


title: Salmonella Typhimurium: Heat-shocked cells vs. control cells and acid-shocked cells vs. control cells

status: Public on May 20 2012

city: Norwich

first: Carmen

last: Pin

address: Colney lane

country: United Kingdom

institute: institute of Food Research

summary: We investigated if the transcriptional response of S. Typhimurium to temperature and acid variations was hysteretic and showed memory, i.e., if the transcriptional regulation caused by environmental stimuli remained after the stimuli ceased. The transcriptional activity of non-replicating stationary-phase cells of Salmonella Typhimurium caused by the exposure to 45°C and to pH 5 for 30 min was monitored by microarray hybridizations before the application of the stress and at the end of the treatment period, as well as immediately and 30 minutes after conditions were set back to their initial values, 25°C and pH 7, respectively. We also investigated if hysteresis was accompanied with higher resistance to inactivation conditions, 50°C and/or pH 3, as well as more efficient growth at extreme conditions, 43°C and/or pH 4.5.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RNA samples for gene expression analysis and culture samples for growth and inactivation experiments were obtained after 30 min with stress (45°C or pH 5), immediately after the removal of stress and 30 min after the removal of stress. A control culture at 25°C and pH 7 was sampled at the same time intervals. Three independent replicates were carried out.


title: Down-regulation of gene expression is a conserved and distinctive feature required for early development of nematode-induced Giant Cells in tomato

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

summary: Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary parasites that affect a high variety of plants with a negative impact in the production of crops such as tomato. The infective RKN induces in the roots 4-7 highly specialized feeding cells (giant cells, GCs) developed into a hypertrophy cellular tissue or visible root swelling called “gall”. During GCs differentiation drastic alterations in genes expression occurs. However, information on genome-wide transcriptional profiles specifically in GCs is still lacking. With the aim to identify potential targets specifically regulated in GCs, we performed a temporal and spatial differential transcription profiling of tomato (Solanum lycopersicum), during the course of Meloidogyne javanica infection hybridizing TOM1 microarrays with hand-dissected galls at 1, 3, 7 and 14 days post-infection (dpi) and GCs exclusively isolated by LASER CAPTURE MICRODISSECTION (LCM) at 3 and 7 dpi. A GCs and galls comparison, at the same stage of development, reveals clear differences between their transcriptional patterns. For this purpose, a fast and efficient method to isolate LCM GCs from cryopreserved galls in the earliest differentiation state described to date: 48-72-hour post-infection (3 dpi), allowing good RNA preservation, was developed.

overall_design: In galls transcriptomic anaylsis, about 3000 galls and 4400 control uninfected root fragments were carefully hand-dissected at 1, 3, 7 and 14 dpi. Thus, more than 12 plates with 8 individual infected plants each, and 18 plates with the same number of plants as controls were used for only one independent experiment in each time point. Total RNA from two independent experiments was equimolarly pooled at each time of infection, in order to achieve a biological replicate for galls or control regardless. Therefore, a total of 6 independent experiments were performed to obtain 3 independent biological replicates for each infection point of galls and control analyzed. Following isolation, total RNA pooled from galls and control were subjected to a single round of linear amplification.   In GCs transcriptomic analysis, independent biological replicates of aRNA from 300 GCs versus 600 control cells (CCs) from control root LCM at 3 and 7 dpi were obtained. Fifty GCs and 100 CCs were independently captured from sections onto separate CapSure HS LCM caps, and total RNA isolation was performed from each cap. RNA from six separate caps was pooled for a single biological replicate of GCs or CCs, respectively. In total, three independent biological replicates were processed. Thus, near to 7000 individual cells were harvested by LCM. The material was obtained from more that 18 independent infection experiments.

first: Mary

last: Portillo

first: Keith

last: Lindsey

first: Jen

last: Topping

first: Javier

last: Cabrera-Chaves

first: Juan

middle: C

last: Oliveros

last: García-Casado

first: Roberto

last: Solano

first: Hinanit

last: Koltai

last: Fenoll

first: Carolina

last: Escobar


title: Molecular Characterization of Laser Microdissected Circumventricular Organs and Third Ventricle Ependyma in the Adult Rat by Microarray Analysis.

