title: Genes differentially expressed as a result of Candida albicans SC5314 exposure to pterostilbene

status: Public on Mar 23 2014

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

institute: PLA General Hospital

summary: Transcriptional profiling of Candida albicans comparing pterostilbene treated cells with untreated cells

overall_design: Wild type Candida albicans strain SC5314 was selected to carry out the expression profile microarray. Two-condition experiment, pterostilbene treated vs. untreated cells. Biological replicates: 3 control, 3 pterostilbene treated, independently grown and harvested. One replicate per array.

first: Lanxue

last: Zhao


title: Human dietary intervention study with blueberry-apple juice

status: Public on Feb 01 2014

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: Human volunteers (N=143; 98 females and 45 males; aged 18-45 years) consumed one litre of blueberry-apple juice per day for four weeks. Before and after the intervention blood was drawn and lymphocytes were isolated for subsequent RNA isolation. Each participant acted as his own control.

overall_design: Each subject acted as his own control, meaning that the fluorescent labeled cRNAs of each subject before and after the intervention were mixed and hybridized on one chip. To rule out any possible dye effect, samples from each subject before and after the intervention were randomly labeled with Cy3 and Cy5.

first: Theo

middle: M

last: de Kok


title: Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

status: Public on Jan 13 2014

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

country: USA

institute: Lineberger Comprehensive Cancer Center

summary: Transcription was assessed in the human H522 NSCLC cell line after reexpression of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by adenovirus infection, after treatment with 5 micromolar 5-deAzacytidine or after treatment with 100nM Trichostatin A.  Control treatments included infection with adenovirus expressing GFP and treatment with DMSO4 (vehicle control).  The goal of the experiment was to identify target genes of the SWI/SNF complex and compart them to changes induced by DNA methylation and histone acetylation modifiers.

overall_design: One biological replicate of each treatment; 4 technical replicates of each treatment.

first: Bernard

middle: E

last: Weissman

first: Mehmet

last: Karaca


title: Identifying vitamin C and RA-regulated genes in the J1 mESCs

status: Public on Jan 21 2014

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

country: China

institute: LVRI

summary: It has been demonstrated that vitamin C enhances reprogramming efficiency during inducing pluripotent stem cells, however, the underlying mechanisms are not fully understood. To find the downstream target genes of vitamin C and investigate the mechanism of vitamin C on reprogramming promotion, we performed Microarray analyses to identify its downstream targets. Retinoic acid (RA), a stimulus molecule for cellular differentiation, is set as negative control. The data show the genes regulated by vitamin C or RA.

overall_design: J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with vitamin C or RA for 24 hours, then total RNA was extracted for analysis.

first: Yongyan

last: Wu

first: Zhiying

last: Ai

first: Xiaoyan

last: Shi

first: Juan

last: Du

first: Ye

last: Liu

first: Zekun

last: Guo


title: Expression profiles of X-ray responsive miRNA in human cells

status: Public on Mar 14 2014

city: Chiba

first: Ken-ichi

last: Ishikawa

state: Chiba

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Charged Particle Therapy

country: Japan

institute: National Institute of Radiological Sciences

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

summary:
MicroRNA (miRNA) is a type of non-coding RNA that regulates the expression of its target genes by interacting with the complementary sequence of the target mRNA molecules. Recent evidence has shown that genotoxic stress induces miRNA expression, but the target genes involved and role in cellular responses remain unclear. We examined the role of miRNA in the cellular response to X-ray irradiation by studying the expression profiles of radio-responsive miRNAs and their target genes in cultured human cell lines. We found that expression of miR-574-3p was induced in the lung cancer cell line A549 by X-ray irradiation. Overexpression of miR-574-3p caused delayed growth in A549 cells. A predicted target site was detected in the 3'-untranslated region of the enhancer of the rudimentary homolog (ERH) gene, and transfected cells showed an interaction between the luciferase reporter containing the target sequences and miR-574-3p. Overexpression of miR-574-3p suppressed ERH protein production and delayed cell growth. This delay was confirmed by knockdown of ERH expression. Our study suggests that miR-574-3p may contribute to the regulation of the cell cycle in response to X-ray irradiation via suppression of ERH protein production.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Global murine neutrophil response to highly and less virulent influenza A (H3N2) virus infections at 3 and 9 h post-infection

status: Public on Mar 19 2014

city: Singapore

first: Vincent

middle: Tak Kwong

last: Chow

state: Singapore

address: 5 Science Drive 2, BLK MD4 (NUS)

department: Microbiology

country: Singapore

institute: National University of Singapore (NUS)

summary: Array analysis of total RNA obtained from MPRO neutrophils collected at 3 and 9 h post-infection with highly and less virulent influenza A (H3N2) viruses. Viruses (designated as LVI, HVI and MPI) were derived from influenza strain virus A/Aichi/2/68 (Aichi68). LVI is Aichi68 propagated in eggs, HVI is mouse adapted Aichi68, and MPI is HVI propagated in MDCK.

overall_design: Infection: lung homogenate (mock), LVI, HVI and MPI; time of sample collection: 3 and 9 h post-infection; two biological replicates for each group.

first: Fransiskus

middle: X

last: Ivan

first: Roy

last: Welsch

first: Jagath

middle: C

last: Rajapakse

middle: T


title: Genomewide expression profile of wire-injured carotid arteries harvested from either miR-126+/+/ApoE-/- or miR-126-/-/ApoE-/- mice during neointima development

status: Public on Feb 19 2014

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: We tried to identify mRNA targets of miR-126 involved in neointima formation in mice with an atherogenic background. Genome-wide expression profiling was carried out in wire-injured carotid arteries of miR-126+/+/ApoE-/- (control group) and miR-126-/-/ApoE-/- (target group) mice on western-type diet. RNA was isolated after 14 days following vascular injury (n=4 each group). Agilent SurePrint G3 Mouse GE Microarrays (8x60K format) were used in combination with a one-color based hybridization protocol. Signals on the microarrays were detected using the Agilent DNA Microarray Scanner. Differential gene expression was identified by applying appropriate biostatistics to the data set. GeneSpring GX11 analysis software was used to normalize and analyze the raw data

overall_design: Genomewide expression profile of miR-126+/+/ApoE-/- and miR-126-/-/ApoE-/- mice were measured at 14 days after vascular injury . 4 animals per group were used.

first: Malihe

last: Nazari-Jahantigh

first: Yuanyuan

last: Wei


title: Microarray profiling of gene expression in ageing murine skeletal muscles

status: Public on Jan 10 2014

city: Perth

first: Tea

last: Shavlakadze

state: WA

address: Anatomy Building, Hackett entrance number 2

department: School of Anatomy, Physiology and Human Biology

country: Australia

institute: the University of Western Australia

summary: We have previously documented a time-course of sarcopenia development in female C57Bl/6J mice, with significant loss of quadriceps muscle mass by 24 m that is more pronounced by 27-29 m. The present study used gastrocnemius muscles from female C57Bl/6J mice aged 3, 15, 24 and 29 months to investigate the expression of genes that coincide with, or potentially precede, muscle loss. The microarray analyses of ageing gastrocnemius muscle indicated that the Functional Theme Protein catabolism was first discernable in 15 and 24 age contrast and then again in the age contrast between 24 m and 29 m.  A common Functional Theme in all age contrasts from the microarray analysis was extracellular matrix suggesting continual remodeling of skeletal muscle during ageing. Metabolic traits, particularly those involving altered fatty acid and glucose metabolism were apparent in the contrast between 24 m and 29 m. This may reflect inefficiency of lipid metabolism with ageing caused by altered mitochondrial function, which has been implicated in ageing processes in other studies. There were no functional themes associated with oxidative stress, inflammation or immune cell infiltration in any age contrast, likely indicating that these factors are not primary drivers of sarcopenia. Ageing was also associated with increased global gene expression variance, consistent with generalised decreased control of gene regulation.

overall_design: Microarray profiling was performed in gastrocnemius muscles from female C57Bl/6J mice aged 3, 15, 24 and 29 months.

first: Mitchell

last: Barns

first: Cedric

last: Gondro

first: Ross

last: Tellam

first: Miranda

middle: D

last: Grounds


title: Transcriptome profiling of T84 colorectal carcinoma cells treated with receptor guanylyl cyclace C agonist (stable toxin)

status: Public on Feb 04 2014

city: Bangalore

first: Sandhya

middle: S

last: Visweswariah

state: Karnataka

address: GA-09, Dept of MRDG, Biological Sciences Building, Indian Institute of Science

department: Molecular Reproduction, Development and Genetics

country: India

institute: Indian Institute of Science

summary: Receptor guanylyl cyclase C (GC-C) is expressed in the intestinal epithelia and plays a key role in intestinal physiology. Activation of GC-C by its ligands has been shown to regulate proliferation and differentiation of enterocytes along the crypt-villus axis. This study aims to identify genes regulated by GC-C activation and elevation of cGMP in colorectal carcinoma cells. This will help understand the molecular targets and biological pathways regulated by GC-C to bring about cancer cell cytostasis.

overall_design: ST (Cy5) Vs. Control (Cy3), ST (Cy5) Vs. Control (Cy3)

first: Nirmalya

last: Basu


title: Human liver, normal adult female vs male

status: Public on Mar 07 2014

city: North Grafton

first: Arlin

middle: B

last: Rogers

state: MA

address: 200 Westoboro Road

department: Biomedical Sciences

institute: Tufts Cummings School of Vet Med

summary: Transcriptional profiling of liver gene expression in adult women and men without primary liver disease

overall_design: Female versus male. Biological replicates: 7 per sex.


title: HCT 116 cells expressing Fucci (fluorescent ubiquitination-based cell cycle indicator); G1 phase vs. S/G2/M phase

status: Public on Jan 09 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary:
Fucci-expressing HCT116 were inoculated into subcutaneous tissue or cecum of NOD/SCID mice. Four weeks after inoculation, Fucci green (mAG; S/G2/M) and red (mKO2;G1) expressing cells were isolated from implanted tumors by FACSAria sorting (BD, Biosciences).
Comparative analyses among green and red cells cultured in vivo were performed to elucidate the molecular basis of cell cycle-dependent motility control mechanism.

