title: Mouse brain microarray, Chronic HDAC inhibitor treatment

status: Public on May 29 2013

middle: Albert

last: Schroeder

address: 185 Cambridge Street

institute: Harvard/MGH

summary: Here, we examined mouse brain trancriptional changes 1 hour after the 10th daily i.p. treament with one of the four following treaments: i) vehicle control (45% saline, 45% PEG-400 and 10% DMSO administered at 7.5mL/kg), ii) Cpd-60, 45mg/kg , administered at 7.5mL/kg or iii) SAHA, 25mg/kg, administered at 5mL/kg) or iv) CI-994, 10mg/kg, administered at 5mL/kg. Cpd-60 is a benzamide HDAC inhibitor with selectivity for class I HDAC subtypes HDAC1 and HDAC2; CI-994 is a benzamide inhibitor with selectivity for HDACs1,2 and 3; SAHA is a hydroxamic acid HDAC inhibitor with selectivity for class I HDAC subtypes 1,2, and 3 and the class II HDAC subtype HDAC 6.   We examined transcript differences using the Illumnia WG-6 2.0 whole genome expression array and profiled 3 specific brain regions (prefrontal cortex, nucleus accumbens, hippocampus)  from each of 36 mice (n=6 mice / treatment group) .   For application to array chips, we pooled two biological replicates from like treatment and brain region-groups such that 36 samples were applied in total: 4 treatment groups x 3 brain regions per treament group x   3 pools of two samples each for each treatment/brain region.

overall_design: Treatment groups: All adult male, C57BL/6 mice  (n=6mice/treatment group) were sacrificed by rapid cervical dislocation and decapitation 1 hour after the tenth daily i.p. injection with one of the four following treaments: i) vehicle control (45% saline, 45% PEG-400 and 10% DMSO administered at 7.5mL/kg), ii) Cpd-60, 45mg/kg , administered at 7.5mL/kg or iii) SAHA, 25mg/kg, administered at 5mL/kg) or iv) CI-994, 10mg/kg, administered at 5mL/kg.   Brains were removed, frozen immediately on dry ice and stored at -80°C until use.  Frozen mouse brains (n = 6/ treatment group) were rapidly dissected at 4°C, isolating medial prefrontal cortex, nucleus accumbens and hippocampus. RNA was isolated using the Qiagen RNeasy Lipid Tissue mini kit, RNA concentration was determined using a NanoDrop spectrophotometer and quality was assessed using Agilent Bioanalyzer PICO chips, with the RNA Integrity Number (RIN) determined at 7.0-8.8 for all samples assayed, indicative of good RNA quality.  For microarray experiments on Illumina MouseWG-6 BeadChips, RNA samples were pooled from two biological replicates such that the total number of samples was 36 (3 treatment groups x 3 brain regions x 3 RNA pools representing two mice per pool). All microarray analysis and gene set analysis (GSA) was performed using GeneSpring software (v.11.5.1) with raw signals adjusted using quantile normalization and baseline transformation with the median signal in all samples set to zero.  Data were included in subsequent analyses if the normalized signal, thresholded at 0.8, was ‘present’ for 3 of 3 replicates for like treatment and tissue groups.

middle: A

first: Douglas

last: Barker

first: Stephen

last: Haggarty

first: Tracey

last: Petryshen


title: Genome-wide analysis of gene expression in adipose tissue of female mice after continuous high fat diet feeding

status: Public on May 10 2013

city: Wuhan

first: Ling

last: Zheng

email: lzheng@whu.edu.cn, ywding0628@gmail.com

address: Wuhan University

department: College of Life Science

country: China

institute: Wuhan University

summary: Analysis of gene expression in adipose tissue of female mice after continuous high fat diet (HFD) feeding for three generations. The hypothesis in this study is that continuous HFD feeding has transgenerational amplification effects to the offspring. Results provide important information on the impacts of over-nutrition over one generation on the offspring, such as transgenerational up-regulated or down-regulated genes.

overall_design: Total RNA was obtained from adipose tissue of the HFD fed mice, including F0, F1 and F2 generations. Normal chow fed mice were used as controls.

first: Yingwen

last: Ding


title: Chromatin regulation by BAF170 controls cerebral cortical size and thickness.

status: Public on May 02 2013

city: Oxford

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary: Increased cortical size is essential to the enhanced intellectual capacity of primates during mammalian evolution. The mechanisms that control cortical size are largely unknown. Here, we show that mammalian BAF170, a subunit of the chromatin remodeling complex mSWI/SNF, is an intrinsic factor that controls cortical size. We find that the conditional deletion of BAF170 promotes indirect neurogenesis by increasing the pool of intermediate progenitors (IPs) and results in an enlarged cortex, whereas cortex-specific BAF170 over-expression results an opposing phenotype. Mechanistically, BAF170 competes with BAF155 subunit in the BAF complex, affecting the euchromatin structure and thereby modulating the binding efficiency of Pax6/REST-corepressor complex to Pax6 target genes that regulate the generation of IPs and late cortical progenitors. Our findings reveal a molecular mechanism mediated by the mSWI/SNF chromatin-remodeling complex that controls cortical architecture.

overall_design: Cortical gene expression is compared between three E12.5 mouse embryos with cortex-specific loss of BAF170 function and three littermate control embryos.

first: Tran

middle: C

last: Tuoc

first: Susann

last: Boretius

middle: N

first: Mara-Elena

last: Pitulescu

first: Jens

last: Frahm

first: Frederick

middle: J

last: Livesey

first: Anastassia

last: Stoykova


title: The effects of MyD88 deficiency on disease phenotype in dysferlin-deficient A/J mice: Role of endogenous toll-like receptor (TLR) ligands

status: Public on Apr 27 2013

city: DC

first: kitipong

last: Uaesoontrachoon

state: Washington

address: 111 Michigan Ave, NW

country: USA

institute: Children's national medical center

summary: Genome wide expression study of the effect of single stranded RNA (ssRNA) in A/JOlaHsd (WT), A/J and A/J-MyD88 deficient mice. The hypothesis for this study was that endogenous TLR ligands released from the leaking dysferlin-deficient muscle fibers engage TLRs on muscle and immune cells and contribute to disease progression.These data point to a clear role for the TLR pathway in the pathogenesis of dysferlin deficiency.

overall_design: Total RNA obtained from isolated tibalis anterior muscles (TA) of A/JOlaHsd (WT), A/J and A/J-MyD88 deficient mice that were subjected to 3 intramuscular injections of ssRNA over the period of 10 days compared to their contraleteral legs that were injected with saline (control).


title: Whole  genome mRNA analysis of virus-specific CD8+ T cells expressing different levels of Id2-GFP following influenza virus infection

status: Public on May 03 2013

city: Parkville

first: Moshe

last: Olshansky

state: Victoria

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

summary: We speculated that distinct levels of Id2 was deterministic in the transcriptional program of antigen-specific CD8+ T cells. To test this hypothesis, we subjected DbNP366-specific effector CD8+ T cells purified according to their differential expression of Id2-GFP (Id2-GFPint and Id2-GFPhigh) to microarray analysis and compared their gene expression profiles to the differentially expressed genes identified by comparing Id2-deficient and wild-type DbNP366-specific CD8+ T cells. This analysis revealed that the transcriptional program of CD8+ T cell differentiation is exquisitely sensitive to the concentration of Id2.

overall_design: PR8-primed Id2gfp/gfp mice were challenged after one month with influenza intranasally HKx31 virus and analysed on day 9 for the expression of Id2-GFP in DbNP366+CD44+ CD8+ T cells. DbNP366-specific CD8+ T cells were then separated into virus-specific CD8+ T cells that expressed intermediate or high levels of GFP. Purified Id2-GFPintermediate (int) and Id2-GFPhigh DbNP366-specific CD8+ T cells were analysed by mRNA whole genome microarray. Three replicates of each group (Id2-GFPint or Id2-GFPhigh) were analysed.

last: Masson

first: Gabrielle

middle: T

last: Belz


title: Gene expression profiles of CD8+ partial memory T cells (Tpm) compared to naive, effector and memory CD8+ T cells (analysis 2, 20 samples)

status: Public on Apr 30 2013

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

summary: Analysis of global gene expression of partial memory T cells compared to naive, effector and memory CD8+ T cells demonstrating that Tpm constitute a unique cell population with distinct global gene expression profile.

overall_design: Total RNA obtained from isolated/FACSorted murine T cells  lysed  in Trizol after isolation.

first: Percy

last: Knolle

first: Jan

last: Böttcher


title: The differentially expressed genes identified in oncospheres derived from CRC105 and its metastatic variants.

status: Public on May 30 2013

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

institute: fudan university

summary: Migrating cancer stem cells (MCSCs) are believed to be tumorigenic initiators of metastasis. However, the relevance of MCSCs for organ-specific metastasis in colorectal cancer remains unclear. Using in vivo selection, transcriptomic analysis and functional verification, we cultured colorectal cancer stem cells and discovered specific cell surface markers of MCSCs exhibiting distinct abilities to metastasize to the liver and lung. These results have important clinical implications as selection criterion for post-operative adjuvant therapy.

overall_design: The human primary colorectal cancer cells from colorectal cancer patient (CRC105) were orthotopically injected into NOG mice. The cancer cells in the liver or lung metastases were orthotopically injected into a new set of mice. After six selection cycles, we obtained cancer cells that produce spontaneous liver (CRC105LM) or lung metastases (CRC105PM). Under serum-free conditions, all individual cells produced nonadherent, multicellular oncospheres. Total RNA extracted from oncospheres of organ-specific metastasizing variants and their parental cells was used to generate biotinylated complementary RNA (cRNA) by following the standard Agilent GeneChip protocol.

first: Qing-Quan

last: Li


title: HUVECs with endogenous or overexpressed GPR4 treated with pH 8.4 (control) or pH 6.4 for 5 h

status: Public on Apr 25 2013

city: Greenville

first: Lixue

last: Dong

state: NC

address: 600 Moye Blvd.

institute: East Carolina University

summary:
Acidic tissue microenvironment is commonly found in a variety of pathophysiological conditions. GPR4 is a proton-sensing G protein-coupled receptor that is fully activated by acidic extracellular pH but has lesser activity at the physiological pH 7.4 and minimal activity at more alkaline pH.
To determine the effects of GPR4 activation by acidosis on vascular endothelial cells, we examined the global gene expression of the acidosis response in primary human umbilical vein endothelial cells (HUVEC) with varying level of GPR4.

overall_design: HUVEC with endogenous or overexpressed GPR4 level (designated as HUVEC/Vector & HUVEC/GPR4 cells). Two treatment conditions: pH 6.4 vs. pH 8.4 for 5 h. Biological replicates: 4 HUVEC/Vector replicates (pH6.4 vs pH 8.4), and 4 HUVEC/GPR4 replicates (pH6.4 vs pH 8.4).

middle: V

last: Yang


title: Transcriptome profile of mouse lung dendritic cell subsets and macrophages.