status: Public on May 24 2012

city: Lyon

first: jacques

last: champier

address: rue Guillaume Paradin

department: neuroonology

summary: We used LCM and microarrays to analyze the transcriptomes of three CVOs, the SCO, the subfornical organ (SFO), and the PG, and the third ventricle ependyma in the adult rat in order to better characterize these organs at the molecular level.

overall_design: Gene expression was performed on laser microdissection of rat Pineal Gland (n=2), Subcommisural Organ (pool of 2), Subfornical Organ (pool of 2) and Third Ventricle Ependyma (pool of 2). Pool of rat total normal brains was used as reference.

first: Alexandru

last: Szathmari

first: Jacques

last: Champier

first: Jean-François

last: Ghersi-Egea

first: Chantal

last: Watrin

first: Anne

last: Wierinckx

first: Michelle

last: Fèvre Montange


title: Xenograft mouse study in C57BL6/SCID mice using A431 cells

status: Public on Oct 20 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary:
In this study four groups involving, Control arm, Rapamycin arm, Nimotuzumab arm and the Combination group were involved. Four tumors from each group was evaluated for microarray analysis they were the two largest and two smallest from each group.
Agilent one-color experiment,Organism: Human ,Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

overall_design: 4 groups: control, rapamycin, nimotuzumab, and rapamycin and nimotuzumab


title: Expression analysis of Linum usitatissimum 25-mers and 60-mers arrays

status: Public on May 15 2012

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité scientifique

institute: University Lille 1

summary:
Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides)
Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology

overall_design: We compared two categories of flax target probes: short (25-mers) oligonucleotides and long (60-mers) oligonucleotides in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. This comparison was realized with two different flax samples and each RNA sample was used for the two categories of arrays. Experiments were realized in order to discriminate specific gene expression profiles of two different flax tissues (outer and inner stem tissues).

first: Stephane

last: Fenart

first: Malika

last: Chabi

first: Sophie

last: Gallina

first: Rudy

last: Huis

first: Godfrey

last: Neutelings

first: Nathalie

last: Riviere

first: Brigitte

last: Thomasset

first: Simon

last: Hawkins

first: Anca

last: Lucau-Danila


title: Fish oil/pectin temporally alters gene expression profiles in exfoliated rat colonocytes throughout oncogenesis

status: Public on Feb 20 2012

city: College Station

first: Youngmi

last: Cho

state: TX

address: 2253 TAMU

department: Faculty of Nutrition

institute: Texas A&M University

summary:
We have demonstrated that fish oil/pectin (FO/P) diets protect against colon cancer compared to corn oil/cellulose (CO/C) by upregulating apoptosis and suppressing proliferation.
To elucidate the mechanisms whereby FO/P diets induce apoptosis and suppress proliferation during the tumorigenic process, we analyzed the temporal gene expression profiles from exfoliated rat colonocytes.
KEYWORDS: Fish oil/pectin, pectin, exfoliated colonocytes, gene expression, apoptosis, colon cancer, chemoprevention

overall_design: Rats consumed diets containing FO/P or CO/C and were injected with azoxymethane (AOM, 2x, 15 mg/kg BW, s.c.). Feces collected at the initiation, aberrant crypt foci (ACF), and tumor stages of colon cancer (24 h (n=20), 7 wk (n=37), and 28 wk (n=28) after AOM injection, respectively) was used for poly A(+) RNA extraction. Gene expression signatures were determined using Codelink arrays.

first: Joanne

last: Lupton

first: Nancy

last: Turner


title: Role of macrophages in invadopodia formation

status: Public on Mar 08 2012

city: Lucknow

first: khemraj

middle: singh

last: baghel

address: Mahatma Gandhi Road

department: Toxicology Division

institute: Central Drug Research Institute

summary: The first experiment involved the DU-145 tumor cell samples cultured with or without macrophages. This experiment was planned with an aim to evaluate the gene expression changes that might occur in DU-145 cells when grown in proximity to macrophages as compared to DU145 cells being grown alone. Similarly, the second experiment, involved the macrophage samples cultured with or without the DU-145 cells. This experiment was planned with an aim to evaluate the gene expression changes that might occur in Macrophages  when grown in proximity to DU-145 cells .