overall_design: The labeled cRNAs were hybridized on 4X44K Agilent Whole Human Genome dual colour Microarrays (G4112F) in two dye swap experiments, resulting in four individual microarrays.

first: Yoshinori

last: Kagawa

first: Masaru

last: Ishii


title: Cell death and regenerative proliferation pathways in hepatocellular carcinoma: The effect of furan on B6C3F1 mouse global gene expression in liver

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine the dose-dependent changes in gene expression upon exposure of B6C3F1 mice to furan in order to better understand furan’s mode of action. Adult female B6C3F1 mice were exposed to 1, 2, 4 or 8 mg/kg bw furan or vehicle control (corn oil) for three weeks and sacrificed four hours after the final exposure.

overall_design: In this study we examined the transcriptional response in liver tissue of female B6C3F1 mice exposed to furan for 3 weeks at four different doses: 1, 2, 4 or 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 4-5 biological replicates. There were a total of 25 samples included in the final analysis. We used a two-colour reference design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).

first: A

middle: F

first: Andrew

last: Williams

first: Leslie

last: Recio

first: Michael

last: Waters

first: Iain

last: Lambert

first: Carole

middle: L

last: Yauk


title: Over-expression of either MECP2_e1 or MECP2_e2 in neuronally differentiated cells (SK-N-SH)

status: Public on Jan 25 2014

city: Toronto

first: john

last: vincent

state: ON

address: 250 College Street

department: Neuroscience Research

institute: Centre for Addiction & Mental Health

summary:
Aim: to detect genes that are differentially transcribed in neuronal cells(SK-N-SH) over-expressing either of the two MECP2 isoforms, MECP2_e1 or MECP2_e2.
Methods: the human neuroblastoma cell line SK-N-SH was stably infected by lentiviral vectors over-expressing MECP2_e1, MECP2_e2, or eGFP, and were then differentiated into neurons. RNA extracted, and used for gene expression microarray analysis

overall_design: 3 replicates for MECP2_e1; 3 replicates for MECP2_e2; 3 replicates for eGFP as control; 3 replicates for MECP2_e1 with 9bp insertion mutation in N-terminal

first: John

last: Vincent

first: Marija

last: Orlic-Milacic


title: Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells.

status: Public on Jan 01 2014

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

type:
Expression profiling by array
Methylation profiling by array

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


title: Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Agilent]

summary: Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level.

overall_design: 22 samples:  1 human NPC, 2 human ESC (UNDIFF), 5 human iPSC (UNDIFF), 2 human ESC (EB_ecto), 5 human iPSC (EB_ecto), 2 human ESC (EB_mesend), 5 human iPSC (EB_mesend)

first: B

last: Mallon

first: R

last: Hamilton

first: O

middle: A

last: Kozhich

first: K

first: Y

last: Fann

first: M

last: Rao

first: P

last: Robey


title: Gene expression profile of wildtype glioblastoma cell lines and their resistant subclones

city: Amsterdam

first: Lotte

last: Hiddingh

address: De Boelelaan 1117

institute: VU University Medical Center

summary: In order to identify factors involved in TMZ-resistance, we engineered different TMZ-resistant glioblastoma cell lines. Wildtype cells were treated twice a week in duplicate with a clinically relevant concentration of TMZ (33 µM) for multiple weeks, until two individual resistant subclones were generated. Gene expression profiling was performed to identify differentially expressed genes in the resistant cells compared to their wildtype cells.

overall_design:
three wildtype glioblastoma cell lines (U87, LNZ308, Hs683) and their resistant subclones, two of each wildtype, were analyzed

The experiments were performed technically as dual channel but processed/normalized as single channel (i.e. two sample records per one raw data file). The raw data file for each sample is indicated in the sample description field but linked as Series supplementary file.

first: Thomas

last: Wurdinger


title: S. coelicolor, Control (untreated) Vs Ciprofloxacin treated

city: Powai, Mumbai

first: Sarika

last: Mehra

state: MH

address: IIT Bombay

department: Chemical Engineering

institute: IIT Bombay

summary:
Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells.
Two-condition experiment, Control Vs CIP treatment. Biological replicates: 3 control, One dye swap replicate.

overall_design: four samples and three biological replicate to study the response of S. coleicolor cells to ciprofloxacin

first: Minal

last: Patkari


title: ERG Overexpression in PC3 cells.

city: Ann Arbor

first: Christopher

last: Maher

state: MI

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

summary: Confirms functional ERG activity.

overall_design: Two-condition experiment: PC3 cells overexpressing ERG compared to PC3 cells overexpressing ERG lacking ETS domain.


title: Platelets direct monocytes differentiation into multinucleated giant foam cells with suppressive response to mycobacterial stimulus

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Co-culture of platelets with monocytes induces the forming of multinucleated giant foam cells (MP-Mac or MP-MNGCs). Compared with normal monocyte differentiated macrophages (M-Mac), the MP-MNGCs can engulf more mycobacteria with suppressed inflammatory responses (releasing more IL-10 with less TNF-gamma). Microarray analysis demonstrated that the MP-MNGCs greatly up-regulated CXCL5, PPBP, NT5E, PDPN, CXCL3 and other M2 related genes, such as ARG1, CXCL1, CD163, etc. GO analysis revealed higher cluster of genes in response to wounding and nuclear division. Immunohistochemistry studies indicated similar high expression of IL-10, CXCL5, CXCL3, PDPN and ARG1 expression in MNGCs of TB granuloma, which indicated that phagocytosis of activated platelets by monocytes might be involved in pathogenesis of TB granuloma.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Yonghong

last: Feng

first: Anca

last: Dohoi

first: Stefan

middle: H

last: Kaufmann


title: Aryl hydrocarbon receptor senses bacterial pigmented virulence factors and orchestrates anti-bacterial defenses (part 2)

summary: The aryl hydrocarbon receptor (AhR) is a highly conserved ligand-dependent transcription factor that senses environmental toxins and endogenous ligands, thereby inducing detoxifying enzymes and modulating immune cell differentiation and responses. We hypothesized that AhR not only evolved to sense pollutants from the environment, but also insults of microbial origin. We demonstrate that bacterial pigmented virulence factors, namely the phenazines pyocyanin and 1-hydroxyphenazine from Pseudomonas aeruginosa and the naphthoquinone phthiocol from Mycobacterium tuberculosis, are ligands of AhR. AhR activation leads to degradation of these virulence factors and regulated cytokine and chemokine production. The relevance of AhR to host defense is underlined by heightened susceptibility of AhR-deficient mice, both to P. aeruginosa and M. tuberculosis. Our data demonstrate that AhR senses distinct bacterial virulence factors and controls anti-bacterial responses. We provide evidence for a previously unidentified role for AhR as an intracellular pattern recognition receptor, and identify bacterial pigmented virulence factors as a new class of pathogen-associated molecular patterns.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Pedro

last: Moura-Alves

first: Erica

last: Houthuys

first: Kellen

last: Faé

last: Dorhoi

first: Hans

middle: J


title: Molecular bases for tumor induced exhaustion in CD8 T cells

status: Public on Dec 31 2013

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

summary: The immune system can recognize and respond to tumors. However there are some conditions in which the genetic instability and heterogeneity of tumor cells leads to the development of variants that can escape the immune system. T cells have infiltrated inside many tumors (Tumor Infiltrating Lymphocytes or TILs), but generally these TILs have lost their functional capacity and are unable to eliminate tumor cells.   We developed a model of autochthonous melanoma in mice that recapitulates some aspects of inflammatory melanoma in humans. These include a systemic Th2/Th17-oriented chronic inflammation, recruitment of immunosuppressive myeloid cells and acquisition by TILs of an “exhausted” phenotype characterized by expression of receptors for multiple inhibitory molecules. To address the molecular bases for the “exhausted” TILs phenotype, we performed transcriptomic analyses on sorted CD8 or T cells from the induced melanomas. These transcriptomes were compared to those of naïve CD8 T cells and of CD8 T cells immunized with a virus.

overall_design: 10 samples, 3 replicates for controls (untreated and infected with AdP1A), 4 replicates for TILs CD8 from melanoma

first: Grégory

last: Verdeil

first: Anne-Marie

last: Schmitt-Verhulst


title: The conserved SUMO ligase Zip3 protein associates differentially with meiotic double-strand break sites and reveals regional variations in the outcome of meiotic recombination

status: Public on Dec 18 2013

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

type: Genome binding/occupancy profiling by array

summary: In meiosis, an excess number of DNA double-strand breaks (DSBs), the initiating DNA lesion, is formed compared to the number of crossovers, one of their repair products that creates the physical links between homologs and allows their correct segregation. It is not known if all DSB hotspots are also crossover hotspots, or if the ratio between DSB and crossovers varies with the chromosomal location. Here, to systematically investigate variation in the DSB/crossover ratio, we have established the genome-wide map of the Zip3 protein binding sites in budding yeast meiosis. We show that Zip3 associates with DSB sites when these are engaged into repair by crossing over, and that Zip3 binding frequency at DSB reflects its tendency to be repaired as a crossover. We further show that the relative amount of Zip3 per DSB varies with the chromosomal location and identify chromosomal features associated with high or low Zip3 per DSB ratio. Among these is the negative regulation by proximity to a centromere and positive by the proximity to axis-associated sequences. This work opens interesting perspectives to understand the role of these extra DSB that are not frequently used for crossover and our findings may extend to mammals that have a large excess of DSB compared to crossovers.

overall_design: ChIP-chip experiment in meiotic diploid SK1 yeast cells - two biological replicates

first: Valérie

last: BORDE


title: miR-27b synergizes with anticancer drugs

status: Public on Jan 07 2014

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

summary: Drug resistance, caused by complex and redundant mechanisms, is a major obstacle in cancer treatment, especially in liver and kidney cancers. Combinational therapy of miRNAs, which concurrently target multiple pathways, with anticancer drugs represent a new strategy to improve the drug response. By a systems approach, we identified that miR-27b, a miRNA deleted in liver and kidney cancers, sensitizes cancer cells to a broad spectrum of anticancer drugs in vitro and in vivo.