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Dendritic cell (DC) are critical initiators and regulators of immunity to pathogens, vaccines, tumors and tolerance to self.  Mouse and human dendritic cells (DCs) are comprised of functionally specialized subsets, but precise interspecies correlation is currently incomplete and hampers the full translation of murine findings to human DC-based clinical therapies.   In this study, we show that murine lung and gut lamina propria CD11b+ DC populations are comprised of two subsets: FLT3- and IRF4-dependent CD24+CD64- DCs and contaminating CSF-1R-dependent CD24-CD64+ macrophages. CD11b+CD24+CD64- DCs are instrumental in inducing Th17 cell immune response in the steady state and upon Aspergillus fumigatus challenge.  We also identified human CD1c+CD11b+ DCs as the functional homologue of mouse mucosal CD11b+ DCs.    Our findings highlight the conservation of key immune functions across species and aid the translation of murine studies to human DC immunobiology. The data for the associated human studies have been stored within GSE35459.

overall_design: Gene Expression from total RNA from specific mouse dendritic cell subsets purified by FACS

first: Andreas

last: Schlitzer

first: Florent

last: Ginhoux

first: Michael

last: Poidinger

first: Pavandip

first: Muzlifah

last: Haniffa

first: Matthew

last: Collin


title: compare of mRNA expression between IA and MMA

city: Changsha

first: Jia

state: Hunan province

address: 110, Xiangya Road

institute: State Key Laboratory of Medical genetics

summary: To exploring the difference of mRNA expression between IA and MMA, we have employed mRNA array expression profiling as a discovery platform to identify genes between the IA and MMA.  It's a compensate experiment after microRNA array, we paired the mRNA data with miRNA targets, finally, these data were used for the functional analysis.

overall_design: 2 IA and 2 MMA tissue were used for the microarray

first: Yugang

last: Jiang

first: Mingming

last: Zhang

first: Hua

last: He

last: Zeng

first: Ranhui

last: Duan


title: In Vivo RNA Interference Screening Identifies a Leukemia-Specific Dependence on Integrin Beta 3 Signaling

status: Public on Apr 24 2013

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: Primary leukemia stem cells (LSCs) reside in an in vivo microenvironment that supports the growth and survival of malignant cells. We used an in vivo short hairpin RNA (shRNA) screening approach to identify novel genes that are essential for primary murine MLL-AF9 acute myeloid leukemia (AML). We found that Integrin Beta 3 (Itgb3) is selectively essential for murine leukemia cells in vivo, and for human leukemia cells in xenotransplantation studies. In leukemia cells, Itgb3 knockdown impaired homing, downregulated LSC transcriptional programs, and induced differentiation. In contrast, loss of Itgb3 in normal HSPCs did not affect engraftment, reconstitution, or differentiation in long term transplantation assays. We explored the signaling pathways downstream of Itgb3 using an additional in vivo shRNA screen and identified Syk as a critical mediator of Itgb3 activity in leukemia. Finally, we confirmed that Itgb3 is dispensable for normal hematopoiesis and required for leukemogenesis using the Itgb3 knockout mouse model. Our results establish the significance of the Itgb3 signaling pathway as a potential therapeutic target in AML, and demonstrate the utility of in vivo RNA interference screens.

overall_design: We examined the effect of Itgb3 knockdown by gene expression profiling in primary leukemia cells.

first: Peter

middle: G

last: Miller

first: Kimberly

last: Hartwell

first: Lisa

middle: P

last: Chu

first: Marcus

last: Järås

first: Rishi

last: Puram

first: Alexandre

last: Puissant

first: Kevin

last: Callahan

first: John

last: Ashton

first: Marie

middle: E

last: McConkey

first: Luke

last: Poveromo

first: Glenn

middle: S

last: Cowley

last: Kharas

first: Myriam

last: Labelle

first: Sebastian

last: Shterental

first: Joji

last: Fujisaki

first: Lev

last: Silberstein

first: Muhammad

last: Al-Hajj

first: Christopher

last: Shelton

first: Scott

last: Armstrong

first: David

last: Root

last: Scadden

first: Richard

middle: O

last: Hynes

first: Siddhartha

last: Mukherjee

last: Stegmaier

first: Craig

last: Jordan

first: Benjamin

last: Ebert


title: Genome-wide analysis of the function of Tlx in regulating mouse brain glioma gene expression

status: Public on Apr 17 2013

city: Heidelberg

first: Hai-Kun

last: Liu

institute: Deutsches Krebsforschungszentrum DKFZ

summary: Analysis of the function of Tlx in regulating brain tumor stem cells (BTSCs) at the gene expression level. Based on our knowledge, we know that Tlx is specifically expressed in the neural stem cells in mouse brain. It also functionally regulates neurogenesis during the postnatal stages. The hypothesis tested in the present study is that Tlx influences the maintenance and progression of mouse brain gliomas through regulating the self-renewal of BTSCs and it is also a specific marker of brain tumor stem cells (BTSCs). Results provide important information about the function of Tlx in brain gliomas.

overall_design: Brain gliomas were initiated from the Nestin-CreERT2;Tlx flox/flox;Nestin-Tva transgenic mouse line. After 2.5 weeks, when the brain gliomas were fully developed, tamoxifen was administered through intraperitoneal injection. Tlx was knocked-out from the Cre-expressing littermates, but the littermates without Cre expression maintained intact Tlx function. Then, total RNA was obtained from mouse brain gliomas with severe neurological symptoms from the Tlx knockout and Tlx intact groups.

first: Zhe

last: Zhu

last: Khan

first: Jan

last: Gronych

first: Olga

last: Bernhardt

first: Andrey

last: Korshunov

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter

first: Hai

middle: K


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]

status: Public on Apr 11 2013

city: San Francisco

first: Abhinav

last: Nellore

state: CA

address: 513 Parnassus Avenue

institute: UCSF

summary: Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease.

overall_design: SVZ monolayer cultures were differentiated in vitro for 1, 2, 4 days, and gene expression changes were measured. SVZ lineage was isolated by FACS using established protocols to separate transit amplifying (TA), neuroblast (NB), activated stem cells (NSCs), and niche astrocytes (astros), and gene expression of each cell type was measured. All arrays are Nimblegen Mouse Gene Expression 12x135K Array.

first: Alexander

last: Ramos


title: Genetic Risk Factors for Type 2 Diabetes:  A Trans-Regulatory Genetic Architecture?

status: Public on Apr 16 2013

city: Chicago

first: Eric

last: Gamazon

state: IL

address: KCBD 3220 900 E 57th Street

institute: University of Chicago

summary: Transcriptional Profiling of Insulin Sensitive and Insulin Resistant Samples

overall_design: Sixty two participants at the tail ends of the distribution of insulin sensitivity adjusted for age, gender and natural logarithm of BMI for each ethnic group separately. Individuals at tail ends were well matched for age, gender, BMI, and percent fat, but were different for insulin sensitivity. Participants were of age 20 years to 55 years, body mass index (BMI) between 19 kg/m2 and 42 kg/m2, and had all biopsies obtained in the fasting state.

middle: R

first: Steven

last: Elbein

first: Swapan

last: Das

first: Neda

last: Rasouli

first: Philip

last: Kern

first: Nancy

last: Cox


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [lncRNA Array]

overall_design: SVZ monolayer cultures were differentiated in vitro for 1,2,4 days, and gene expression changes were measured. SVZ lineage was isolated by FACS using established protocols to separate transit amplifying (TA), neuroblast (NB), activated stem cells (NSCs), and niche astrocytes (astros), and gene expression of each cell type was measured. All arrays are custom lncRNA arrays.


title: Gene expression profiles of CD8+ partial memory T cells (Tpm) compared to naive, effector and memory CD8+ T cells

first: Joachim

last: Schultze

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

overall_design: Refer to individual Series


title: MicroRNA and Gene signatures of young and replicative senescent human umbilical vein endothelial cells

status: Public on Apr 05 2013

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

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


title: Genome-wide analysis of tissue-specific gene expression by Ly6Chi inflammatory monocytes during Toxoplasma gondii infection

status: Public on May 25 2013

city: Bethesda

first: John

last: Grainger

state: Maryland

address: Building 4, 4 Center Drive,

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Analysis of Ly6Chi monocytes from small intestine lamina propria (SILP) and blood of day 8 Toxoplasma gondii infected mice at gene expression level. The hypothesis tested in the present study was that Ly6Chi monocytes from SILP have altered expression of regulatory factors to blood monocytes. Results provide  important information on the regulatory to effector balance of genes expressed by Ly6Chi monocytes during an acute inflammatory response.

overall_design: Ly6Chi inflammatory monocytes were sorted by FACS from the blood or small intestine lamina propria (SILP) of Toxoplasma gondii infected C57BL/6 mice. Cells were isolated at day 8 after infection and total RNA obtained from sorted populations. Three biological replicates were acquired for both blood and SILP from pooled animals.

first: Nicolas

last: Bouladoux

first: Yasmine

last: Belkaid


title: Gene signature of young and replicative senescent human umbilical vein endothelial cells (HUVECs)

summary: MicroRNAs regulate various cellular processes. While several genes associated with replicative senescence have been described in endothelial cells, miRNAs that regulate these genes remain largely unknown. The present study was designed to identify miRNAs associated with replicative senescence and their target genes in HUVECs. Gene profiling was established using the same RNA input as that used for miRNA profiing. We have employed Agilent Whole Human Genome microarray platform  to evaluate the expressions of 19,596 human genes .