overall_design: Agilent one-color experiment, Organism: Human, Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Khemraj

middle: S

last: Baghel

first: Smrati

last: Bhadauria


title: Gender dependent differences in molecular electrophysiological targets in failing and nonfailing human hearts

status: Public on Feb 01 2012

city: St. Louis

first: Christina

middle: Marie

last: Ambrosi

state: MO

address: 1 Brookings Drive

department: Biomedical Engineering

institute: Washington University in St. Louis

summary: Previous epidemiological studies have shown that males tend to have an increased overall lifetime risk of developing atrial fibrillation (AF), whereas females tend to be more susceptible to the development of ventricular tachyarrhythmias resulting from long-QT syndrome and drug-induced Torsades de Pointes.  In this study, we compared the transcript-level expression of 89 ion channel subunits, calcium handling proteins, and other transcription factors in the left atria (LA) and ventricles (LV) of human hearts of both genders.

overall_design: Total RNA from the LA and LV of failing male (n=9), failing female (n=7), nonfailing male (n=9), and nonfailing female (n=9) hearts was probed using a custom-designed Taqman gene array from Applied Biosystems.  Tissues from LA (n=22), LV (n=22), LV endocardium (n=12), and LV epicardium (n=12) were analyzed by the Applied Biosystems SDS 2.3 software using the threshold cycle (Ct) relative quantification method with GAPDH as an endogenous control.

first: Kathryn

middle: A

last: Yamada

first: Jeanne

last: Nerbonne

first: Igor

last: Efimov


title: Genome-wide profiling of responses to cadmium in the diatom Phaeodactylum tricornutum

status: Public on Aug 02 2011

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

summary: The only group of organisms in which a biological function for cadmium has been shown is the diatoms, which are unicellular phytoplankton. Yet diatoms exhibit similar sensitivity to Cd as other groups of phytoplankton. We have investigated responses of Cd on molecular, metabolic and physiological levels in the diatom Phaeodactylum tricornutum. P. tricornutum apparently has a high tolerance to Cd; only minor responses were observed on growth, pigment and transcriptional changes at cadmium concentrations of 123 µg/l. No significant changes in chlorophyll and xanthophyll levels were observed, and the very few transcripts affected strongly indicate that the cells were able to respond to the increased Cd2+ levels without changing proteins levels. At 10 times this concentration, 1230 µg/l, a much clearer response was observed, including transcripts encoding proteins involved in metal transport, cell signalling and detoxification processes. Our results point towards putative pathways for the removal or detoxification of Cd and its metabolites, as well as a possible Cd uptake mechanism. We predict that ATPase5-1B is involved in removal of Cd by pumping Cd2+ ions out of the cell, whereas VIT1/CCC1 sequesters Cd2+ in the vacuole.

overall_design: Cultures of Phaeodactylum tricornutum were treated with two concentrations of Cd2+, 123 µg/l and 1230 µg/l. The reference samples were grown in artificial seawater base AK modified with added f/2-medium nutrients. Three biological replicates were harvested for all samples.

first: Tore

last: Brembu

first: Margrethe

last: Jørstad

first: Kristin

last: Valle

first: Atle

last: Bones


title: Transcriptom analysis of the interaction Medicago truncatula – Ralstonia solanacearum

status: Public on Sep 10 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: affy_ralstonia_medicago - Ralstonia solanacearum is the causal agent of the devastating bacterial wilt disease. Its infection process was studied with an in vitro inoculation procedure on intact roots of Medicago truncatula. The pathosystem involved susceptible A17 and resistant F83005.5 M truncatula lines infected with the pathogenic strain GMI1000. The mutant A17 line, Sickle, which showed a resistant phenotype was also part of the experiment. To identify host signaling pathway triggered by R. solanacearum infection with a focus on the involvment of ethylene, we used the Medicago Affymetrix array to monitore the expression profiles and the molecular process associated with initial symptoms development (12hpi) and colonization (72hpi). In order to maximize chances to observe differential gene expression, RNA samples were extracted from the root infection zone (root tips) -Three Medicago truncatula lines, A17, F83005.5 and sickle were inoculated with GMI1000 Ralstonai solanacearum strain (107 cfu/ml). RNA were extracted from root extremities (1 cm above the root tip) at time 0, 12h and 72h post inoculation. Three biological repeats were conducted

overall_design: normal vs disease comparison, time course, 27 arrays - Medicago

first: Marie-françoise

last: Jardinaud

first: Sandrine

last: Balzergue

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Functional genomics study of endogenous free fatty acid overproduction in Escherichia coli