overall_design: Two samples transfected with nontarget miRNA control or miR-27b mimics followed by 48 hours doxorubicin treatment

first: Wenjing

last: Mu

first: Chaobo

last: Hu


title: Sca-1 expression defines different developmental stages of mouse PDC that show functional heterogeneity in the endosomal but not lysosomal TLR9 response

status: Public on Dec 21 2013

city: Bergisch-Gladbach

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Plasmacytoid dendritic cells (PDC) play an important role in innate and adaptive immunity and were shown to be identical to previously described natural IFN-α-producing cells (NIP). Here, we describe two functionally distinct PDC subpopulations that are characterized by the differential expression of stem cell antigen-1 (Sca-1; Ly-6A/E). Sca-1- PDC are mainly found in the bone marrow, appear first during development, show a higher proliferative activity and represent the more precursor phenotype. Sca-1+ PDC are mostly located in secondary lymphoid organs and show higher expression of MHC class II molecules. Sca-1- PDC give rise to a Sca-1+ subset upon activation or in response to tissue-specific factors. Interestingly, in contrast to Sca-1- PDC, Sca-1+ PDC are defective in type I IFN production upon endosomal TLR9 stimulation, whereas lysosomal signaling via TLR9 is functional in both subsets. Gene expression analysis revealed that osteopontin (Opn) is strongly upregulated in Sca-1- PDC. This data provides evidence for the molecular basis of the observed functional heterogeneity, as the intracellular isoform of Opn couples TLR9 signaling to IFN-α expression. Taken together, our results indicate that Sca-1- PDC are an early developmental stage of PDC with distinct innate functions representing the true murine NIP.

overall_design: The dataset comprises eight samples divided into two sample groups consisting of Sca-1(-) and Sca-1(+) PDCs collected from in vitro culture of differentiated bone marrow precursor cells using mFlt3-L

first: Marina

last: Niederquell

first: Andrzej

last: Dzionek

first: Ian

last: Johnston

first: Marco

last: Colonna

first: Stefanie

last: Kurig

first: Jens

last: Fischer


title: PU.1 promotes cell cycle exit in the murine myeloid lineage associated with down-regulation of E2F1

status: Public on Dec 11 2013

city: London

first: Rodney

middle: P.

last: DeKoter

address: 1151 Richmond Street

department: Microbiology & Immunology

institute: University of Western Ontario

summary: A doxycycline-inducible system was used to induce PU.1 expression in cultured myeloid cell lines. The parent cell line used was BN (Kamath et al., Leukemia 22:1214-1225, 2008).

overall_design: RNA was prepared from uninduced cells (3) and cells induced with 1000 ng/ml doxycycline for 72 hours (3)

first: R

last: Ziliotto

first: S

last: Podder

middle: P


title: Involvement of Nr4a in a Treg-specific transcriptional program and suppression of　Th2/Tfh response

status: Public on Dec 23 2013

city: Ichikawa

first: Takashi

last: Sekiya

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

summary: Regulatory T (Treg) cells, as central mediators of immune suppression, play crucial roles in many aspects of immune system physiology and pathophysiology. Treg cells are characterized by a distinct pattern of gene expression, including upregulation of immune-suppressive genes and silencing of inflammatory cytokine genes. However, the molecular mechanisms that establish and/or maintain such gene regulation in Treg cells remain largely unknown. We recently reported that Nr4a family nuclear orphan receptors are essential for the development of Treg cells. The fact that Treg cells maintain high levels of expression of all Nr4a family components suggests that they may also play critical roles beyond Treg cell development. Here, we show that Nr4a factors are essential for maintaining Treg-specific gene expression programs, mediating two defined characteristics of Treg cells: lineage stability and suppressive activity. A compound knockout mouse strain in which all Nr4a genes were specifically deleted in Treg cells developed systemic immunopathology with accelerated Th2/Tfh/IgE reactions. Treg cells in these mice showed global reduction of 'Treg signature' gene expression, including Foxp3, Il2ra and Ikzf4. These findings demonstrate that Nr4a controls a genetic program indispensable for Treg cell maintenance and function.

overall_design: mRNA from wild-type and Nr4a-deficient Treg cells were analyzed.

first: Akihiko

last: Yoshimura


title: RNA methylation destabilizes developmental regulators in murine embryonic stem cells (MoGene-2)

status: Public on Jan 06 2014

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

summary:
Recent methylome studies have located N6-methyladenosine (m6A) RNA modification on thousands of mammalian transcripts.  However, its functional mechanism remains unclear.  In this study, we examined the role of m6A methylation in mouse embryonic stem cells.
To gain an understanding of dynamic changes in cells depleted with (proposed) methyltranferases at molecular level, we examined the time-series gene expression pattern in mESC lines using microarray analysis.

overall_design:
After 0, 4 and 8 h incubation with scramble, shRNA for Mettl3 or Mettl14, mESC cells were collected and RNAs were isolated for microarray analysis using Affymetrix Genechip Mouse Gene 2.0 ST array.
After 0 h incubation with scramble, shRNA for Mettl3 or Mettl14, mESC cells were collected and RNAs were isolated for microarray analysis using Affymetrix Genechip Mouse Gene 2.0 ST array.

first: Yang

last: Wang

first: Zhaolei

last: Zhang

first: Jing

last: Zhao


title: Molecular Signatures of Neurogenesis in the Hippocampal Subgranular Zone of Rodents

status: Public on Dec 04 2013

city: Seattle

first: Jeremy

last: Miller

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary:
We sought to find molecular signatures of the SGZ cell types, and to characterize the molecular pathways and transcription factor cascades that define the neurogenic niche. We used laser capture microdissection and DNA microarrays to profile gene expression in the inner (SGZ) and outer portions of the dentate gyrus (DG).  Since the vast majority of the cells in the DG are mature granule cells, we compared the expression of the inner and outer portions to reveal molecular markers for the less numerous populations of the SGZ.
This data set is part of a larger study assessing conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates.  Using a combination of selective SGZ transcriptional profiling with laser microdissection and DNA microarrays as well as in situ hybridization (ISH), we developed an extensive molecular characterization of the mouse SGZ, identifying 367 genes enriched in the SGZ compared to mature granule neurons.  These genes displayed a wide range of cellular expression patterns reflecting the cellular milieu of the SGZ, including progenitor and dividing cells, immature granule cells, astrocytes, oligodendrocytes, and GABAergic interneurons.   We next used a comparable microarray data set in rhesus monkey that profiled the SGZ across postnatal development to identify genes related to developmentally regulated granule cell neurogenesis.  The rhesus monkey SGZ showed highly significant similarity to mouse, whereas network analysis of these data identified SGZ-enriched gene sets with different temporal profiles reflecting differential time-courses for maturation of glia and granule neurons.  One neurogenesis-related gene network showed a steady decrease in expression across postnatal rhesus development from birth to adulthood.  This temporal pattern is highly correlated with the number of proliferating cells in the dentate gyrus, and the neurogenic transcription factors Sox4 and Sox11 are central hub genes for this gene network.  A number of the genes in this network showed a similar postnatal downregulation in mouse, suggesting a general conservation of molecular mechanisms underlying developmental and adult neurogenesis in rodents and primates.
Primate data available at: http://www.blueprintnhpatlas.org/

overall_design: Brains from 10- to 11-week-old C57BL/6 male mice housed in three conditions (no running, 4 days of running, 30 days of running) were sectioned and the dentate gyrus was isolated.  For each brain, the inner granule cell layer (containing the subgranular zone) and outer GCL were separated using laser capture microdissection, and RNA from each region was collected and processed as described in the protocols.

first: Jason

last: Nathanson

first: Ed

last: Lein

first: Fred

last: Gage


title: Impact of Visceral Fat on Gene Expression Profile in Peripheral Blood Cells

first: Norikazu

last: Maeda

department: Graduate School of Medicine

institute: Osaka University

summary: We profiled gene expression in peripheral blood cells from 28 obese patients by microarray analysis and visceral fat accumulation caused the gene expression proliles especially in circadian rhythm, inflammation, oxidative stress, and immune response.

overall_design: Obesity was defined as body mass index (BMI) greater than 25 kg/m2 according to the Japanese criteria and visceral fat area (VFA) was estimated by abdominal bioelectrical impedance analysis. Subjects with type 1 diabetes mellitus, autoimmune diseases, malignant diseases, and infectious diseases were excluded. Patients treated with statin and/or thiazolidinediones were also excluded.

first: Masaya

last: Yamaoka

first: Seiji

last: Nakamura

first: Ken-ichi

last: Matsubara

first: Tohru

last: Funahashi

first: Iichiro

last: Shimomura


title: Effects of fluvastatin treatment on monocyte gene expression in SLE patients

status: Public on Mar 12 2014

city: Cordoba

first: Rosario

last: Lopez Pedrera

address: Avda. Menendez Pidal s/n

country: Spain

institute: IMIBIC

summary: The present gene expression array study of fluvastatin effects on monocytes from SLE patients show that fluvastatin has a global anti-inflammatory effect on monocytes, which includes attenuated expression of several proinflammatory cytokines, and regulated expression of molecules mediating lipoprotein signaling and cholesterol metabolism, as well as atherosclerosis and inflammatory signaling.

overall_design: Twenty seven SLE patients were given 20mg/day fluvastatin for one month. Blood samples were obtained before the starting of the treatment and at the end of treatment. Total RNA from monocytes was extracted using TRIzol reagent. RNA quality control was performed in a 2100 Bioanalyzer. Complementary RNAs from six SLE patients (four before treatment and two after treatment) were prepared for hybridization in an Agilent G4112F platform (Whole human Genome microarray 44K) using the One-color gene expression system (Agilent technologies).