overall_design: Gene expression profiles were established for young and replicative senescent HUVECs

first: Hui-Lan

last: Jong

first: Mohd

last: Mustafa

first: Paul

middle: M

last: Vanhoutte

first: Sazaly

last: AbuBakar


title: KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [array]

status: Public on Apr 03 2013

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

summary: A multilayered transcription regulatory system is unveiled, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an essential step of erythropoiesis

overall_design: Analyses of transcriptional profiles and chromatin state in KAP1 WT and KO cells

first: Isabelle

last: Barde

first: Benjamin

last: Rauwel

first: Ray

last: Marin-Florez

first: Andrea

last: Corsinotti

first: Elisa

last: Laurenti

first: Sandra

last: Offner

first: Sonia

last: Verp

first: Julien

last: Marquis

first: Jiri

last: Vanicek

first: Didier

last: Trono


title: Comparison of the transcripts in control and Blimp-1-deficient keratinocytes

status: Public on Apr 02 2013

city: Taipei

first: Ming-Feng

last: Chiang

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia sinica

summary: We performed microarray analysis to examine the differential gene expression profiles between Prdm1 (Blimp-1)-deleted and control keratinocytes. Keratinocytes isolated from Prdm1-floxed K5-CreER positive (CKO) mice were cultured in the presence of 4OHT to induce deletion of the Prdm1 allele in vitro. Prdm1-floxed K5-CreER positive (CKO) keratinocytes treated with the ethanol solvent control (EtOH) or Prdm1-floxed K5-CreER negative (control) keratinocytes treated with 4OHT or EtOH served as controls. Microarray analyses revealed that there were 93 genes up-regulated and 109 genes down-regulated by more than 2-fold in the CKO + 4OHT group in comparison with the CKO + EtOH, Ctrl + 4OHT or Ctrl + EtOH groups. Several corneocytes-related genes, including Rptn, Lce1f, Krt1 and Lce1d, are significantly down-regulated and several cytokines/chemokines, including Cxcl1, Cxcl2, Cxcl5 and Il24, are significantly up-regulated upon the deletion of Prdm1 in vitro.

overall_design: We analyzed the transcription profiles in control and Blimp-1-deficient keratinocytes using the GeneChip® Mouse Expression Array 430A.

first: Ming

middle: F

first: I

middle: Y

last: Lin

first: K

middle: I


title: compare of expression between IA and MMA

first: Jia

last: Li


title: Genome-wide identification of genes differentially expressed between wild-type and Prdm14-deficient ES cells grown in 2i culture conditions.

status: Public on Apr 01 2013

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Analysis of Prdm14 function in mouse embryonic stem cells. Prdm14 null and overexpressing ES cells were generated and analyzed by microarray, immunoflurescence, flow cytometry, ELISA, qPCR in different culture conditions.

overall_design: 2 samples (wild-type control and knockout) were analyzed in biological triplicates

first: Nils

last: Grabole

first: Julia

last: Tischler

first: M

middle: A

last: Surani


title: Genome-wide identification of genes differentially expressed between control and Prdm14 overexpressing ES cells grown in serum conditions.

overall_design: 2 samples (control and overexpression) were analyzed in biological triplicates


title: Amygdala-Dependent Fear Is Regulated by Oprl1 in Mice and Humans with PTSD

city: Atlanta

first: Raul

last: Andero Gali

state: GA

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

summary: Analysis of amygdala RNA expression 2 hours after auditory fear expression test in mice with and without previous exposure to acute immobilization stress.

overall_design: Total RNA from three groups was obtained: 1) Home Cage (HC) 2) Fear Expression / Extinction 3) Immobilization (IMO) + Fear Expression / Extinction.

first: Kerry

last: Ressler

first: Raül

last: Andero


title: Gene expression profiling of colitis-associated and sporadic colorectal tumors in mice

city: Erlangen

first: Clemens

last: Neufert

address: Ulmenweg 18

department: First Department of Medicine

summary: To uncover molecular mechanisms specifically involved in the pathogenesis of colitis-associated colon cancer (CAC), we studied tumorigenesis in experimental models of CAC and sporadic CRC that mimic characteristics of human CRC. Using comparative whole genome expression profiling, we observed differential expression of epiregulin (Ereg) in mouse models of colitis-associated, but not sporadic colorectal cancer. Similarly, highly significant upregulation of Ereg expression was found in cohorts of patients with colitis-associated cancer in inflammatory bowel disease but not in sporadic colorectal cancer. Furthermore, tumor-associated fibroblasts were identified as major source of Ereg in colitis-associated neoplasias. Functional studies showed that Ereg-deficient mice, although more prone to colitis, are strongly protected from colitis-associated tumors, and data from serial endoscopic studies revealed that Ereg promotes growth rather than initiation of tumors.

overall_design: 4 samples of individual distal colitis-associated tumors (CAC) from 4 mice, 2 samples of tumor-free distal colon epithelium with a pool of 5 mice per sample (CAC contr), 5 samples of individual Apcmin/+ tumors from the distal colorectum of 5 mice (sporCRC) and 3 samples of tumor-free distal colon epithelium (pool of 4 mice per sample)  (sporCRC contr). Colitis-associated tumorigenesis was performed by intraperitoneal injection of Azoxymethane (10mg/kg) (Sigma) into C57BL/6J wildtype mice followed by 3 cycles of Dextran Sodium Sulfate (DSS) in drinking water. Each DSS-cycle was composed of DSS (2.5% (w/v) (MP Biomedicals) in drinking water for 7 days, followed by a recovery phase with regular drinking water for 14 days. Sporadic tumors were from C57BL/6J-ApcMin/+/J mice. All tumors were obtained from the from the lower 6th of the large intestine and they had the same size covering between ¼ and up to ½ of the colonic circumferenc as evaluated by mini-endoscopy.

first: Oezlem

last: Tuereci

first: Ugur

last: Sahin

first: Markus

last: Neurath


title: Alteration of gene expression in differentiating C2C12 cells upon inhibition of PCAF by embelin

status: Public on Mar 31 2013

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: KAT2B (PCAF) belongs to GNAT family of lysine acetyltransferases (KAT), which specifically acetylates histone H3K9 residue and several nonhistone proteins. PCAF is also a transcription coactivator. Due to the lack of PCAF, KAT specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here we report that a hydroxy benzoquinone class of natural compound, embelin, specifically inhibits H3Lys9 acetylation in mice and recombinant PCAF mediated acetylation with near complete specificity in vitro. Further, using embelin, we have identified the PCAF regulated gene networks during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation, apart from regulation through MyoD acetylation.

overall_design: C2C12 cells were treated with either DMSO or 10uM embelin in GM/DM for either 24 or 48h.

first: Rahul

last: Modak

first: Narendra

last: Bharathi

first: Vinay

last: Kumar Rao

first: Reshma

last: Taneja


title: Alteration of gene expression in two cell lines upon inhibition of PCAF by embelin

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Alteration of gene expression in HEK 293T cells upon inhibition of PCAF by embelin

overall_design: HEK 293T cells were treated with DMSO (solvent control) and 20uM embelin for 24h. Cells were harvested and total RNA was extracted by Trizol method. RNA was cleaned up using RNeasy MinElute Cleanup Kit (Qiagen) and reverse transcribed, labelled and subsequently hybridized to Agilent human 4X 44k array slide.


city: Tokushima

first: Le

middle: Tan

last: Dat

state: Tokushima

address: 3-18-15, Kuramoto-cho

department: Genome center

country: Japan

institute: Tokushima university

summary: Gene expression profiles of 5 cancer cell lines, including lung cancer (SBC-5 (duplicate samples), ACC-LC319/bone2, NCI-H1048); and breast cancer (ZR75.1, HCC1397) were analyzed.

overall_design: Cells were cultured following the guidelines published somewhere, and at confluent ~ 80% cells were extracted RNA for microarray analysis.

first: Taisuke

last: Matsuo

first: Tetsuro

last: Yoshimaru

first: Toyomasa

last: Katagiri


title: Prdm14

first: Charles

last: Bradshaw


title: Epigenetic Silencing of DKK3 in Medulloblastoma.

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary: Medulloblastoma (MB) is one of the most common malignant pediatric brain tumor. The aim of our study was to understand which mechanisms are involved in aberrant activation of Wnt pathway and its association with MB tumor development. We studied the expression profiles of 19 MBs tumors using a genome-wide approach, furthermore we have included the data obtained from four independent public Datasets of gene expression (see README file below) to increase the statistical power of the study. The expression profiles identified the Wnt inhibitor gene, DKK3, significant down-regulated. DKK3 down-regulation was confirmed by qPCR in 80% of samples (27/33 MB tumors and in 3/5 MB human cell lines). Since DKK3 was found methylated in several cancers we also investigated the status of methylated CpG sites within the three promoters by a combination of two approaches: the MSP and pyrosequencing. MSP showed no methylation in all promoters while the pyrosequencing, a quantitative technique, indicated a very low level of methylation. To verify the epigenetic involvement on DKK3 silencing, we also studied the effect of Trichostatin A (TSA) in 4 MB cell lines (DAOY; D283; D425; D458). After TSA treatment we observed a significant DKK3 mRNA expression increase in 3/4 cell lines compared to the no treated cells. DAOY cells, that have a normal DKK3 expression value, did not change significantly the DKK3 expression after TSA treatment. To further validate the role of histone tail modifications as an epigenetic silencing mechanism for DKK3 in MB, we performed Chromatin Immunoprecipitation (ChIP) experiment using antibodies against acetylated histones. According to our earlier results, TSA treatment increased the signal of the histone modification meH3K4 which is related to a transcriptionally active gene respect to the untreated controls. Finally, we evaluated the DKK3 protein in three MB cell lines (DAOY; D283; D425) after 24h of TSA treatment, by immunofluorescence.