status: Public on May 24 2011

city: Madison

first: Rebecca

last: Lennen

state: WI

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

summary: Comparative analysis of changes in gene and protein expression and fatty acid profiles between Escherichia coli K-12 MG1655 ΔfadD ΔaraBAD expressing an acyl-acyl carrier protein thioesterase from Umbellularia californica (BTE) or a non-functional mutant thioesterase (BTE-H204A) to determine the functional basis for losses in cell viability, membrane integrity, or other stresses and metabolic perturbations that may be present. New hypotheses obtained from the study will assist in metabolic engineering efforts of improved strains exhibiting higher fatty acid yields and productivities.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Cultures of fatty acid overproducing (BTE-expressing) and negative control (non-functional BTE-H204A-expressing) strains of Escherichia coli K-12 MG1655 delta-fadD delta-araBAD (deficient in beta-oxidation and L-arabinose catabolism) were sampled under two different sets of media/induction/antibiotic conditions. These conditions were shake flasks at 37C, 250 rpm shaking, in EZ rich defined medium supplemented with 0.2% glucose and 0.01 mM biotin (EZglu), and in fermentors at 37C with controlled air sparging, agitation, and pH in EZ rich defined medium supplemented with 0.4% glycerol and 0.01 mM biotin (EZgly). Two strains were analyzed in the EZglu experiment, the background strain harboring either pTrc99A-BTE (fatty acid overproducing) or pTrc99A-BTE-H204A (control phenotype). Three strains were analyzed in the EZgly experiment, with the background strain haboring either pBAD35-BTE and pBAD33 (fatty acid overproducing), pBAD35-BTE and pBAD33-ACC (fatty acid overproducing, ACC are the 4 subunits of E. coli K-12 acetyl-CoA carboxylase expressed as an artificial operon accDABC in plasmid pBAD33), and pBAD35-BTE-H204A and pBAD33 (control phenotype). RNA was extracted from harvested cell pellets from biological triplicates (EZglu) or biological duplicates (EZgly) of each strain at three different sampling times as defined in each sample description. Due to a hybridization or scanning problem, biological duplicates rather than triplicates were analyzed at the mid-stationary phase sampling point in the EZglu experiment for the control strain harboring pTrc99A-BTE-H204A. Multiple technical replicates at either the hybridization or sample level were analyzed from the biological duplicates of the fermentor experiment. The form of technical replicate (sample or hybridization) is specified in each EZgly sample description.

first: Max

last: Kruziki

first: Kritika

last: Kumar

first: Robert

last: Zinkel

last: Burnum

first: Mary

last: Lipton

first: Spencer

last: Hoover

first: Don

middle: R

last: Ranatunga

first: Tyler

last: Wittkopp

first: Wesley

middle: D

last: Marner

first: Brian

middle: F

last: Pfleger


title: Comparison of whole brain expression data between selectively bred P and NP, alcohol naïve rats

status: Public on Apr 19 2011

city: Aurora

first: Laura

last: Saba

state: CO

address: 12801 E. 17th Avenue

department: Pharmacology

institute: University of Colorado Denver

summary: Gene expression was analyzed in brains of 4 male selectively-bred alcohol-preferring (P) rats (generation 63) and 3 male alcohol non-preferring (NP) rats (generation 62) that were obtained from Dr. Richard L. Bell, Indiana University School of Medicine, Indianapolis, IN.  These rats had never been exposed to alcohol.

overall_design: Individual rats from each group were hybridized separately to individual arrays (one array per rat).  No duplicates are present.  Originally, four NP samples were analyzed, but one was dropped because of quality control standards.

first: Boris

last: Tabakoff


title: Estrogens and selective estrogen receptor modulators regulate gene and protein expression in the mesenteric arteries