first: Lopez

last: Chary


title: BEAS-2B cells: Control versus chemical exposure

status: Public on Dec 01 2013

city: Mol

first: Sylvie

last: Remy

state: Antwerp

address: Boeretang 200

country: Belgium

institute: VITO

summary: Transcriptonal profiling of BEAS-2B cells: Control versus skin sensitizers; Control versus respiratory sensitizers; Control versus non-sensitizing irritants

overall_design: Replicates: 3 biological replicates; Exposure: 10 different chemicals versus solvent, 1 exposure concentration (IC20); Exposure time: 3 different exposure time points;

first: Sandra

last: Verstraelen

first: Rosette

last: Van Den Heuvel

first: Inge

last: Nelissen

first: Jef

last: Hooyberghs

first: Greet

last: Schoeters


title: Glomerulonephritis in BXSB/MpJ-Yaa mice

city: Sapporo

first: Junpei

last: Kimura

address: Kita 18-Nishi 9, Kita-ku

department: Department of Biomedical Sciences

institute: Graduate School of Veterinary Medicine, Hokkaido University

summary: Analysis of glomeruli isolated from kidneys of 4 month male BXSB/MpJ-Yaa. The  BXSB/MpJ-Yaa mouse strain is a lupus-prone model. Results provide insight into the pathogenic mechanisms linked to glomerulonephritis in BXSB/MpJ-Yaa mice.

overall_design:
The glomeruli were isolated from 6 BXSB/MpJ-Yaa (glomerulonephritis model) and BXSB/MpJ-Yaa+ (control). 6 glomerular populations of each strain were devided into 3 groups (1 group / 2 populations). 3 glomerulonephritis models versus 3 controls analysis was performed.
BXSB/MpJ-Yaa is a recombinant inbred strain developed originally from a C57BL/6 female mouse and a SB/Le male mouse. Yaa (Y-linked autoimmune accelerator locus) localizing on the Y chromosome of BXSB/MpJ-Yaa male mice is the result of a duplication of an about 4 Mbp telomeric segment near the pseudoautosomal region of the X chromosome onto the Y chromosome. BXSB/MpJ-Yaa+ (control)  male mice carry the wild-type Y chromosome in place of the mutant Yaa-containing Y chromosome of BXSB/MpJ-Yaa male mice.

first: Osamu

last: Ichii


title: In Vitro Global Gene Expression Analyses Support the Ethnopharmacological Use of Achyranthes aspera

city: Miami

first: Subbarayan

middle: R.

last: Pochi

state: FL

department: Medicine

institute: University of Miami

summary: Examining of the global gene expression changes in cultured human pancreatic cancer cells effected by the extract of A. aspera leaves. Comparison of cells treated for 24, 48 and 72 hours with the respective controls (untreated) allowed to select key genes that may be of interest as a response markers.

overall_design: Two-condition experiment, treated vs. untreated cells at 3 time points. Biological replicates: 6 control and 6 treated replicates for 24 hours time point; 4 control and 4 treated replicated for 48 hours time point; 2 control and 2 treated replicates for 72 hours time point.

first: Pochi

last: Subbarayan

first: Malancha

last: Sarkar

first: Lubov

last: Nathanson

first: Nikesh

last: Doshi

first: Balakrishna

last: Lokeshwar

first: Bach

last: Ardalan


title: 29 untreated breast cancer cell lines vs. pool of all 29 cell lines.

status: Public on Nov 27 2013

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

country: New Zealand

institute: University of Otago, Dunedin School of Medicine

summary:
Expression profiling of 29 untreated breast cancer cell lines using Agilent 4x44K V1 (G4112F) dual color oligonucleotide microarrays
The primary study objective was to establish a research resource for comparative transcriptomic analysis of a series of commercially available breast cancer cell lines representative of diverse histopathologic and molecular subtypes, generated on the Agilent oligonucleotide platform.
A specific study objective was to perform a comparative transcriptional analysis of three cell lines established from a patient with triple negative metaplastic inflammatory breast cancer developed by Drs. Felding Habermann and Smider at the Scripps Research Institute, San Diego, CA. Cancer Res 2011;71(24 Suppl):Abstract nr PD03-07.

overall_design: Commercial cell lines were cultured in replete media using manufacturer-recommended conditions and harvested during exponential growth phase using TRIzol Reagent. Total RNA was prepared from each cell line and a pooled reference was generated containing an equimolar concentration of RNA from all cell lines. Individual cell lines were differentially labeled relative to the reference pool and hybridized to Agilent Commercial V1 4x44K oligonucleotide microarrays.

middle: E

first: Pilar

last: Ramos

first: Megan

last: Russell

first: Amy

last: Stone

first: Amanda

last: Willis

first: Brunhilde

last: Felding-Habermann

first: Vaughn

middle: V

last: Smider


title: Gene expression profiling of liver-specific NCOR knockout mice

status: Public on Nov 25 2013

city: Houston

first: Zheng

last: Sun

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: We profiled gene expression in livers depleted of NCOR (nuclear receptor corepressor) along with wild-type livers as control.

overall_design: NCOR floxed mice were intravenously injected with adeno-associated virus (AAV) expressing Cre or GFP. Livers were harvested at 2-weeks post-injection at 5pm (ZT10). Total RNA was extracted and hybridized to Affymetrx Mouse Gene 2.0 array.

first: Bin

last: Fang

first: Mitchell

last: Lazar


title: Basal-like Breast Cancer Cells Induce Phenotypic and Genomic Changes in Macrophages

status: Public on Nov 15 2013

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: Basal-like breast cancer (BBC) is an aggressive subtype of breast cancer that has no biologically targeted therapy. The interactions of BBCs with stromal cells are important determinants of tumor biology, with inflammatory cells playing well-recognized roles in cancer progression. Despite the fact that macrophage–BBC communication is bidirectional, important questions remain about how BBCs affect adjacent immune cells. This study investigated monocyte-to-macrophage differentiation and polarization and gene expression in response to coculture with basal like versus luminal breast cancer cells. Changes induced by coculture were compared with changes observed under classical differentiation and polarization conditions. Monocytes (THP-1 cells) exposed to BBC cells in coculture had altered gene expression with upregulation of both M1 and M2 macrophage markers. Two sets of M1 and M2 markers were selected from the PCR profiles and used for dual immunofluorescent staining of BBC versus luminal cocultured THP-1s, and cancer-adjacent, benign tissue sections from patients diagnosed with BBCs or luminal breast cancer, confirming the differential expression patterns. Relative to luminal breast cancers, BBCs also increased differentiation of monocytes to macrophages and stimulated macrophage migration. Consistent with these changes in cellular phenotype, a distinct pattern of cytokine secretion was evident in macrophage–BBC cocultures, including upregulation of NAP-2, osteoprotegerin, MIG, MCP-1, MCP-3, and interleukin (IL)-1b. Application of IL-1 receptor antagonist (IL-1RA) to cocultures attenuated BBC-induced macrophage migration. These data contribute to an understanding of the BBC-mediated activation of the stromal immune response, implicating specific cytokines that are differentially expressed in basal-like microenvironments and suggesting plausible targets for modulating immune responses to BBCs.Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and/or stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk. Methods: We studied gene expression data in cancer-adjacent tissue from 158 BC patients. Complementary in vitro cocultures were used to study cell-cell communication between fibroblasts and specific breast cancer subtypes. Results: Our results suggest that intrinsic tumor subtypes are reflected in histologically normal cancer-adjacent tissue. Gene expression of cancer-adjacent tissues shows that triple negative (Claudin-low or Basal-like tumors) exhibit increased expression of genes involved in inflammation and immune response. While such changes could reflect distinct immune populations present in the microenvironment of different breast cancer subtypes, altered immune response gene expression was also observed in cocultures in the absence of immune cell infiltrates, emphasizing that these inflammatory mediators are secreted by breast-specific cells. In addition, while triple negative BCs are associated with upregulated immune response genes, Luminal breast cancers are more commonly associated with estrogen-response in adjacent tissues. Conclusions: Specific characteristics of BCs are reflected in the surrounding benign tissue. This commonality between tumor and surrounding tissue may underlie second primaries and local recurrences. Biomarkers derived from cancer-adjacent tissue may be helpful in defining personalized surgical strategies or in predicting recurrence risk.

overall_design: reference x sample

first: Delisha

last: Stewart

first: Yinmeng

last: Yang

first: Liza

last: Makowski


title: Gene expression profiling of Akt3 over-expressing breast cancer cells after estrogen and tamoxifen treatment

city: Stockton

first: Jesika

last: Faridi

state: California

address: 751 Brookside Road

department: Physiology & Pharmacology

institute: University of the Pacific

summary: The aim of this study is to identify the differentially expressed genes in upon Akt3 over-expression after estrogen and tamoxifen treatment.

overall_design: RNA were extracted from three independently treated respective breast cancer cell lines and processed for further microarray experiments.

first: Kshama

last: Mehta

first: Khyati

middle: N

last: Shah


title: Transcriptional responses to engineered nanoplatforms for drug delivery in primary human aortic endothelial cells.

status: Public on Dec 20 2013

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary:
This study evaluated transcriptional effects of nanomaterials that have been proposed for use as platforms for drug delivery. We tested SiO2 that had been surface modified to have a positive zetapotential of different geometries as well PAMAM dendrimers with different surface charges. We tested these materials on human aortic endothelial cells (HAECs) since we were interested in determining if there was a toxicogenomic response in endothelial cells that may come into contact with drug delivery nanoplatforms.
The most pronounced transcriptional response resulted from the SiO2 treatement - the most prevelant responses were cell cycle, lipid metabolism and pro-inflammatory responses - with fewer responses from the PAMAM dendrimers.  The lipid metabolism responses may relate to teh positive surface character as this response was not observed in the G3.5-COOH dendrimers. Indeed, the G3.5-COOH dendrimers were non-toxic and did not demonstrate any consistent transcriptional response.

overall_design:
Primary human aortic endothial cells (HAECs) were grown in 6 well plates (in 2 ml of medium) until they were >80% confluent by visual inspection. Daily media changes allowed continued growth for HAECs that demonstrate contact inhibition. The cells were then incubated with nanomaterials: surface modified SiO2 with worm and sphere goemetries (the spheres were 200 nm in diameter and the worm's cylindrical diameter 200 nm and the length was ~ 1000 nm); and PAMAM dendrimers with different surface charges (G3.5-COOH are negative and G4-NH2 are positive). RNA was collected after 4 and 24 hrs (one SiO2 worm sample was at 1.5 hrs due to space available on the 4-pack microarrays).
Triplicate biological samples (indicated by the 'a', 'b', and 'c' designations in the sample names) were evaluated for gene expression changes by microarray analysis.