overall_design: We analysed 19 Medulloblastoma tumor  from pediatric patients, a commercial pool (Clontech) of 24 normal cerebellum from female and male Caucasians (ages: 16-70 years; cause of death: sudden death) and a pool of 10 normal cerebellum from children (6 Caucasians and 4 African Americans; ages: 0-16 years;  cause of death: sudden death) using 44K whole genome oligonucleotids microarray

first: Francesca

last: Valdora

first: Simona

last: Coco

first: Sara

last: Stigliani

first: Stefano

last: Moretti

first: Gian

last: Tonini


title: Differential induction of TLR3-dependent innate immune signaling by closely related parasite species_I

status: Public on Mar 29 2013

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: The closely related protozoan parasites Toxoplasma gondii and Neospora caninum display similar life cycles, subcellular ultrastructure, invasion mechanisms, metabolic pathways, and genome organization, but differ in their host range and disease pathogenesis.   Type II (γ) interferon has long been known to be the major mediator of innate and adaptive immunity to Toxoplasma infection, but genome-wide expression profiling of infected host cells indicates that Neospora is a potent activator of the type I (α/β) interferon pathways typically associated with antiviral responses.  Infection of macrophages from mice with targeted deletions in various innate sensing genes demonstrates that host responses to Neospora are dependent on the toll-like receptor Tlr3 and the adapter protein Trif.  Consistent with this observation, RNA from Neospora elicits TLR3-dependent type I interferon responses when targeted to the host endo-lysosomal system.  Although live Toxoplasma fail to induce type I interferon, heat-killed parasites do trigger this response, albeit much weaker than Neospora, and co-infection studies reveal that T. gondii actively suppresses the production of type I interferon.  These findings reveal that eukaryotic pathogens can be potent inducers of type I interferon and that related parasite species interact with this pathway in distinct ways.

overall_design: In vitro cultures of bone marrow-derived macrophages from WT or IFNAR2-/- mice were infected with either Toxoplasma gondii (VEG strain) or Neospora caninum (Nc2 strain) for 17 hours.  RNA was collected from biological replicates for expression profiling by microarray.  Uninfected controls for both WT and IFNAR2-/- were used as a reference.

first: Daniel

last: Beiting

first: David

last: Roos


title: Differential induction of TLR3-dependent innate immune signaling by closely related parasite species


title: Gene expression changes with loss of H3f3b

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis


title: The multifaceted responses of human monocytes to IFN-gamma and IL-4 are not reducible to M1/M2 polarization of Macrophages

status: Public on Mar 15 2013

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

summary: Macrophages are known to be polarized into inflammatory (M1) and immunoregulatory (M2) cells when they are stimulated by agonists such as IFN-gamma and IL-4, respectively. If circulating monocytes may be polarized in response to T cell signals is often misguidedly deduced from macrophage results. Here the transcriptional responses of human CD14+ monocytes to IFN-gamma and IL-4 were analyzed using whole genome microarrays. A principal component analysis and hierarchical clustering showed that monocyte and macrophage responses were distinct. Monocytes stimulated with IFN-gamma and IL-4 for 6 hours exhibited some features of macrophage polarization. Indeed, when 80 genes considered as M1 and M2 genes were analyzed, we found that M1 genes were modulated in response to IFN-gamma and that M2 genes were modulated in response to IL-4. The M1 polarization of monocytes was transient because only M2 genes were modulated when monocytes were stimulated with IFN-gamma and IL-4 for 18 hours. However, the activation of monocytes by IFN-gamma and IL-4 could not be reduced to M1/M2 polarization status. Indeed, monocytes exhibited early specific signatures composed of 46 and 39 up-regulated genes in response to IFN-gamma and IL-4, respectively, and a late signature common to both molecules that consisted of 57 up-regulated genes. Taken together, these results demonstrated the extreme plasticity of human monocytes and suggested the existence of a core transcriptional termination program. Using early and late signatures might be pertinent to investigate monocyte activation in inflammatory or infectious diseases.

overall_design: Monocytes were stimulated with IFN-gamma (20ng/mL) or IL-4 (20ng/mL) for 6 and 18 hours or culture for 6 and 18 hours without agonist (Unstimulated samples).  Monocytes-derived-macrophages (MDM) stimulated with IFN-gamma and IL-4 for 18 hours were used as controls. Each microarray is derived from a single biological sample.

first: Vikram

last: Mehraj

first: Amira

last: Ben Amara

first: Adil

last: El Filali

first: Eric

last: Ghigo

first: Christian

last: Capo

first: Jean-Louis

last: Mege


title: Endothelial cells require miR-214 to secrete exosomes that suppress senescence and induce angiogenesis in human and mouse endothelial cells

status: Public on Mar 22 2013

city: Utrecht

first: Bas

middle: van

last: Balkom

address: Heidelberglaan 100

department: Nephrology and Hypertension

country: Netherlands

institute: UMC Utrecht

summary: Signalling between endothelial cells, endothelial progenitor cells and stromal cells is crucial for the establishment and maintenance of vascular integrity and involves exosomes, among other signalling pathways. Exosomes are important mediators of intercellular communication in immune signalling, tumour survival, stress responses and angiogenesis. The ability of exosomes to incorporate and transfer mRNAs encoding for ‘acquired’ proteins or miRNAs repressing ‘resident’ mRNA translation suggests that they can influence the physiological behaviour of recipient cells. We here demonstrate that miR-214, a miRNA that controls endothelial cell function and angiogenesis, plays a dominant role in exosome-mediated signalling between endothelial cells. Endothelial cell-derived exosomes stimulated migration and angiogenesis in recipient cells, whereas exosomes from miR-214 depleted endothelial cells failed to stimulate these processes. Exosomes containing miR-214 repressed the expression of Ataxia Telangiectasia Mutated in recipient cells, thereby preventing senescence and allowing blood vessel formation. Concordantly, specific reduction of miR-214 content in exosome-producing endothelial cells abolishes the angiogenesis the angiogenesis stimulatory function of the resulting exosomes. Collectively our data indicate that endothelial cells release miR-214 containing exosomes to stimulate angiogenesis through silencing of Ataxia Telangiectasia Mutated in neighbouring target cells.

overall_design: Gene expression analysis of HMEC endothelial cells exposed to supernatant containing either HMEC derived exosomes (miR-214 high), HMEC derived exosomes depleted of miR-214 (miR-214 low) or containing no exosomes (no exosomes). Each sample was analysed in duplo.

middle: W

last: van Balkom

first: Michiel

last: Smits

first: Olivier

last: De Jong

first: Jolanda

last: Brummelman

first: Krista

last: den Ouden

first: Petra

last: de Bree

first: Monique

last: van Eijndhoven

first: D

last: Pegtel

first: Willem

last: Stoorvogel

first: Thomas

last: Würdinger

first: Marianne

middle: C

last: Verhaar


title: Effects of far-infrared rays to human prostate cancer cell line PC-3

status: Public on Mar 14 2013

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

institute: SHIMA Institution for Quantum Medicine

summary:
Far-infrared rays activated DNA repair genes in human prostate cancer cells, PC-3, after 12days' exposure to far-infrared rays.  As a far-infrared rays emitter, synthetic/natural rubber (RB) was used.

Keywords: comparative genomic hybridization

overall_design: Two-condition experiment,RB-treated  vs.non-RB-treated cells.: 2  reference control without RB,  independently grown and harvested. One replicate per array.

first: Jun

last: Qiu

first: Yoshie

last: Yoshikawa


title: mRNA Expression data from transverse aortic constriction hearts (cardiovascular disease) and sham hearts in mice.

city: Guelph

first: Elena

last: Tsimakouridze

address: 50 Stone Rd E

country: Canada

institute: University of Guelph

summary:
We used transverse aortic constraction pressure overload hypertrophy mouse hearts as a model of cardiovascular disease to study the genetic changes between TAC and SHAM (normal) mouse hearts and over 1 circadian cycle (24h). This is one approach to identify diurnal genetic biomarkers of cardiovascular disease.
The micorarray approach allowed to see the gene expression in all genes in cardiovascular disease and sham hearts.

overall_design: There are 36 samples of cardiovascular disease (TAC) and normal SHAM hearts.  For TAC: There were 3 mice sacrificed at each time point as biological replicates, for 6 timepoints over 24 hrs.  For SHAM: There were 3 mice sacrificed at each time point as biological replicates, for 6 timepoints over 24 hrs.

first: Tami

last: Martino

middle: V


title: Expression data for 2-month-old wild type and Tfam-SCKO (MPZ-Tfam KO) sciatic nerves

status: Public on Mar 13 2013

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

summary:
Gene expression analysis of 2-month-old Ctrl and Tfam-SCKO mice. At this age mitochondrial function is disrupted in the Schwann cells of Tfam-SCKO mice ,but their nerves display only very limited pathology.
Mitochondrial dysfunction is a common cause of peripheral neuropathy. Much effort has been devoted to examining the role played by neuronal/axonal mitochondria, but how mitochondrial deficits in peripheral nerve glia (Schwann cells, SCs) contribute to peripheral nerve diseases remains unclear. Here, we investigate a mouse model of peripheral neuropathy secondary to SC mitochondrial dysfunction (Tfam-SCKOs). We show that disruption of SC mitochondria activates a maladaptive integrated stress response through actions of heme-regulated inhibitor kinase (HRI), and causes a shift in lipid metabolism away from fatty acid synthesis toward oxidation. These alterations in SC lipid metabolism result in depletion of important myelin lipid components as well as in accumulation of acylcarnitines, an intermediate of fatty acid b-oxidation. Importantly, we show that acylcarnitines are released from SCs and induce axonal degeneration. A maladaptive integrated stress response as well as altered SC lipid metabolism are thus underlying pathological mechanisms in mitochondria-related peripheral neuropathies.

overall_design: Total RNA samples were prepared by isolating and pooling RNA from three different 2-month-old MPZ-Tfam KO and Ctrl mice. 2 replicates per genotype were used in this experiment and they were prepared entirely independently.

first: Andreu

last: Viader

first: Jeffery

last: Milbrandt


title: Expression data from asynchronous HUH7 cells

first: Kenneth

middle: S.