status: Public on Jul 06 2011

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Estrogen is a reproductive steroid hormone that has both beneficial and detrimental effects on the cardiovascular system. Selective estrogen receptor modulators (SERMs) exhibit partial estrogen agonist/antagonist activity in estrogen target tissues.  Since we still have an incomplete picture of the gene targets of estrogen in the vasculature, and our understanding of SERM gene targets in the vasculature is even less well-developed, it is important to broaden the available information on this subject.  The present study tested the hypothesis that estrogens (ethinyl estradiol, estradiol benzoate, and equilin) and SERMs (tamoxifen and raloxifene) cause differential gene and protein expression in the vasculature.  DNA microarray and real-time RT-PCR were used to investigate gene expression in the mesenteric arteries of estrogen and SERM treated ovariectomized rats. The genes shown to be differentially expressed included stearoyl-CoA desaturase (SCD), soluble epoxide hydrolase (sEH), secreted frizzled related protein-4 (SFRP-4), insulin-like growth factor-1 (IGF-1), phospholipase A2 group 1B (PLA2-G1B), and fatty acid synthase (FAS).  Western blot further confirmed the differential expression of sEH, SFRP-4, FAS, and SCD protein.  These results reveal that estrogens and SERMs cause differential gene and protein expression in the mesenteric artery.  Consequently, the use of these agents may be associated with a unique profile of functional and structural changes in the mesenteric arterial circulation.

overall_design:
Goal of the experiment:  To examine the effects of three formulations of estrogen (ethinyl estradiol, equilin, and estradiol benzoate) and of the selective estrogen receptor modulators, tamoxifen and raloxifene, on gene expression in the mesenteric arteries of the rat.

Keywords:  rat, artery, gene expression, mesentery, estrogen, tamoxifen, raloxifene

Experimental factors:  hormone treatment, drug treatment

Experimental design:  Prepubertal female Sprague Dawley rats (Harlan, Indianapolis, IN) were ovariectomized at 4 weeks of age, prior to the initiation of regular ovarian cycles.  The animals were allowed to recover for 2 weeks before the experimental protocol was initiated.  The rats were randomly divided into 6 groups (n=3-4/group) and treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN).
After 3 weeks of treatment, the rats were euthanized and the mesentery obtained.  Total RNA was extracted from each individual sample and used for the synthesis of labeled cRNA for microarray analysis.
After the final gavage treatment on day 21, the rats were deeply anesthetized with isoflurane and euthanized by decapitation.  The mesenteric arterial tree was isolated and harvested and stored in RNAlater (Ambion) at -80ºC.  The mesenteric arteries were dissected free from veins and surrounding fat and homogenized in TRI reagent (MRC, Cincinnati, OH).
Mesenteric artery RNA was extracted and purified using an RNeasy Mini Kit (Qiagen).  Any potentially contaminating DNA was removed by treatment with RNase-free DNase (Qiagen) on the RNeasy column.  Total RNA was quantified and RNA integrity was assessed using the Agilent Bioanalyzer (Santa Clara, CA).  Following analysis, the RNA was stored at -80ºC until it was used for gene expression studies.
DNA microarray:  CodeLink Whole Rat Genome Bioarrays (Applied Microarrays, Tempe, AZ) were used.  Five μg total RNA was used from each mesenteric arterial sample for the microarray analysis.  Complementary RNA was synthesized per company protocol (Ambion).  A set of bacterial RNAs was added to each total RNA sample and carried through the synthesis and labeling reactions as controls and for nor¬malization of the data.  The microarrays were scanned with the GenePix 4000B (Axon Instruments, Union City, CA) with GenePix Pro 5.0 software (Axon Instruments).  Analysis of the microar¬rays was performed with the CodeLink Expression Analysis software (Applied Microarrays) and Acuity 3.1 software (Axon), and statistical analysis was performed with GeneSpring 7.1 software (Agilent, Santa Clara, CA).  A sample of n=3 was completed with the microarrays for each treatment.

Quality control steps:  The cRNA that was synthesized from each mesenteric artery treatment sample was used for hybridization to a single CodeLink (Applied Microarrays) whole rat genome microarray.  Only one sample was hybridized with each slide and only one dye (streptavidin-Alexa 647) was used so no dye swaps were used.  Bacterial control spikes were used per manufacturer's instructions.

Samples used, extract preparation and labeling:
The origin of each biological sample:  The samples were isolated mesenteric arteries from individual Sprague Dawley rats that had been treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN).

Manipulations of biological samples and protocols used:  Ovariectomized female rats were treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN).
After the final gavage treatment on day 21, the rats were deeply anesthetized with isoflurane and euthanized by decapitation.  The mesenteric arterial tree was isolated, harvested, and stored in RNAlater (Ambion) at -80ºC.  The mesenteric arteries were dissected free from veins and surrounding fat and homogenized in TRI reagent (MRC, Cincinnati, OH).