title: Gene expression signature of subcutaneous abdominal and subcutaneous gluteal adipose tissue

city: Hamburg

first: Sandra

last: Gehrke

address: Unnastraße 48

department: Applied Skin Biology

institute: Beiersdorf AG

summary: To identify genes differentially expressed in abdominal and gluteal adipose tissue, we determined the mRNA transcription profile of 10 abdominal and 10 gluteal female adipose tissue sections using Agilent Whole Human Genome Microarrays.

overall_design: RNA of 10 subcutaneous abdominal and 10 subcutaneous gluteal fat depot samples was processed by Miltenyi Biotech GmbH (Bergisch Gladbach, Germany) and loaded on single-color Whole Human Genome 4x44K microarrays (G4112F) from Agilent Technologies.

first: Marc

last: Winnefeld

first: Sabine

last: Hagemann


title: A Global Transcriptome Analysis of BMSC Senescence

status: Public on Nov 21 2013

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Bone marrow stromal cells (BMSCs) can be expanded by serial passage, but expansion is limited by cell senescence.  The nature of changes associated with BMSC serial passages was assessed. Transcriptome analysis of 10 early and 15 late passage samples from 5 subjects revealed 2193 differentially expressed genes; those highly expressed in early passage cells were overrepresented in skeletal system development, embryonic morphogenesis, tube morphogenesis, etc, while those highly expressed in the late passage BMSCs were overrepresented in nucleosome assembly; chromatin assembly, DNA packaging, etc. 57 BMSC samples from 7 donors were further analyzed for the transition from an early to late passage; 155 genes were highly correlated with BMSC senescence and a set of 24 genes was predictive of BMSCs lifespan. The change from an early to a late passage molecular signature occurred between passage 3 and 5. In contrast, senescence associated beta-galactosidase staining began to increase after passage 6 or 7 and colony formation efficiency began to fall after passage 7. These data indicated that the onset of molecular changes associated with BMSC passage varied among individuals and preceded changes in commonly used indicators of BMSC senescence. The set of 24 BMSC lifespan predictive genes will be useful in assessing the quality of clinical BMSC products.

overall_design: We performed gene expression profiling on serial passages of BMSCs from 7 healthy donors (09FC20, 09FC37, 09FC43, 09FC44, 09FC45, 09FC49, and W10003).


title: Der f/SEB-induced skin inflammation

status: Public on Dec 10 2013

city: La Jolla

first: Tomoaki

last: Ando

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease. We recently described an animal model in which repeated epicutaneous applications of a house dust mite extract and Staphylococcal enterotoxin B induced eczematous skin lesions. In this study we showed that global gene expression patterns are very similar between human AD skin and allergen/staphylococcal enterotoxin B–induced mouse skin lesions, particularly in the expression of genes related to epidermal growth/differentiation, skin barrier, lipid/energy metabolism, immune response, or extracellular matrix. In this model, mast cells and T cells, but not B cells or eosinophils, were shown to be required for the full expression of dermatitis, as revealed by reduced skin inflammation and reduced serum IgE levels in mice lacking mast cells or T cells (TCRb-/- or Rag1-/-). The clinical severity of dermatitis correlated with the numbers of mast cells, but not eosinophils. Consistent with the idea that T helper type 2 (Th2) cells play a predominant role in allergic diseases, the receptor for the Th2-promoting cytokine thymic stromal lymphopoietin and the high-affinity IgE receptor, FceRI, were required to attain maximal clinical scores. Therefore, this clinically relevant model provides mechanistic insights into the pathogenic mechanism of human AD.

overall_design: A total of six samples were analyzed. Back skin samples from healthy or AD-induced C57BL/6, PLC-beta 3 KO (C57BL/6 background), and NC/Nga mice were collected for total RNA extraction. Pooled RNA from 2-4 mice per condition were used for analysis.

first: Wenbin

last: Xiao

first: Peisong

last: Gao

first: Siavash

last: Namiranian

first: Kenji

last: Matsumoto

first: Yoshiaki

last: Tomimori

first: Hong

last: Hong

first: Hirotaka

last: Yamashita

first: Miho

last: Kimura

first: Jun-ichi

last: Kashiwakura

first: Haley

last: Glatthorn

first: Brandon

last: Dolan

first: Tissa

last: Hata

last: Izuhara

first: Michael

last: Gurish

first: Axel

last: Roers

first: Nicholas

middle: M

last: Rafaels

first: Kathleen

middle: C

last: Barnes

first: James

last: Lee

first: Stephen

last: Galli

first: Colin

last: Jamora

first: Yuko

last: Kawakami

first: Toshiaki


title: Expression data from mouse liver over-expressing either GFP alone or biotinylated-TRb1 and GFP

city: Boston

first: Preeti

last: Ramados

address: 3 Blackfan Cir

institute: Beth Israel Deaconess Medical Center

summary:
We over-expressed biotinylated-thyroid hormone receptor beta 1 (TRb1) in mouse liver using an adenovirus in order to perform ChIP-seq experiments. These microarrays were performed to determine gene expression changes in response to tri-iodothyronine (thyroid hormone; T3) stimulation. A control GFP adenovirus was used and gene expression from these livers was also done as a comparison.
We performed microarrays from Ad-GFP-infected propylthiouracil (PTU)-fed livers injected with either saline or T3 and Ad-TRb1-GFP infected livers injected with either saline or T3.

overall_design: RNA was extracted from livers of biotin ligase (BirA)-expressing mice that had been infected with either Ad-GFP or Ad-TRb1, fed with PTU for 3 weeks followed by saline or T3 injections for 4 consecutive days.

first: P

last: Ramadoss

first: B

last: Abraham

first: L

last: Tsai

first: Y

last: Zhou

first: R

last: Costa-e-Sousa

first: F

last: Ye

first: M

last: Bilban

first: K

last: Zhao

first: A

last: Hollenberg


title: Gene epxression profiling in murine bone marrow Lin- cells transduced with BCR-ABL and/or IRF8 followed by Flt3L culture for 5 days

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To understand the effect of BCR-ABL and IRF8 on gene expression pattern during in vitro dendritic cell differentiation, microarry analysis was performed.

overall_design: Murine bone marrow Lin- cells were transduced with retroviruses carrying human BCR-ABL cDNA and/or mouse Irf8 cDNA, and then cultured with Flt3L for 5 days. Two independent experiments were performed.

first: Tomoya

last: Watanabe

first: Akira

last: Nishiyama


title: HNSCC Cells: ctrl vs six tumour lethal miRNAs transfected

status: Public on Nov 06 2013

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary:
Some microRNAs have antiproliferative effects in cells and are believed to act as tumour suppressors. We used a retroviral human microRNA expression library to identify six microRNAs, miR-181a, miR-323, miR-326, miR-342, miR345 and miR-371, that induce antiproliferative effects in head and neck squamous cell carcinoma (HNSCC), but do not in normal oral keratinocytes. By gene expression profilling we showed that the ataxia telangiectasia mutated (ATM) gene is a common target for three of these microRNAs.
Transcriptional profilling of head and neck cancer cells comparing transiently transfected with either one of the six miRNAs to the cells transfected with a control vector.

overall_design: One-condition experiment, ctrl vs miRNA transfected, Biological replicates: 2 replicates for each miRNA transfected, 4 replicates for ctrl transfected

first: Marlon

last: Lindenbergh-van der Plas

first: Sanne

last: Martens-de Kemp

first: Michiel

last: de Maaker

first: Wessel

last: van Wieringen

first: Bauke

last: Ylstra

first: Reuven

last: Agami

first: Francesco

last: Cerisoli

first: René

last: Leemans

first: Boudewijn

last: Braakhuis

first: Ruud

last: Brakenhoff


title: Gene expression in response to fluconazole vs. the combination of  fluconazole and berberine

status: Public on Nov 14 2013

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

institute: PLA General Hospital

summary: Transcriptional profiling of Candida albicans comparing fluconazole treated cells with fluconazole- and berberine-treated cells, as well untreated cells with berberine treated cells

overall_design: Three different clinical FLC-resistant strains (0304103, 01010 and 632) were selected to carry out the expression profile microarray. Two-condition experiment, fluconazole-treated vs. fluconazole- and berberine-treated cells, and untreated cells vs. berberine-treated cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested. One replicate per array.

first: Yi

last: Xu

first: Yan

last: Wang

first: Yuanying

last: Jiang


title: Expression profiling of TSC2 overexpressing cells

status: Public on Nov 05 2013

city: Bangalore

first: Shalmali

last: Pradhan

state: Karnataka

address: Indian Institute of Science

department: MRDG

institute: Indian Institute of Science

summary: In order to identify the genes regulated by TSC2, gene expression profiling of two clones stably overexpressing TSC2 was performed.

overall_design: The gene expression profiles of two stable transfectant clones overexpressing the full-length TSC2 in KB cells were compared with the gene expression profile of a vector control clone carrying an empty plasmid.

first: Mohammad

middle: I

last: Rather

first: Ankana

last: Tiwari

first: Arun

last: Kumar


title: Quorum sensing in CD4+ T cells homeostasis : IL-2 coordinates the interplay between IL-2p and regulatory T cells.

status: Public on Nov 01 2013

city: Paris

first: Antonio

middle: Angelo

last: Freitas

address: 25 Rue du Dr. Roux

department: Lymphocyte Population Biology Unit

institute: Institut Pasteur

summary: Many species of bacteria use quorum sensing to sense the amounts of secreted metabolites and adapt their growth according to their population density. We asked whether similar mechanisms would operate in lymphocyte homeostasis. We investigated the regulation of the size of Interleukin-2-producing CD4+ T-cell (IL-2p) pool using different IL-2-reporter mice. We found that in the absence of either IL-2 or regulatory CD4+ T-cells (Treg) the number of IL-2p-cells increases. Administration of IL-2 decreases the number of cells of the IL-2p-cell subset and pertinently, abrogates their ability to produce IL-2 upon in vivo cognate stimulation, while increasing Treg-cell numbers. We propose that control of the IL-2p-cell numbers occurs via a quorum-sensing-like feedback loop where the produced IL-2 is sensed by both the activated CD4+ T-cell pool and by Treg-cells, which reciprocally regulate cells of the IL-2p-cell subset. In conclusion, IL-2 acts as a self-regulatory circuit integrating the homeostasis of activated and regulatory T cells as CD4+ T-cells restrain their growth by monitoring IL-2 levels thereby preventing uncontrolled responses and autoimmunity.