last: Zaret

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

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

summary:
During mitosis, RNA polymerase and most transcription factors are excluded from the chromosomes and transcription ceases.  The transcriptional re-activation of the genome, following mitosis, requires the re-setting of cell-type specific programs that were initially established during development.  However, only about one-fifth of transcription factors are retained on chromosomes throughout mitosis and a subset of these have been shown to facilitate target gene reactivation during mitotic exit.  How such “bookmarking” factors bind to chromatin in mitosis and re-activate transcription is central to the stability of transcriptional programs across multiple cell cycles.  We compared a diverse set of transcription factors involved in liver differentiation and found different modes of mitotic chromosome binding.  The pioneer transcription factor FoxA1, which is among the first to bind liver genes in development, exhibits virtually complete mitotic chromosome binding, whereas other liver factors bind with a range of efficiencies.  Yet genome-wide analysis shows that only about 15% of the FoxA1 interphase target sites are bound in mitosis; the latter include sites at genes for maintaining cell differentiation.  FoxA1 mutants that perturb specific and nonspecific DNA binding reveal a significant contribution of nonspecific binding events in mitotic chromatin.  Such nonspecific binding appears to spread from interphase FoxA1 targets and may serve as storage sites.  The hierarchy of specific binding, nonspecific binding, partial chromatin binding, and failure to bind mitotic chromosomes reflects the temporal sequence of the factors’ developmental roles in gene activation.
Gene expression was assessed in asynchronously cycling cells in order to determine whether FoxA1 is disposed to bind to high- or low-expressed genes during mitosis. Heatmap analysis shows that FoxA1's mitotic targets are among the highest-expressed genes in asynchronous cells.

overall_design: Total RNA was collected from three different plates with asynchronous HUH7 cells using the RNeasy mini kit (Qiagen Valencia CA). Expression microarrays were performed with a Human Gene 1.OST array (Affymetrix) at the UPenn Microarray Core Facility and assessed using Partek.

first: Juan

last: Caravaca

first: Greg

last: Donahue

first: Justin

last: Becker


title: Gene expression alterations due to defective Fbw7-dependent cyclin E ubiquitination in bone marrow erythroid cells

city: Chicago

first: Yanfei

last: Xu

address: 303 E. Superior Street., Lurie 5-250

department: Medicine

institute: Northwestern University

summary: A novel knock-in mouse model was reported (Minella et al., Genes Devel 2008) to have a mixed hyper-proliferative and defective maturation phenotype in the erythroid series. Microarray analyses were performed to identify gene expression alterations resulting from dysregulated cyclin E control.

overall_design: Analysis of gene expression changes in cyclin E (T74A T393A) knock-in erythroblasts (Ter119-positive, CD71-high) isolated by FACS sorting. Comparison is to cells similarly isolated from littermate controls.

first: Alex

last: Minella


title: Genome-wide analysis of gene expression in VAV1-/- versus VAV1+/+ bone marrow (BM)-macrophages

status: Public on Mar 08 2013

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Analysis of differential gene expression profiles in VAV1-/- versus VAV+/+ BM-macrophages , respectively. A distinct expression profile in VAV1-/- versus VAV1+/+ (wild-type) BM-macrophages  allows to resolve molecular mechanisms.

overall_design: Total RNA was obtained froms BM-macrophages of VAV1+/+ and VAV1-/- mice

first: Bettina

last: Jux

first: Andrea

last: Staratschek-Jox

middle: L

first: Waldemar

last: Kolanus


title: Effect of Trp63 deletion on the developing vagina

city: Columbus

first: Takeshi

last: Kurita

state: OH

address: 460 W. 12th Avenue,

department: Molecular Virology, Immunology & Medical Genetics

institute: Ohio State University

summary: Gene expression in the neonatal uterus and vagina from transformation related protein 63 (Trp63) conditional heterozygous and null mice was analyzed in order to identify upstream and downstream of Trp63 in the developing vagina. Differential gene expression between vaginal (Trp63 positive) and uterine (Trp63 negative) tissues should reflect both the upstream and downstream of Trp63 expression, whereas the comparison between conditional knockout and heterozygous vaginae should identify what is downstream of Trp63. Thus, the three-way comparison should identify what is upstream of Trp63.

overall_design: Total RNA was extracted from the Trp63 conditional heterozygous (Trp63 flox/wt ; Pax2-cre) uteri and vaginae, and Trp63 conditional knockout (Trp63 flox/floxt ; Pax2-cre) vaginae. Total 12 samples (3 different genotype/tissue groups x 4 independent samples each).

first: Kazutomo

last: Ishi


title: miR-139-5p induced gene expression alteration in glioma cells

status: Public on Mar 01 2013

city: Nanjing

first: Huibo

last: Wang

state: Jiangsu

address: 300# Guangzhou Rd.

department: Department of Neurosurgery

institute: First Affiliated Hospital of Nanjing Medical University

type: Expression profiling by high throughput sequencing

summary: To evaluate gene expression alteration following miR-139-5p transfection in glioma cells. We find a significant downregulation of two transcriptional factors, E2F3 and HoxA9.

overall_design: Total RNA were extracted from U87, LN229 and U251 glioma cells transfected with miR-139-5p or miRNA negative control.

first: Wanghao

last: Chen

first: Ning

last: Liu


title: Gene-expression changes in cerium chloride-induced injury of mouse hippocampus

status: Public on Mar 05 2013

city: Suzhou

first: fashui

last: Hong

address: Renai Road 199

institute: Medical College of Soochow University

summary:
Our findings suggested that exposure to CeCl3 led to hippocampal lesions, apoptosis, oxidative stress and impairment of spatial recognition memory. Furthermore, microarray data showed marked alterations in the expression of 154 genes involved in learning and memory, immunity and inflammation, signal transduction, apoptosis and response to stress in the 2 mg/kg CeCl3 exposed hippocampi.
Cerium is widely used in many aspects of modern society, including agriculture, industry and medicine. It has been demonstrated to enter the ecological environment, is then transferred to humans through food chains, and causes toxic actions in several organs including the brain of animals. However, the neurotoxic molecular mechanisms are not clearly understood. In this study, mice were exposed to 0.5, 1, and 2 mg/kg BW cerium chloride (CeCl3) for 90 consecutive days, and their learning and memory ability as well as hippocampal gene expression profile were investigated. Our findings suggested that exposure to CeCl3 led to hippocampal lesions, apoptosis, oxidative stress and impairment of spatial recognition memory. Furthermore, microarray data showed marked alterations in the expression of 154 genes involved in learning and memory, immunity and inflammation, signal transduction, apoptosis and response to stress in the 2 mg/kg CeCl3 exposed hippocampi. Specifically, the significant up-regulation of Axud1, Cdc37, and Ube2v1 caused severe apoptosis, and great suppression of Adcy8, Fos, and Slc5a7 expression led to impairment of mouse cognitive ability. Therefore, Axud1, Cdc37, Ube2v1, Adcy8, Fos, and Slc5a7 may be potential biomarkers of hippocampal toxicity caused by CeCl3 exposure.

first: Zhe

last: Cheng

first: Yuguan

last: Ze

first: Junju

last: Su

first: Bing

last: Li

first: Lei

last: Sheng

first: Liyuan

last: Zhu

last: Guan

first: Suxin

last: Gui

first: Xuezi

last: Sang

first: Xiaoyang

last: Zhao

first: Qingqing

last: Sun

first: Ling

first: Jie

first: Renping

last: Hu

first: Fashui

first: Haiquan


title: Expression Analysis and Genomic Analysis of Microdissected Inflammatory Breast Cancer

city: Houston

first: Takahiro

last: Kogawa

state: TX

address: 1515 Holcomb Blvd

department: Breast Medical

institute: MD Anderson

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Expression Analysis of Microdissected Inflammatory Breast Cancer

summary: Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status.

overall_design: Gene expression profiling of 20 inflammatory breast cancer (IBC), 20 non-IBC and 5 normal was studied.

first: Wendy

last: Woodward

first: Naoto

middle: T

last: Ueno


title: Whole genome microarray analysis of mouse liver subjected to Leishmania donovani infection

city: Kolkata

first: Suvendra

middle: Nath

last: Bhattacharyya

state: West Bengal

address: 4, Raja S.C.Mullick Road

department: Molecular and Human Genetics

institute: Indian Institute of Chemical Biology

summary: Balb/c mice were infected with Leishmania donovani and liver mRNA expression were studied at two months post infection

overall_design: Total RNA was isolated from liver tissue from uninfected and two months infected mouse and whole genome microarray was performed

first: June

last: Ghosh

middle: N


title: Comparison of monocytic cells from naïve mice and day 14 LCMV Armstrong and day 14 LCMV Clone 13 infected mice

status: Public on Feb 25 2013

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary: Infection with acute and chronic strains of LCMV (Armstrong (ARM) and Clone 13 (C13), respectively) leads to massive proliferation of monocytic cells contemporaneously with peak of the anti-viral CD8+ T cell response. These cells return to naïve levels following ARM infection.  However, during C13 infection these cells are sustained at high levels and gain a T cell suppressive function at day 14 post infection.  The mechanisms by which these cells are induced to proliferate and impair T cell function during chronic LCMV infection are largely unknown.  To address this, we analyzed gene expression profiles using microarray analysis of purified splenic monocytic cells (CD11b+ Ly6Chi Gr-1low) from naïve mice, or day 14 LCMV ARM or LCMV C13 infected mice.

overall_design: We sought to determine the unique genetic profile of monocytic cells from either acutely or chronically infected mice relative to that of monocytic cells from naïve mice.   We performed a meta-analysis using the expression profiles of naïve splenic monocytic cells (CD11b+ Ly6Chi Gr-1low), splenic monocytic cells from day 14 post LCMV ARM infection, and splenic monocytic cells from day 14 post LCMV C13 infection.

first: Brian

last: Norris

first: Bali

last: Pulendran


title: Gene expression in E18.5 Tex19.1-/- mouse placenta

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

institute: MRC Human Genetics Unit

summary: Microarray experiment to identify changes in gene expression in 18.5 day post coitum Tex19.1-/- mouse placenta. Tex19.1 is expressed in trophectoderm-derived cells in the placenta. Tex19.1-/- placentas are small and have defects in junctional zone and labyrinth layers of the placenta, Tex19.1-/- embryos exhibit intra-uterine growth retardation. Data provides insight into the changes in gene expression and cell composition in Tex19.1-/- placentas.

overall_design: Six E18.5 Tex19.1-/- placentas (KO: four XX, two XY), four E18.5 Tex19.1+/- littermate control placentas (HET: four XX), and two E18.5 Tex19.1+/+ littermate control placentas (WT: two XY) are included in the analysis.