Experimental factor:  hormone treatment, drug treatment

Technical protocols:  The mesenteric arteries were minced with scalpels and TRI reagent (MRC) was added.  The tissue was homogenized with a Polytron homogenizer.  Bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

	Labeled cRNA was prepared using the Message Amp II-Biotin Enhanced Kit from Ambion, following the manufacturer's Instruction Protocol.  5.0 microgram of rat mesenteric artery total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on spin columns included in the Ambion kit.  The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on spin columns from the Ambion kit.  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of biotinylated cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides (CodeLink Whole Rat Genome Bioarrays), and hybridized for 18 hours at 37C.
	The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The streptavidin-Alexa 647 fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

first: Connie

middle: J

last: Mark-Kappeler

first: Douglas

last: Martin


title: Differential gene expression profile of y79 retinoblastoma cells in response to stress conditions

status: Public on Mar 11 2011

first: Genotypic

last: technology

summary: The Y79 retinoblastoma cells were exposed to oxidative stress conditions with hydrogen peroxide exposure. The differential gene expression profile on this condition was evaluated by comparing with untreated control Y79 cells. The cellular responses based on the differential gene expression was studied.

overall_design: One-color experiment,Organism: Human , Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd.  (Agilent-27114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Suryanarayan

last: Vandhana


title: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [protein binding microarray]

status: Public on Sep 15 2011

city: Cambridge

first: Xinchen

last: Wang

state: MA

address: 32 Vassar St, D514

institute: MIT

summary: Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specific AS event that changes the DNA binding preference of the forkhead family transcription factor FOXP1. We show that the ESC-specific isoform of FOXP1 stimulates the expression of transcription factor genes required for pluripotency including OCT4, NANOG, NR5A2 and GDF3, while concomitantly repressing genes required for ESC differentiation. Remarkably, this isoform also promotes the maintenance of ESC pluripotency and the efficient reprogramming of somatic cells to induced pluripotent stem cells. These results reveal an AS switch that plays a pivotal role in the regulation of pluripotency through the control of critical ESC-specific transcriptional programs.

overall_design: Protein binding microarray (PBM) experiments were performed for two isoforms of the DNA binding domain of the human FOXP1 gene. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 4*44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.

first: Mathieu

last: Gabut

first: Payman

last: Samavarchi-Tehrani

first: Valentina

last: Slobodeniuc

first: Dave

last: O’Hanlon

first: Hoon-Ki

last: Sung

first: Manuel

last: Alvarez

first: Shaheynoor

last: Talukder

first: Qun

last: Pan

first: Knut

last: Woltjen

first: Esteban

middle: O

last: Mazzoni

first: Stephane

last: Nedelec

first: Hynek

last: Wichterle

first: Timothy

last: Hughes

first: Peter

last: Zandstra

first: Andras

last: Nagy

first: Jeffrey

last: Wrana

first: Benjamin

last: Blencowe


title: Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

status: Public on Dec 02 2010

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting 3 (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkable evolutionary success. Given a set of modules with defined 3-base specificities, modular assembly also presents a way to construct artificial proteins with specific DNA-binding preferences. However, a recent survey of a large number of three-finger ZFAs engineered by modular assembly reported high failure rates (~70%), casting doubt on the generality of modular assembly. Here, we used protein-binding microarrays to analyze 28 ZFAs that failed in the aforementioned study. Most (17) preferred specific sequences, which in all but one case resembled the intended target sequence. Like natural ZFAs, the engineered ZFAs typically yielded degenerate motifs, binding dozens to hundreds of related individual sequences. Thus, the failure of these proteins in previous assays is not due to lack of sequence-specific DNA-binding activity. Our findings underscore the relevance of individual C2H2-ZF sequence specificities within tandem arrays, and support the general ability of modular assembly to produce ZFAs with sequence-specific DNA-binding activity.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 20 artificial zinc finger arrays (ZFAs). Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.