overall_design: 2 populations of conventional CD4+ T cell are analysed. 5 replicates for each. GFP- is the control one.

first: Inês

middle: F

last: Amado

first: Julien

last: Berges

first: Rita

last: JLuther

first: Marie-Pierre

last: Mailhé

first: Sylvie

last: Garcia

last: Bandeira

first: Casey

last: Weaver

first: Adrian

last: Liston

last: AFreitas


title: Gene expression profiles of C57BL/6 murine hepatocytes, murine embryonic stem cells (D3) and murine hepatocyte-reprogrammed induced Tissue Stem cells (iTSCs)

status: Public on Oct 29 2013

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary: We have recently developed a new generation of induced stem cells that we have called “induced Tissue Stem cells” (iTSCs) which are generated by using low doses of non-integrative vectors encoding several embryonic reprogramming factors permitting to de-differentiate the cells without passing through a pluripotent state. ITSCs are thus multipotent stem cells rather than pluripotent stem cells. Using this technology we have produced endodermic iTSCs by de-differentiation of murine hepatocytes and shown that they are able to differentiate in vitro and in vivo into tissues restricted to endodermic layers. We report the gene expression profiles of two subclones of murine hepatocytes-reprogrammed iTSCs and of hepatocytes parental cells and murine embryonic stem cells (D3).

overall_design: Adherent liver cultures were established from 6 to 8 week old mice and one million of hepatocytes were infected with adenovirus encoding Oct4, Sox2, cMyc and Klf4. After 5 days of infections, cells were manually pooled and plated on mitomycin C-arrested Mouse Embryonic fibroblasts (MEF) in daily changed ES cell culture medium. In this manner, more than 50 colonies have been isolated and for two of them (clones 3 and 6), single cells were added in a 96-well cell culture plate for subcloning. Two subclones ; 6.6 and 3.8 were evaluated by microarray. The transcriptome was analyzed with Affymetrix microarray technology (GeneChip ® Mouse Gene 2.0 ST Array) and the data were normalized by the RMA method and annotated with Partek GS and R Bioconductor softwares.

first: Christophe

last: Desterke

first: Frank

last: Griscelli

first: Annelise

last: Bennaceur-Griscelli


title: Polarization profiling of renal macrophages in stone model mice

status: Public on Oct 22 2013

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

institute: Nagoya City University Graduate School of Medical Sciences

summary: We recently reported elimination of renal crystals and migration of macrophages (Mφ) around crystals in hyperoxaluric mice, suggesting Mφs might eliminate crystals. Mφs are of 2 phenotypes: inflammatory (M1) and anti-inflammatory (M2). Because M2Mφs are considered to be involved in tissue repair and regeneration, we focused attention on their suppressive role in renal crystal formation. Hence, we investigated the gene array profiling of renal macrophages in stone model mice and CSF-1-deficient stone model mice.

overall_design: B6C3Fe a/a-Csf1op/J wild type/homozygous mice were admistered 80mg/kg gyyoxylate (GOX) for 6days, then the kidneys were extracted and sorted CD11b+/CD11c+ macrophages using autoMACS. The gene expression of WT- and op/op-macrophages were investigated using bone marrow derived M1/M2 macrophages as controls.

first: Hiroshi

last: Kitamura


title: Sex-specific control of CNS autoimmunity by p38 MAPK signaling in myeloid cells

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

summary: Objective: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system (CNS), characterized by a global increasing incidence driven by relapsing-remitting disease in females. p38 MAP kinase (MAPK) has been described as a key regulator of inflammatory responses in autoimmunity, but its role in the sexual dimorphism in MS or MS models remains unexplored. Methods: Toward this end, we used experimental autoimmune encephalomyelitis (EAE), the principal animal model of MS, combined with pharmacologic and genetic inhibition of p38 MAPK activity and transcriptomic analyses. Results: Pharmacologic inhibition of p38 MAPK selectively ameliorated EAE in female mice. Conditional deletion studies demonstrated that p38α signaling in macrophages/myeloid cells, but not T cells or dendritic cells, recapitulated this sexual dimorphism. Analysis of CNS inflammatory infiltrates showed that female, but not male mice lacking p38α in myeloid cells exhibited reduced immune cell activation compared with controls, while peripheral T cell priming was unaffected in both sexes. Transcriptomic analyses of myeloid cells revealed differences in p38α-controlled transcripts comprising female- and male-specific gene modules, with greater p38α dependence of pro-inflammatory gene expression in females. Interpretation: Our findings demonstrate a key role for p38α in myeloid cells in CNS autoimmunity and uncover important molecular mechanisms underlying sex differences in disease pathogenesis. Taken together, our results suggest that the p38 MAPK signaling pathway represents a novel target for much needed disease modifying therapies for MS

overall_design: WT vs. p38alphaCKO macrophages, male vs. female

first: D

first: R

last: Noubade

first: J

last: Dragon

first: K

last: Otsu

first: M

last: Rincon

first: C

last: Teuscher


title: Gene Expression Analysis of Host Immune Responses in the UV inactivated SARS-CoV-immunized mice following Lethal SARS-CoV Infection

status: Public on Oct 01 2013

city: Shinnjuku-ku

first: Naoko

last: Iwata-Yoshikawa

state: Tokyo

address: 1-23-1 Toyama

institute: National institute of infectious diseases

summary: To better understand the biological pathways by which UV inactivated SARS-CoV-induced pulmonary eosinophilia occurs, we examined global transcriptional changes in mouse lungs.

overall_design: Female BALB/c mice were used at 21 weeks of age.  Mice were subcutaneously immunized with UV inactivated SARS-CoV (UV-V) or UV-V and Toll like receptor (TLR) ligands at 6 and 1 weeks prior to mouse-adapted SARS-CoV (n=6 per group).  PBS was used in three mice as control immunization.  Mice were intranasally challenged with 1E+6TCID50 in 30μL.  Mice were sacrificed and collected lungs at 1 days after challenge. These mice were used for the analysis of microarray.

first: N

first: A

last: Uda

first: Y

last: Sato

last: Tsunetsugu-Yokota

first: T

last: Sata

first: H

last: Hasegawa

last: Nagata


title: Transcriptome analysis of a clinical phase Ia Mycobacterium bovis BCG vaccination study (sex and age matched European (Caucasian) males, 25-35 years, performed in Germany)

status: Public on Oct 31 2013

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
Global transcriptome analyses provide an excellent basis for the identification and definition of biomarkers with high relevance in infection processes, therapeutic intervention and protective immunity. The measurement applies three different state of the art transcriptomic technologies for global expression profiling to vaccine development. Different microarray platforms in conjunct to next generation sequencing (NGS) will build the basis for comparative approaches, such as up-down classification and correlation coefficients. This measurement is based on Agilent microarrays and a clinical trial phase Ia study with M. bovis BCG vaccination, using two different tuberculin skin test (PPD negative and PPD positive) groups.
• Surrogate measurement using PBMCs
• 4 time points: d0 (naïve, pre-immunization) and d29, d57, d180 post m. bovis BCG immunization
• Responses of PPD negative and PPD positive study groups
• Group size of approximately 9 individuals
European network of vaccine research and development (TRANSVAC)

overall_design: Microarray experiments were performed as single-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays

first: Stefan

last: Kaufmann


title: Gene expression data in Mouse Lung Epithelial cells MLE-12 transfected with inhibitors and precursors for miR-30a, miR-30d, miR-23b, miR-125 and miR-337, miR-466a, miR466d, miR-476c, respectively

status: Public on Oct 18 2013

first: christian

middle: lacks

last: lino cardenas

address: 185 Cambridge st Room 3224

department: division of cardiovascular

institute: Massachusetts general hospital-Harvard medical school

summary: The regulation of gene expression in cells, including by microRNAs (miRNAs), is a dynamic process. Current methods for identifying microRNA targets by combining sequence, miRNA and mRNA expression data do not adequately utilize the temporal information and thus miss important miRNAs and their targets. We developed a new method, mirDREM, that uses probabilistic modeling to reconstruct dynamic regulatory networks which explain how temporal gene expression is jointly regulated by microRNAs and transcription factors (TFs). We used mirDREM to study the regulation of postnatal lung development in mice. The reconstructed network for this process identified several known miRNAs and TFs and provided novel predictions about additional miRNAs and the specific developmental phases they regulate. Microarray data of Mouse Lung Epithelial cells MLE-12 after transfection with inhibitors for miR-30a, miR-30d, miR-23b and miR-125 and with precursors for miR-337, miR-466a, miR466d and miR-476c. The results provide a general insight into the gene expression profile which was modulated by the inhibition or overexpression of these microRNAs. We experimentally validated several predictions and show that miR-30d, miR-30a, and miR-467c are new regulators of proliferation in lung cells. Our analysis establishes new links between identified miRNAs and lung diseases, supporting recent evidence that such diseases may represent reversal of lung differentiation.

overall_design: We first analyzed the endogenous expression of miR-30a, miR-30d, miR-23b, miR-125, miR-337, miR-466a, miR466d and miR-476c in MLE-12 cells. Then, we transfected the MLE-12 cells with inhibitors ( miR-30a, miR-30d, miR-23b and miR-125) for the highly expressed and precursos for those that were almost undetectable (miR-337, miR-466a, miR466d and miR-476c). RNA level of the 8 microRNAs was verify by qRT-PCR in order to  validate the transfection efficiency. Finally, 0.5ug of total RNA was used to performe the gene expression microarrays for each condition

first: Christian

middle: L

last: Cardenas

first: Kusum

last: Pandit

first: Naftali

last: Kaminski


title: Intestinal gene expression in 10-day Giardia duodenalis GS infected mice

status: Public on Oct 21 2013

city: Washington

first: Steven

last: Singer

state: DC

address: 37th & O Sts, NW

department: Biology

institute: Georgetown University

summary:
C57BL/6 mice were infected with the GS strain of G. duodenalis and total RNA prepared from the duodenum on day 10. Age matched controls were compared using Affy chips to determine changes in gene expression induced by infection.
The majority of induced transcripts are invlved in antibody production. Genes exhibiting the greatest increase in expression are all mast cell transcripts.