middle: R

first: Judith

last: Reichmann


title: Gene expression profiles of CD8+ partial memory T cells (Tpm) compared to naive, effector and memory CD8+ T cells (analysis 1, 17 samples)

status: Public on Apr 30 2013

first: Joachim

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

institute: University of Bonn

summary: Analysis of global gene expression of partial memory T cells compared to naive, effector and memory CD8+ T cells demonstrating that Tpm constitute a unique cell population with distinct global gene expression profile.

overall_design: Total RNA obtained from isolated/FACSorted murine T cells  lysed  in Trizol after isolation.

first: Percy

last: Knolle

first: Jan

last: Böttcher


title: Genome-level Cell Responses to Digital Microfluidic Manipulation

status: Public on May 01 2013

city: Toronto

first: Sam

last: Au

state: ON

address: 160 College St. Room 440

institute: University of Toronto

summary: Analysis of mammalian cell responses to digital microfluidic manipulation. BA/F3 cells were manipulated on devices with 15 min continuous actuation at 400Vpp at 1 kHz or 18 kHz and compared to untreated control cells and cells heat shocked at 42C, 47C or 52C.

overall_design: Total RNA isolated from Ba/F3 murine cells, untreated or exposed to digital microfludic manipulation or heat shock.

first: Au

last: Sam

first: Fobel

last: Ryan

first: Wheeler

last: Aaron


title: Variability of gene expression profiles in neutrophils from Germ-free mice

status: Public on Mar 30 2013

first: Flavia

last: Lakschevitz

address: 150 College st room 221

department: Faculty of Dentistry

summary: Neutrophils, key cells of the innate immune system, are responsible for preventing bacterial infections. It was already demonstrated that albeit neutrophils synthesize lower levels of protein and RNA they are able to marked change its gene expression after bacteria exposure. The absence of microbial stimulation has consequences on development of the mucosal immune system as demonstrated using germ-free mice as a model. We are interested in understanding if commensal flora induces changes in the gene expression profile of neutrophils in its site of production, the bone marrow.

overall_design: Total RNA obtained from isolated neutrophils from Bone Marrow from Germ-free mice and control

middle: S

first: Dana

last: Philpot

first: Michael

last: Glogauer


title: Postnatal glucocorticoids suppress myelination in a dose-dependent manner by genomic mechanism

status: Public on Feb 27 2013

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary:
Objective: Postnatal glucocorticoids (GCs) are widely used in the prevention of chronic lung disease in premature infants. However, their use is associated with neurodevelopmental delay and cerebral palsy. We hypothesized that postnatal dexamethasone or betamethasone in high-dose, but not low-dose, would induce hypomyelination, astrogliosis, and motor impairment in premature rabbit pups.  Additionally, these effects would be mediated by glucocorticoid receptors (GRs).

Methods: Preterm rabbit pups, delivered by C-section at E29 (term=32d), were treated with a high dose of dexamethasone or vehicle. Myelin basic protein (MBP), glial fibrillary basic protein (GFAP), oligodendrocyte proliferation and maturation, and alteration of transcriptomic profile were evaluated in these pups. Neurobehavioral assessments were performed at 14d.

Results: High-dose dexamethasone treatment reduced MBP expression and induced motor-impairment compared with controls. High-dose dexamethasone induced astrogliosis and altered genes associated with myelination, cell-cycle, GR, and MAP-Kinase signaling.

Interpretation: High-dose postnatal dexamethasone arrested maturation of oligodendrocytes, and induced hypomyelination, gliosis and motor deficits. GC treatment reduced myelination by genomic GR-dependent mechanisms, and caused astrogliosis by non-genomic mechanisms.

overall_design: Two-condition experiment: forebrains of HDD (high dose dexamethasone) vs. CTR (saline) post-natally exposed rabbit pups. Biological replicates: 4 CTR replicates, 4 HDD replicates.

first: Muhammad

last: Zia

first: Govindaiah

last: Vinukonda

first: Linnea

last: Vose

first: Bala

middle: B

last: Bhimavarapu

first: Sanda

first: Nishikant

last: Pandey

first: Ann

middle: M

last: Beall

first: Edmund

middle: F

last: LaGamma

first: Praveen

last: Ballabh


title: PRENATAL EXPOSURE TO CORTICOSTEROIDS: HYPOTHALAMIC CHANGES RELEVANT FOR POSTNATAL BEHAVIORAL IMPAIRMENTS

status: Public on Mar 06 2013

summary: Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters, peptides and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the ARC of rats prenatally exposed to either betamethasone or saline. The expression of transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. Total of 18,094 unigenes were quantified in the hypothalamic ARC of P14 male and female rats prenatally exposed to betametasone used in this experiment. Out of these genes, Kyoto Encyclopedia for Genes and Genomes (http://www.genome.jp) selected 112 for the dopaminergic synapse, 75 for the GABAergic and 97 for the glutamatergic synapse. We further analyzed composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission). Finally we investigated the “transcriptomic landscape” of the GSF in the ARC of P14 males (M) and females (F) prenatally (G15) exposed to betamethasone (B) or saline (S). We combined in one measure (PWR = Pair-Wise Relevance) expression levels, controls and coordination of all pairs that can be formed by synapse genes with the other synapse genes, higher PWRs indicating larger influence of that gene pair to the fabric modulation. We found that prenatal exposure to betamethasone caused sex-dependent changes in the dopaminergic/GABA/glutamatergic synapse genes:. In males, 10 dopaminergic (9%), 4 GABAergic (5%) and 5 glutamatergic synapse genes (5%) were down-regulated. While in females, 9 dopaminergic (8%), 3 GABAergic (4%) and 6 glutamatergic (6%) synapse genes were downregulated. The data indicate that in both sexes the dopaminergic synapse was the most affected. In contrast, in control animals, no significant differences between male and female were present in these synapse genes. Since the most noticeable transcritpomic changes were found in the transcriptome of DA glutamatergic synapse, we investigated the expression of tyrosine-hydroxylase (TH) NMDA receptor subunits in the ARC. The western blot analyses and immunohistochemistry confirmed the sex-specific differences between prenatally betamethasone-exposed and saline-exposed P15 rats. Accordingly to the changes in gene expression, prenatal exposure to synthetic corticosteroids was associated with postnatal changes in behavior and susceptibility to certain types of seizures. While we did not find any significant impairements in normal behavioral patterns (open field activity), there was a sex-specific change in the novel object recognition test. We found that behavioral lateralization in females is lost after prenatal betamethasone exposure and both male and female prenatally betamethasone exposed rats were avoiding novelty. This trait is similar to children with autism and suggests that certain elements of autistic behaviors can be present after prenatal exposure to synthetic corticosteroids. Additionally, there were changes in the search patterns in the Morris water maze as well as in the Barnes maze.  In conclusion, our work is consistent with findings of profound reprogramming changes in the brain after prenatal corticosteroid exposure associated with alterations cognitive functions and seizure susceptibility.

overall_design: Two-sexes (M, F) x two-condition (B = betamethasone prenataly exposed vs S = saline prenataly exposed) experiment. Biological replicates: 4 MS, 4 FS, 4 MB, 4 FB.

middle: A

first: Tamar

last: Chachua

first: Galyna

last: Sidyelyeva

first: C

last: Goletiani

first: Jana

last: Velíšková

first: Libor

last: Velíšek


title: Transcriptomics in response to internal exposure in Flemisch adults

status: Public on Feb 21 2013

city: Ghent

first: Sam

last: De Coster

address: De Pintelaan 185

department: Study Centre for Carcinogenesis and Primary Prevention of Cancer

country: Belgium

institute: Ghent University

summary: Transcriptomic analysis of the effects of environmental exposure to cadmium, lead, PCBs, dioxin, hexachlorobenzene, p,p'-DDE, benzene and PAHs on the gene expression in blood in humans (biomonitoring study)

overall_design: Correlation analysis of 9 biomarkers of exposure with gene expression levels in peripheral blood lymphocytes of 20 females or 20 males.

first: Danitsja

last: van Leeuwen

first: Danyel

middle: G

last: Jennen

first: Gudrun

last: Koppen

first: Elly

last: Den Hond

first: Vera

last: Nelen

first: Greet

last: Schoeters

first: Willy

last: Baeyens

first: Joost

middle: H

last: van Delft

first: Jos

last: Kleinjans

first: Nicolas

last: van Larebeke


title: Characterization of T-rapamycin cells by gene expression profiling

status: Public on Feb 15 2013

city: Bethesda

first: Luciano

last: Castiello

address: 10 Center Drive

department: DTM

institute: NIH/CC

summary:
Gene expression profiling of CD4+ T cells cultured in vitro in presence of IL-2, IL-4, Rapamycin for 12 days
Sources tested: Day 0 CD4+ T cells (6 samples), Day 6 T-rapamycin cells (6 samples), Day 12 T-rapamycin cells (6 samples)

overall_design: 3 time points were compared: day 0 (cells before start the culture), Day 6 and Day 12 (cells at the end of the culture)

first: Miriam

last: Mossoba


title: Cyclophilin D extramitochondrial signaling controls cell cycle progression and chemokine-directed cell motility.