first: Kathy

last: Lam

last: van Bakel

first: Atina

middle: G

last: Cote

first: Anton

last: van der Ven


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

status: Public on Feb 13 2011

city: Boston

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

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

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

first: Stanislav

last: Karsten

first: Anatol

last: Bragin

first: Lili

last: Kudo

first: Lauren

last: Gehman

first: Josephine

last: Ruidera

first: Daniel

middle: H

last: Geschwind

first: Jerome

last: Engel Jr


title: Lieb SDQ4051_LEM2_N2_MXEMB

status: Public on Dec 22 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3154
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: To complement our extensive ChIP-chip characterization of chromosomal regulators in C. elegans, in select experiments we also isolate total RNA from parallel cultures of staged animals.  Labeled cDNA will be prepared and used to probe either gene-specific microarrays, or genomic tiling microarrays to assess the transcriptional state of genomic sequences flanking the protein-binding regions localized by ChIP-chip and ChIP-seq.  To investigate possible correlations between putative regulatory proteins and transcription state, data from such experiments (i.e., protein binding sites and steady-state mRNA levels) will be integrated during downstream analysis.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius

first: Ikegami

last: Kohta

first: Jason

last: Lieb


title: Responses of Zea mays root tissue to inoculation with the necrotrophic root pathogen Phytophthora cinnamomi

status: Public on Mar 02 2011

city: Waurn Ponds

first: Jane

last: Allardyce

state: Victoria

address: Pigdons Road

institute: Deakin University

summary: Phytophthora cinnamomi is a devastating soil-borne oomycete with a very broad host range however there remains a major gap in the understanding of plant resistance responses to the pathogen, furthermore, necrotrophic plant-pathogen interactions, particularly those of root pathogens, remain poorly understood. Zea mays exhibits non-host resistance to the pathogen and has been well characterised as a model species. Using the maize Affymetrix GeneChip array we conducted genome-wide gene expression profiling to elucidate the defence genes and pathways which are induced in the root tissue of a resistant plant species to the pathogen.

overall_design: Each experimental repeat consisted of 60 Z. mays seedlings in total: 15 control and 15 inoculated plants per timepoint. Root tissue was harvested and snap frozen in liquid nitrogen and stored at -80°C until required. All harvested root tissue within each treatment group at each time point was pooled for total RNA extractions. Three technical repeats were conducted resulting in a total of 180 sampled plants and 12 samples of purified total RNA for microarray analysis. Total RNA was labelled, hybridised and scanned using standard Affymetrix protocols and resulted in 12 .CEL files. Raw data was processed using Partek Genomics Suite software and normalised using Robust Multi-Chip Average Software. Differentially expressed genes were defined by a fold difference of >1.5 (log2) and those with a P value cutoff of <0.05 were considered statistically significant.


title: Retinal pigment epithelium and photoreceptor and choroidal cells

status: Public on May 30 2010

city: Amsterdam

first: arthur

last: bergen

address: Meibergdreef 47

institute: NIN

summary: Background: To identify and functionally annotate cell type-specific gene expression in the human retinal pigment epithelium (RPE), a key tissue involved in age-related macular degeneration and retinitis pigmentosa. Methodology: RPE, photoreceptor and choroidal cells were isolated from selected freshly frozen healthy human donor eyes using laser microdissection. RNA isolation, amplification and hybridization to 44k microarrays was carried out according to Agilent specifications. Bioinformatics was carried out using Rosetta Resolver, David and Ingenuity software. Principal Findings: Our previous 22k analysis of the RPE transcriptome showed that the RPE has high levels of protein synthesis, strong energy demands, is exposed to high levels of oxidative stress and a variable degree of inflammation. We currently use a complementary new strategy aimed at the identification and functional annotation of RPE-specific expressed transcripts. This strategy takes advantage of the multilayered cellular structure of the retina and overcomes a number of limitations of previous studies. In triplicate, we compared the transcriptomes of RPE, photoreceptor and choroidal cells and we deduced RPE specific expression. We identified at least 114 entries with RPE-specific gene expression. Thirty-nine of these 114 genes also show high expression in the RPE, comparison with the literature showed that 85% of these 39 were previously identified to be expressed in the RPE. In the group of 114 RPE specific genes there was an overrepresentation of genes involved in (membrane) transport, vision and ophthalmic disease. More fundamentally, we found RPE-specific involvement in the RAR-activation, retinol metabolism and GABA receptor signaling pathways. Conclusions: In this study we provide a further specification and understanding of the RPE transcriptome by identifying and analyzing genes that are specifically expressed in the RPE.

overall_design: Six RPE samples, three phot samples, three choroid samples

first: Judith

last: Booij

first: Arthur

last: Bergen


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

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

overall_design: Refer to individual Series