overall_design: This is a 4X4 comparison, 4 infected mice and 4 uninfected mice

first: Erenst

last: Tako


title: TEL-JAK2 dependent transcriptome

status: Public on Sep 28 2013

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

institute: Institut Curie

summary:
TEL-JAK2 is a fusion oncogene resulting from a t(9;12) chromosomal translocation in T-ALL, translated as a constitutively activated TEL-JAK2 tyrosine kinase. Mice carrying a TEL-JAK2 transgene develop T-ALL.
Gene deregulated in TEL-JAK2 T-ALL cells as compared to  mouse thymocytes were identified

overall_design: Leukemic cells were collected from the thymus of terminally-ill  TEL-JAK2 mice; thymocytes were collected from the thymus of 2 months-old mice. All mice on C57B/6 background. RNA was extracted from each sample and processed for hybridization to Affymetrix arrays.

first: J

last: Ghysdael


title: Relationship of mammographic density and gene expression: analysis of normal breast tissue surrounding breast cancer

city: Chapel Hill

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

institute: University of North Carolina at Chapel Hill

summary: Purpose: Previous studies of breast tissue gene expression have demonstrated that the extratumoral microenvironment has substantial variability across individuals, some of which can be attributed to epidemiologic factors.  To evaluate how mammographic density (MD) and breast tissue composition relate to extratumoral microenvironment gene expression, we used data on 121 breast cancer patients from the population-based Polish Women’s Breast Cancer Study.Design: Breast cancer cases were classified based on a previously reported, biologically-defined extratumoral gene expression signature with two subtypes: an Active subtype, which is associated with high expression of genes related to fibrosis and wound response, and an Inactive subtype, which has high expression of cellular adhesion genes. MD of the contralateral breast was assessed using pre-treatment mammograms and a quantitative, reliable computer-assisted thresholding method. Breast tissue composition was evaluated based on digital image analysis of tissue sections. Results:The Inactive extratumoral subtype was associated with significantly higher percentage mammographic density (PD) and dense area (DA) in univariate analysis (PD: p=0.001; DA: p=0.049) and in multivariable analyses adjusted for age and body mass index (PD: p=0.004; DA: p=0.049).  Inactive/higher MD tissue was characterized by a significantly higher percentage of stroma and a significantly lower percentage of adipose tissue, with no significant change in epithelial content.   Analysis of published gene expression signatures suggested that Inactive/higher MD tissue expressed increased estrogen response and decreased TGF-ß signaling. Conclusions:By linking novel molecular phenotypes with MD, our results indicate that MD reflects broad transcriptional changes, including changes in both epithelia- and stroma-derived signaling.

overall_design: reference x sample

first: Xuezheng

last: Sun

first: Aleix

last: Prat

middle: A


title: Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors [Expression array]

status: Public on Oct 11 2013

city: Hanover

first: Gavin

middle: D

last: Grant

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine

summary: We identified the cell cycle-regulated mRNA transcripts genome-wide in the osteosarcoma derived U2OS cell line.  This resulted in 2,140 transcripts mapping to 1,871 unique cell cycle-regulated genes that show periodic oscillations across multiple synchronous cell cycles.  We identified genomic loci bound by the G2/M transcription factor FOXM1 by Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associated these with cell cycle-regulated genes.  FOXM1 was bound to cell cycle-regulated genes with peak expression in both S phase and G2/M phases.  ChIP-seq genomic loci were shown to be responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase.  Analysis of ChIP-seq data from a panel of cell cycle-transcription factors (E2F1, E2F4, E2F6, and GABPA) from ENCODE and ChIP-seq data for the DREAM complex, found that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors.  These data identify the cell cycle regulated genes in a second cancer derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle.

overall_design: Cell cycle-regulated gene expression identified from three double thymidine time courses and one thymidine nocodazole time course.

first: Michael

last: Whitfield


title: Gene expression of the human choroid plexus epithelium (CPE)

status: Public on Sep 27 2013

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

institute: Netherlands Institute for Neuroscience

summary: We investigated the gene expression of the human CPE.We isolated CPE cells from healthy human donor choroid plexus tissues with laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

overall_design: We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 7 replicates of human CPE samples from 7 different donors.

first: Arthur

last: Bergen


title: Sub-chronic forestomach transcriptional response in adult male MutaTMMouse following oral exposure to benzo(a)pyrene

city: Ottawa

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

summary: Benzo(a)pyrene is a well-established human carcinogen in humans and rodents. In the present study, we sought to determine the dose- and time-dependent changes in gene expression upon oral exposure to benzo(a)pyrene. Adult male MutaTMMouse were exposed to three doses of benzo(a)pyrene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the forestomach transcriptional response of male mice exposed to BaP for 28 days at three different doses, including D1 (25 mg/kg BW/day), D2 (50 mg/kg BW/day), and D3 (75 mg/kg BW/day) and vehicle control.  Each dose group was examined 72 hours following the final exposure.  Each dose group and time point had 4-5 biological replicates. There were a total 17 samples (arrays) included in the final analysis using a two-colour reference design.

first: Andrew

last: Williams

first: Sabina

last: Halappanavar

first: Charles

last: Guo

first: Carole

last: Yauk

first: Paul

last: White


title: Gene expression of the choroid plexus epithelium (CPE)

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome analysis of a clinical phase Ib Mycobacterium bovis BCG vaccination study (sex and age matched African males, 25-35 years, performed in South-Africa)

first: Hans-Joachim

last: Mollenkopf

summary:
Global transcriptome analyses provide an excellent basis for the identification and definition of biomarkers with high relevance in infection processes, therapeutic intervention and protective immunity. The measurement applies three different state of the art transcriptomic technologies for global expression profiling to vaccine development. Different microarray platforms in conjunct to next generation sequencing (NGS) will build the basis for comparative approaches, such as up-down classification and correlation coefficients. This measurement is based on Agilent microarrays and a clinical trial phase Ib study with M. bovis BCG vaccination.
• Surrogate measurement using whole human blood
• 4 time points: d0 (naïve, pre-immunization) and d14, d28,d56, d168 post m. bovis BCG immunization
• Responses of PPD  positive study groups
• Group size of approximately 6 individuals
European network of vaccine research and development (TRANSVAC)

first: Stefan

middle: H

last: Kaufmann


title: Low paternal dietary folate alters the sperm epigenome and is associated with negative pregnancy outcomes

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

institute: McGill University

summary: We hypothesized that the availability of folate, a soluble B vitamin, would alter the levels of DNA methylation in spermatogenesis with consequences for the sperm epigenome and pregnancy outcomes. We fed male mice with either a folate-deficient or a folate-sufficient diet throughout life. Males fed the folate-deficient diet had offspring with increased birth defects, which included craniofacial and musculoskeletal malformations. These phenotypes corresponded to developmental genes with altered methylation in sperm. To determine if there was transmission of epigenetic effects from sires to offspring, global gene expression levels were assessed in placenta from 18.5 dpc fetuses sired by either a folate-sufficient or folate-deficient male.

overall_design: Gene expression was measured in placenta of 18.5 dpc fetuses sired by either a folate sufficient male (n=4 placentas from different litters and different fathers) or a folate deficient (FD) male (n=4 placentas from different litters and different fathers).

last: Kimmins


title: Inhibition of RUNX2 transcriptional activity blocks the proliferation, migration and invasion of epithelial ovarian carcinoma cells

status: Public on Sep 23 2013

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

department: Medicine

institute: Laval university

summary: Previously, we have identified the RUNX2 gene as hypomethylated and overexpressed in post-chemotherapy (CT) primary cultures derived from epithelial ovarian cancer (EOC) patients, when compared to primary cultures derived from matched primary (prior to CT) tumors. However, we found no differences in the RUNX2 methylation in primary EOC tumors and EOC omental metastases, suggesting that DNA methylation-based epigenetic mechanisms have no impact on RUNX2 expression in advanced (metastatic) stage of the disease. Moreover, RUNX2 displayed significantly higher expression not only in metastatic tissue, but also in high-grade primary tumors and even in low malignant potential tumors. Knockdown of the RUNX2 expression in EOC cells led to sharp decrease of cell proliferation and significantly inhibited EOC cell migration and invasion. Gene expression profiling and consecutive network and pathway analyses confirmed these findings, as various genes and pathways known previously to be implicated in ovarian tumorigenesis, including EOC tumor invasion and metastasis, were found to be downregulated upon RUNX2 suppression, while a number of pro-apoptotic genes and some EOC tumor suppressor genes were induced.  Taken together, our data are indicative for a strong oncogenic potential of the RUNX2 gene in EOC progression and suggest that RUNX2 might be a novel EOC therapeutic target. Further studies are needed to more completely elucidate the functional implications of RUNX2 and other members of the RUNX gene family in ovarian tumorigenesis.

overall_design: To better understand the molecular mechanisms of RUNX2 gene action in ovarian cancer cells, we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon RUNX2 suppression in SKOV3 cells. We compared the gene expression of the previously selected clone shRNA- RUNX2-knockdown clone 3 (cl3) against the corresponding control clone. The microarray experiments were performed in duplicates, as two hybridizations were carried out for the RUNX2-suppressing cell clone against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.


title: Effects of Brazilian propolis on gene expression of stromal cells in mesenteric adipose tissue of ob/ob mice

status: Public on Sep 25 2013

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

summary: A hive product propolis has been used for folk medicine for more than 4, 000 years. So far, several line of studies demonstrated that propolis improved glucose metabolism in obese models. In this study, we inverstigated whether  propolis modulates stromal cells of mesenteric adipose tissue of ob/ob mice.

overall_design: Male ob/ob mice were inhjected with Brazilian propolis ethanol extract  (100mg/kg ip, twice a week) or vehicle for 12 weeks. Subsequently, vasucular stromal fraction was prepared from mesenteric adipose tissue. Total cellular RNA extracted from the fraction was used for microarray analysis. Biological triplicates were subjected.