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: Mitochondria control bioenergetics and cell fate decisions, but whether they also participate in extra-organelle signaling is not understood.  Here, we show that interference with cyclophilin D (CypD), a mitochondrial matrix protein and apoptosis regulator, causes accelerated cell proliferation and enhanced cell migration and invasion.  These responses are associated with global transcriptional changes in CypD-/- cells, predominantly affecting chemokines and their receptors, and resulting in increased activating phosphorylation of Signal Transduction and Activator of Transcription 3 (STAT3).  In turn, STAT3 signaling promotes increased proliferation of CypD-/- cells via accelerated S-phase entry and supports Cxcl12-directed paracrine cell motility.  Therefore, mitochondria-to-nuclei transcriptional signaling globally affects cell division and motility.  As immunosuppressive therapies often target CypD, this pathway may predispose the tissue microenvironment of these patients to oncogenic transformation.

overall_design: Three wild type (WT) and three CypD-/- knock-out mouse embryonic fibroblasts (MEFs) have been compared.

first: Dario

last: Altieri


title: mRNA and miRNA analysis during hepatitis C virus infection

status: Public on Feb 17 2013

city: Nantes

first: Cyrille

last: Féray

address: 1 rue Gaston Veil

institute: Faculté de médecine de Nantes


title: Smooth muscle specific deletion of N-deacetylase-N-sulfotransferase 1 (Ndst1) results in increased arterial elasticity in mice

status: Public on Feb 16 2013

city: Minneapolis

first: Neeta

last: Adhikari

state: Minnesota

address: 312 Church Street SE

department: Lillehei Heart Institute

institute: University of Minnesota

summary: The hypothesis tested was that loss of Ndst1 in smooth muscle would lead to significant changes in gene expression and alter functional properties in large and small vessels. The increase in aortic elasticity was increased in mice lacking Ndst1 was associated with significant changes in genes that modify mechano-sensing, contractility and elasticity.

overall_design: Total RNA extracted from aorta from smooth muscle specific Ndst1 deficient mice (SM22αcre+Ndst1-/-) was compared to aorta from wild type (WT, SM22αcre-Ndst1wt/wt ) control mice.

first: Jennifer

last: Hall

first: Rod

last: Staggs


title: Studies in a murine B16 melanoma model show that persistent antigen at vaccination sites induces CD8+ T cell sequestration, dysfunction and deletion

status: Public on Mar 02 2013

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: To understand why cancer vaccine-induced T cells often fail to eradicate tumors, we studied immune responses in mice vaccinated with gp100 peptide emulsified in incomplete Freund's adjuvant (IFA), commonly used in clinical cancer vaccine trials. After gp100 peptide/IFA vaccination, tumor-specific CD8+ T cells (adoptively transferred from gp100-specific TCR-transgenic pmel-1 mice) accumulated not in tumors but at the persisting, antigen-rich vaccination site. Once there, primed T cells became dysfunctional and underwent antigen-driven, IFN-γ and FasL-mediated apoptosis, resulting in systemic hyporesponsiveness to subsequent vaccination. Provision of anti-CD40 antibody, TLR7 agonist and interleukin-2 (covax) reduced T cell apoptosis but did not prevent vaccination site sequestration. A non-persisting vaccine formulation shifted T cell localization towards tumors, inducing superior anti-tumor activity. Short-lived formulation also reduced systemic T cell dysfunction and promoted memory formation, as shown by gene expression profiling and other measures. Persisting peptide/IFA vaccine depots, currently used to vaccinate cancer patients, can induce specific T cell sequestration at vaccination sites followed by dysfunction and deletion; short-lived depot formulations may overcome these limitations and result in greater therapeutic efficacy of peptide-based cancer vaccines.

overall_design: To study the fate of melanoma-specific CD8+ T cells after peptide vaccination, we tracked T cell receptor-transgenic pmel-1 T cells in mice vaccinated with heteroclitic gp100_25-33 peptide emulsified in IFA. Splenic pmel-1 CD8+ T cells were purified at 6 and 21 days after vaccination with either gp100/IFA/covax or gp100/saline/covax, and then their total RNA was extracted and used for comparison by gene expression profiling.

first: Yared

last: Hailemichael

first: Zhiqiang

last: Wang

first: R

middle: E

last: Davis

first: Willem

middle: W

last: Overwijk


title: Comparison of gene expression in Dnmt1+/+ and Dnmt1-/- MEFs

status: Public on Feb 12 2013

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL

summary: DNA methylation and the Polycomb Repression System are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. By genome-wide mapping of the Polycomb Repressive Complex 2 (PRC2)-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and PRC2 from Polycomb-target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining PRC2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.

overall_design: Three replicates of each sample are compared

first: Richard

last: Meehan


title: JAR cells: Control vs. siIMP1 transfected

city: Taichung

first: yeunting

last: hsieh

address: Chugong Road Section3, 160

department: GYN

institute: TCVGH

summary:
To acquire an overall picture of IMP1 regulating network, we compared the global transcription pattern in IMP1 inhibited JAR cells with control cells by DNA microarray.
Specific siRNA to IMP1 or universal negtive control siRNA were transfected into JAR cells respectively, the total RNA was extracted after 72hr incubation. Then went into the microarray assay procedure.

overall_design: one control vs. one siIMP1

first: Yeunting

last: Hsieh

first: Jenn

middle: J

last: Tseng

first: Hong

last: Chen


title: Retinoic acid signaling is essential for HSC development

status: Public on Mar 12 2013

first: Bhaskar

last: Chanda

address: 101 College Street

summary: To find signaling regulators that modulate transition from endothelial (AA4.1/VEC+CD45-) to hemogenic endothelial (AA4.1/VEC+ CD45+) cell

overall_design: This microarray was performed between  AA4.1/VEC single +ve or AA4.1/VECCD45+ cells were sorted from E11.5 AGM and Total RNA was extracted.

first: Andrea

last: Ditadi

first: Norman

last: Iscove

first: Gordon

last: Keller


title: TCR affinity-dependent functional inhibition via PD-1 and SHP-1 phosphatase

status: Public on Feb 11 2013

city: Boston

first: Lukas

last: Baitsch

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: To investigate gene expression changes associated with stimulation of TCRs of different affinity, primary CD8 T cells were transduced with sequence optimized TCRs of various affinities and stimulated for 6h.

overall_design: Gene expression was measured at baseline (0h) and after 6h after stimulation with low dose NY-ESO-1 multimer

first: N

last: Rufer

first: M

last: Hebeisen

first: L


title: Posterior Second Heart Field (pSHF) transcriptomes of wild-type and Shh mutant mouse embryos

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

institute: universty of Chicago

summary: To understand Sonic hedgehog homolog (Shh)-mediated molecular networks in the posterior second heart field (pSHF), we have employed whole genome microarray expression profiling as a discovery platform to identify genes with Shh-dependent expressional changes.  We microdissected the pSHF from E9.5 embryos and compared the Shh mutant samples with than of wild-type using Agilent 4x44k Mouse Whole Genome Arrays (n = 4 WT pools and 4 Shh - /- pools).

overall_design: Microdissected pSHF from E9.5 mouse embryos was molecularly verified by real-time PCR.  Shh mutant embryos were compared with wild-type embryos. Four independnet pools of RNAs from each biological group were measured on 1-color Agilent Mouse Whole Genome Arrays (n = 3 WT pools and 4 Shh -/- pools).

first: Andrew

middle: D

last: Hoffmann

first: Ivan

last: Moskowitz


title: A panel of breast cell lines

status: Public on Feb 22 2013

city: Santa Monica

first: Judy

last: Dering

state: CA

address: 2825 Santa Monica Blvd. Suite 200

institute: UCLA School of Medicine

summary: RNA expression patterns of breast cell lines were compared with a breast cell line mixed reference.

overall_design: Gene expression profiles of 52 individual breast cell lines relative to a breast cell line reference mix containing equal amounts of 10 breast cell lines.

last: Finn

first: Hsiao

first: Charles

last: Ginther

first: Dennis

last: Slamon


title: Posterior Second Heart Field (pSHF) Transcriptomes of Wild-type and Tbx5 Mutant Mouse Embryos

status: Public on Feb 08 2013

state: IL

summary: To understand Tbx5-Hedgehog molecular networks in the posterior second heart field (pSHF), we have employed whole genome microarray expression profiling as a discovery platform to identify genes with Tbx5-dependent expression changes.  We microdissected the pSHF from E9.5 embryos and compared the Tbx5 mutant samples with than of wild-type using Agilent 4x44k Mouse Whole Genome Arrays (n = 4 WT pools and 4 Tbx5 -/+ pools).

overall_design: Microdissected pSHF from E9.5 mouse embryos was molecularly verified by real-time PCR.  Tbx5 mutant embryos were compared with wild-type embryos. Four independnet pools of RNAs from each biological group were measured on 1-color Agilent Mouse Whole Genome Arrays (n = 4 WT pools and 4 Tbx5 -/+ pools).


title: Constitutive expression of activated NOTCH1 in fetal Sertoli cells dysregulates factors required for proper gonocyte maintenance and survival.

city: Urbana

first: Thomas

middle: Xavier

last: Garcia

address: 2001 S. Lincoln Ave

department: Department of Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary:
Genome-wide analysis of whole embryonic day 14.5 mouse testes constitutively expressing the activated intracellular domain of NOTCH1 in Sertoli cells. The goal of the study was to identify Sertoli cell expressed genes regulated by Notch signaling, which are critical to gonocyte maintenance and survival.
The mouse model was generated by intercrossing anti-Müllerian hormone (Amh)-cre transgenic mice and RosaNICD transgenic mice.

overall_design: Testes were dissected free from mesonephroi and testis pairs from a single fetus were pooled to generate a single sample. Littermates not expressing Amh-cre were used as controls. Testes from one control and one overexpressor fetus per dam from three separate dams were used for analysis.

first: Marie-Claude

last: Hofmann


title: Analyses of X-inactivation status in female human induced pluripotent stem cells

status: Public on Feb 06 2013

city: San Francisco

first: Kiichiro

last: Tomoda

address: 1650 Owens Street

institute: The Gladstone Institutes, UCSF

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

overall_design: Refer to individual Series


title: Xi-reactivation in female human induced pluripotent stem cells (hiPSCs)

summary: Female human induced pluripotent stem cell (hiPSC) lines exhibit considerable  variability in X-inactivation status. Some lines maintain one transcriptionally  active X chromosome (Xa) and one inactive X (Xi) from donor cells. However,  hiPSC lines that have two Xas are infrequently produced. We show here Xinactivation  status in female hiPSC lines depends on derivation conditions. hiPSC  lines generated using the Kyoto method, which employs leukemia inhibitory factor  (LIF)-expressing SNL feeders, frequently had two Xas. Lines derived on other  feeders maintained an Xi. In addition, there appears to be a window in which SNL  feeders promote Xi-reactivation. Upon differentiation, Xa/Xa hiPSCs silenced one  X. The efficient production of Xa/Xa hiPSC lines provides unprecedented  opportunities to understand human X-reactivation and inactivation.

overall_design: Gene expression patterns were compared between several human embryonic stem cell (hESC) and hiPSC lines. Gene expression ratios between genes on X and those on autosomes were calculated from each cell lines.