first: Yoshinori

last: Naoe


title: Lipopolysaccharide-induced microRNA-146a targets CARD10 and involves in angiogenesis of human umbilical vein endothelial cells

status: Public on Sep 10 2013

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: This study was designed to explore the role of miRNA-146a (miR-146a) and its target genes in the endothelial cells. In this study we have demonstrated that lipopolysaccharide (LPS) induced upregulation of miR-146a in the human umbilical vein endothelial cells (HUVEC) and the induction was blocked by the silencing of the toll-like receptors (TLRs) adaptor molecules MyD88 and nonspecific NF-κB inhibitor BAY 11-7082. In addition, knockdown of miR-146a by transfection of the locked nucleic acid (LNA)-antimiR-146a significantly decreased the increased cell migration and tube formation induced by LPS. A combined analysis of the bioinformatics miRanda algorithms and the whole genome expression microarray of the immunoprecipitated Ago2 ribonucleoprotein complex identified 14 transcripts as the potential target genes. Subsequent transfection with miR-146a precursor pre-miR-146a into the HUVEC validated that the CARD10 was the target gene of the miR-146a both in the transcript and protein level.

overall_design: immunoprecipitation of RNA-induced silencing complexes (RISC) with an Ago2-specific monoclonal antibody followed by RNA extraction and subsequent quantification of mRNAs on microarrays was utilized to identify mRNAs that are associated with the RNA-silencing machinery and are therefore targets of cellular miRNAs. In brief, 100 μg of total protein was diluted with 200 μL of PBS buffer (pH 7.4). For each sample, 25 μL of Protein A/G plus agarose (Santa Cruz, Dallas, TX) was washed with PBS and incubated with 2 μg of rabbit anti-Ago2 (Abcam, Cambridge, MA) or rabbit normal IgG (Santa Cruz) antibodies for 2 h at 4°C. The beads containing the immobilized anti-Ago2 antibody were then added to 400 μL of diluted serum and incubated for 4 h at 4°C. The beads were washed 3 times with 1% NT-2 buffer (1% Nonidet P-40, 50 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 2 mM EDTA) and the mixture was split in half. Each sample was eluted in 600 μL of lysis/binding buffer for total RNA extraction and subsequent whole genome array experiment. Microarray analyses. Microarray experiments were performed on the total RNA samples from the Ago2 immunoprecipitate (pooling from n=4 in each group) from 1×106 HUVEC with or without 1 μg/mL LPS treatment for 24 h in the presence or absence of miR-146a knockdown by LNA-antimiR-146a or LNA-control, respectively. The procedures were carried out following the manufacturer’s protocols. Briefly, 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies) and labeled with Cy3-CTP or Cy5-CTP (PerkinElmer, Waltham, MA) during the in vitro transcription process. RNA from the experimental groups and control group was labeled by Cy5 and Cy3, respectively. A total of 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies) at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Whole Human Genome 4x44k oligo microarray (Agilent Technologies) at 60°C for 17 h. After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

first: Cheng-Shyuan

last: Rau

first: Johnson

last: Yang

first: Shao-Chun

last: Wu


title: Gene expression of the human trabecular meshwork (TM) of the eye

status: Public on Sep 12 2013

city: Amsterdam

first: Sarah

last: Janssen

summary: We investigated the gene expression of the human TM. We isolated TM cells from healthy human donor eyes. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

overall_design: We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 2 replicates of human TM samples from 2 different donors.

last: Bergen


title: Programmed cell senescence during embryonic development

city: Madrid

first: Daniel

last: Muñoz

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: CNIO

summary: Cellular senescence disables the proliferation of damaged cells and it is relevant for cancer and aging. Here, we show that cellular senescence occurs during mammalian embryonic development. Specifically, we have focused on the mouse regressing mesonephros and the endolymphatic sac of the inner ear. Senescence is characterized by SAβG activity, heterochromatinization, and proliferative arrest. Mechanistically, developmentally-programmed senescence at the mesonephros and endolymphatic sac is strictly dependent on p21, but independent of DNA damage, p53 or other cell cycle inhibitors, and it is regulated by the TGFβ/SMAD and PI3K/FOXO pathways. Developmentally-programmed senescence is followed by macrophage infiltration and clearance of senescent cells. Abrogation of senescence by p21 deletion is only partially compensated by apoptosis and originates detectable developmental abnormalities. Importantly, high levels of p21 are also associated to the regressing mesonephros and endolymphatic sac in human embryos. These findings place cellular senescence as a relevant morphogenic process during embryonic development.

overall_design: We microdissected mesonephric tubules from senescent (WT) and non-senescent (p21-null) embryos to get information about this new senescence that occurs during embryogenesis.

last: Muñoz-Espin

first: Antonio

last: Maraver

first: Marta

last: Cañamero

first: Gonzalo

last: Gómez-López

first: Julio

last: Contreras

first: Silvia

last: Murillo-Cuesta

first: Isabel

last: Varela-Nieto

first: Jesús

last: Ruberte

first: Manuel

last: Collado

last: Serrano


title: Wildtype, miR-1-1 KO, miR-1 Double het P2 mixed strain heart analysis (MoGene 2.0 ST Arrays).

status: Public on Oct 19 2013

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

summary:
Neonatal hearts (P2) from wildtype, miR-1-1 null and miR-1-2 +/-: miR-1-1 +/- double heterozygote animals were isolated and total RNA was extracted with TRIzol (Invitrogen), following the manufacturer’s suggested protocol.
Genomic DNA was removed using a gDNA eliminator column (Qiagen).  Samples were hybridized to Affymetrix mouse genechip ST 2.0 arrays.

Mouse strain for all samples is: Mixed 129 x C57BL/6

overall_design: Three groups: miR-1-1, miR-1 double het, wildtype, all compared against each other. Samples are all from neonatal hearts.

first: Amy

last: Heidersbach


title: Determine the effects of mTORC1 inhibition by rapamycin on mouse liver transcriptome

city: Providence

first: Joan

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

summary: Liver from RICTOR knockout mice show normal levels of mTORC1 signaling in response to refeeding.  With this experiment we sought to compare the effects of Rictor depletion to the effects of mTORC1 inhibition by rapamycin in liver from mice that were fasted and refed.

overall_design:
Mice were either fasted for 24hr (n=5), or fasted for 22hr then treated with either 10mg/kg rapamycin suspended in 0.9% NaCl and 2% ethanol at a concentration of 1mg/ml (547mM), or vehicle only.  After an additional 2 hr, one group of mice (0 hr time, n=3) was sacrificed, the liver immediately removed, and flash frozen in liquid nitrogen.  The remaining mice were given ad libitum access to food and sacrificed after 3hr (n=3), 6hr (n=3), or 12 hr (n=3).
Two other nonfasted groups of mice (n=2) were injected with either vehicle or rapamycin and sacrificed after 24hr.
Submitter cannot locate the CEL files.

first: Dudley

middle: W

last: Lamming

first: David

last: Sabatini

first: Tao

last: Peng

first: Philip

last: Gruppuso


title: Expression data from Sf3b1 heterozygous Lineage-c-Kit+Sca-1+ (LSK) bone marrow cells

status: Public on Sep 20 2013

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

institute: Kumamoto University

summary: Recent studies have shown that multiple components of the mRNA splicing machinery are mutated in myelodysplastic syndrome (MDS) patients.  SF3B1 is frequently mutated in refractory anemia with ringed sideroblasts (RARS)-MDS patients, however, the pathophysiological role of SF3B1 mutations has not been elucidated yet.  In this study, we examined the function of Sf3b1 in murine hematopoiesis.

overall_design: Since Sf3b1 null homozygotes died during preimplantation development, in this study, we utilized Sf3b1 heterozygous mice showing grossly normal growth.  We harvested bone marrow stem/progenitor (LSK) cells from wild type (WT) and Sf3b1+/- mice (n=4) at 20 weeks old.  In addition, to exclude the possibility of indirect effect from bone marrow environment, we transplanted total bone marrow cells from WT or Sf3b1+/- (CD45.2+) mice into lethally irradiated CD45.1+ recipient mice, and then harvested (CD45.2+) LSK cells from the recipients (n=5) at 9 months-post transplantation.

first: Atsushi

last: Iwama


title: Maternal folic acid supplementation alters gene expression in the offspring brain

status: Public on Sep 09 2013

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

state: NY

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

summary: Studies have indicated that altered maternal micronutrients and vitamins influence the development and susceptibility of newborns to chronic diseases. Among these, folic acid (FA) plays a key role in the synthesis and repair of DNA, along with maintenance of epigenetic DNA methylation. Deficiency of FA has been associated with the pathogenesis of neural tube defects. Since FA can modulate DNA methylation and affect gene expression, we investigated the effect of gestational FA supplementation on the expression of genes in the offspring brain. Our results suggest that a maternal ten-fold increase in FA supplementation alters the expression and dysregulates a number of genes in the offspring brain, including many involved in development. While a number of genes that were dysregulated were common to both male and female pups, there were sex differences in gene expression changes.

overall_design: C57BL/6J female mice were separated into two groups of ten mice and supplemented with a custom diet.  One week prior to mating the low-dose group of female mice were fed a custom AIN-93G amino acid–based diet (Research Diet, Inc. New-Brunswick, NJ), with FA at 0.4 mg/kg, while the high-dose group received FA at 4 mg/kg diet.  Tissues from the cerebral hemisphere of three independent pups of same gender were pooled together. A total of three microarray gene expression studies have been performed (0.4mg/kg or 4mg/kg both male and female) and the mean was used for comparison.

first: Subit

last: Barua

first: Kathryn

middle: K

last: Chadman

first: Salomon

last: Kuizon

first: W

middle: T

last: Brown


title: Transcriptome profiling of breast cancer cells with Insulin like growth factor binding protein 2 (IGFBP2) knockdown

status: Public on Sep 06 2013

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

institute: Indian Institute of Science Bangalore

summary: The study was carried out to identify the genes regulated upon IGFBP2 modulation in breast cancer. This will help to understand the molecular targets and biological pathways targeted by IGFBP2 in breast cancer.

overall_design: C5 (Cy5) Vs. Vector(Cy3), C5 (Cy5) Vs. Vector(Cy3), C12 (Cy5) Vs. Vector(Cy3), C12 (Cy5) vs. Vector(Cy3)

first: Priyanka

last: Sahagal

last: Kumar

first: Paturu

last: Kondaiah