first: Shinya

last: Yamanaka

first: Barbara

last: Panning

first: Kazutoshi

last: Takahashi

first: Megumi

last: Narita


title: Decidual Endothelial Cells (DEC) and endothelial cells from human skin (ADMEC)

status: Public on Feb 01 2013

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

institute: Centro di Riferimento Oncologico

summary: BACKGROUND: endothelial cells (ECs) form a continuous barrier between blood and tissues and gate the traffic of molecules and cells across the vessel wall playing an active role in hemostasis, inflammation and immunity. Decidual endothelial cells (DECs) are located in a very special district from the immunological and inflammatory point of view since decidua has immunoregulatory and pro-angiogenic functions. The aim of this study was to compare the phenotype of microvascular ECs isolated from decidua with microvascular ECs isolated from other vascular districts. METHOD: we analyzed the differences in molecules involved in angiogenesis and leukocyte recruitment between DECs and endothelial cells from human skin (ADMECs) which are normally involved in inflammatory response by microarray analysis.   RESULTS: our results showed that DECs are able to produce high amount of the growth factors HGF, VEGF-A and IGFBP3, important for the control of angiogenesis and express the adhesion molecules ICAM2 and ICAM3 in basal condition, important molecules for the control of leukocyte recruitment and function. We demonstrated also that DECs do not up-regulate the expression of ICAM1 in response to pro-inflammatory cytokines and produce high amount of the chemokines CXCL9/MIG and CXCL10/IP-10 in response to IFN-a. CONCLUSION: we conclude that the phenotype of these cells strongly differs from that of other endothelial cells such as ADMECs which have to be quickly able to response to infections and other pro-inflammatory stimuli. These data suggest that endothelial cells may play an active in the control of local immune response at foeto-maternal interface.

overall_design: Single color gene expression in human endothelial cells. Six independent experiments (3 DEC vs 3 ADMEC) were performed using different donors for each experiment.

first: Elisa

last: Masat

first: Roberta

last: Bulla


title: Orientia tsutsugamushi, the agent of scrub typhus, induces an inflammatory program in human macrophages

status: Public on Jan 29 2013

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary: Scrub typhus is a life-threatening disease caused by Orientia tsutsugamushi, a bacterium that mainly infects endothelial cells in vitro and in vivo. Evidence suggests that the interaction of O. tsutsugamushi with myeloid cells may play a pivotal role in O. tsutsugamushi infection. We showed here that O. tsutsugamushi intensively replicated within human monocyte-derived macrophages. Bacterial organisms stimulated the expression of a large panel of genes including type I interferon, interferon-stimulated, inflammatory, apoptosis-related genes and induced an M1-type gene response in macrophages. This transcriptional signature was accompanied by functional consequences such as the release of inflammatory cytokines such as Tumor Necrosis Factor and interleukin-gamma. Live O. tsutsugamushi organisms were necessary for type I interferon response and, to a lesser degree, to inflammatory response. As interferon-gamma is known to elicit M1 polarization, we assessed the effect of interferon-gamma on O. tsutsugamushi fate in macrophages. Exogenous interferon-gamma partly inhibited O. tsutsugamushi replication within macrophages. Our results suggest that the inflammatory response induced by O. tsutsugamushi may account for the local and systemic inflammation observed in scrub typhus and that interferon-gamma may be useful as an adjuvant treatment of patients with scrub typhus.

overall_design: Macrophages (4 × 10.5 cells per assay) were incubated with O. tsutsugamushi at a bacterium-to-cell ratio of 20:1 for 8 hours.  RNA samples (four samples per experimental condition) were processed for microarray analysis.

first: Wiwit

last: Tantibhedhyangkul

first: Amira

last: Amara

first: Eric

last: Ghigo

first: Christian

last: Capo

first: Jean-Louis

last: Mège


title: Interferon-related transcriptional program is induced by chronic hepatitis E infection in kidney-transplant recipients

summary:
Background: Hepatitis E Virus (HEV) is a new causative agent of chronic hepatitis in solid organ transplant recipients in Europe. Factors associated with the occurrence and persistence of chronic HEV infection remain largely unknown but chronic evolution seems to be the consequence of host’s immunological factors rather than of viral factors.
Method: In a prospective case-control study, we have determined in whole blood of chronically HEV-infected kidney-transplant recipients the host response using microarray technology.
Results: Chronically HEV-infected kidney-transplant recipients exhibited a specific transcriptional program, in which interferon effectors were prominent. The intensity of expression of each signature’s gene was significantly lower in patients who were subsequently cleared of HEV than in patients who were not. Furthermore, in patients who were cleared of HEV, a higher expression of these genes was associated with a longer delay until HEV clearance.
Conclusions: The specific transcriptional program determined in chronically HEV-infected kidney-transplant recipients suggests an activation of type I interferon response. Intensity of interferon-stimulated genes expression could be useful to forecast the outcome of infection. High expression of interferon-stimulated genes could signify a dysregulation in the interferon response that might favour the persistence of the HEV infection.
Trial’s registration number: NCT01090232; Registry’s URL: http://clinicaltrials.gov/ct2/show/study/NCT01090232?term=kidney+transplant+recipients&cntry1=EU%3AFR&rank=2

overall_design: Total RNA was extracted from whole-blood sample or monocytes of kidney-transplant patients with or without chronic hepatitis E (CHE) infection. Control patients were matched up with CHE patients for age, sex, time since kidney transplant and immunosuppressive treatment.

first: Valérie

last: Moal

last: Ben Amara

first: Vikram

last: Mehraj

first: Yvon

last: Berland

first: Philippe

last: Colson

last: Mege


title: Genome-wide analysis of host mRNA translation during hepatitis C virus infection

first: Cyrille

last: Féray

summary: Sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells.

overall_design: Huh7 cells were infected with HCV JFH-1 strain. Controls consisted in non-infected cells and infected cells treated with an anti-protease. 3 days after infection, cell lysates were subjected to sucrose-gradient centrifugation in order to isolate polysome-free RNAs from polysome-bound (translated) RNAs. The non-polysomal, polysomal as well as cytosolic (non fractionned) RNAs, from infected, non-infected, and infected-treated cells were subject sur microarray analysis.

first: Hélène

last: Colman

first: Catherine

last: Le Berre-Scoul

first: Céline

last: Hernandez

first: Sandra

last: Pierredon

first: Audrey

last: Bihouée

first: Rémi

last: Houlgatte

first: Stephan

last: Vagner

first: Arielle

middle: R

last: Rosenberg


title: Transcriptional response to aneuploidy in mouse epidermis

status: Public on Jan 22 2013

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

institute: University Medical Center Groningen

summary: Analysis of the transcriptional response to aneuploidy in mouse epidermis. In this study we measured the transcriptional response to aneuploidy by aboragting the spindle checkpoint in mouse epidermis. We found that, whereas spindle checkpoint inactivation in the epidermis is tolerated, but results in metabolic deranged cells, SAC abrogation kills bulge stem cells

overall_design: Mad2; K14-Cre mice were sacrificed at indicated timepoints and epidermis was separated from dermis using overnight trypsin. RNA was isolated and expression patterns were compared between K14-Cre; Mad2f/f and Cfre negative animals for all timepoints.


title: Illumina SNP and CNV data for the HuRef individual

city: Toronto

first: Andy

last: Pang

address: MaRS Centre - East Tower, 101 College Street, Room 14-701

institute: The Centre for Applied Genomics

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation.  Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. We applied a multi-step sequence and microarray-based analysis to identify numerous previously unknown SVs within the first genome sequence reported from an individual.

overall_design: An Illumina SNP array experiment was performed according to the manufacturer's directions on DNA extracted from a lymphoblastoid cell line (HuRef).


title: Immune and tumor cell gene expression from node positive and node negative breast cancers' primary tumor, lymph nodes and peripheral blood

status: Public on Jan 11 2013

city: Duarte

first: Peter

last: Lee

address: 1500 E Duarte Rd.

department: Cancer Immunotherapeutics and Tumor Immunology

institute: City of Hope

summary: Analysis of purified immune and breast tumor cells from three major compartments where cancer and immune cells interact: primary tumor, tumor draining lymph nodes (tumor invaded or tumor free), and peripheral blood.  The results suggests that node-positive patients’ immune regulation and functionality is down-regulated compared to node-negative patients.

overall_design: CD45+ Immune and ESA+ tumor cells were purified from breast cancer patients' primary tumor, tumor-draining lymph node, and peripheral blood (ficoll) and placed onto Agilent microarrays using the dye-swap method. A universal human reference was used as a reference for the patient samples.

first: Hongxiang

last: Yu

first: Diana

middle: L

last: Simons


title: IL-27, PXN, CXCR4, GZMA, PRF1 and Foxp3 genes are differentially expressed in CD4+ T cells of HTLV-1-infected individuals.

status: Public on Jun 01 2013

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

summary: HTLV-1 preferentially infects CD4+ T cells and these cells play a central role in HTLV-1 infection. In this study, we investigated the global gene expression profile of circulating CD4+ T cells from distinct clinical status of HTLV-1-infected individuals in regard to Tax expression levels. CD4+ T cells were isolated from asymptomatic HTLV-1 carrier (HAC) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients, in order to identify genes involved in the HAM/TSP development. Hierarchical clustering analysis showed that healthy controls (CT) and HTLV-1-infected samples clustered separately. We also observed that HAC and HAM/TSP groups clustered separately regardless Tax expression. The gene expression profile of CD4+ T cells was compared among CT, HAC and HAM/TSP groups. The IL-27, PXN, CXCR4, GZMA, PRF1 and Foxp3 genes were differentially expressed between HAC and HAM/TSP groups and the frequency of CD4+Foxp3+ regulatory T cells (Treg) were higher in HTLV-1-infected individuals. These findings suggest that CD4+ T cells activity is distinct between HAC and HAM/TSP groups as expected.

overall_design: In order to study the transcriptional changes in CD4 T cell from HTLV-1-infected individuals, immunomagnetically purified CD4+ T-cells from the peripheral blood of 4 asymptomatic HTLV-1 carrier individuals (HAC) and 4 individuals with HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP), as well as from 4 healthy controls (CT) were isolated and processed the microarray assay according Agilent's protocol. The differential expressed genes, molecular characterization and networks analysis were evaluated using robust bioinformatic tools, then  the real time PCR was done to validate the genes.

first: Mariana

middle: T

last: Pinto

first: Tathiane

last: Malta

first: Evandra

middle: S

last: Rodrigues

first: Rodrigo

last: Panepucci

first: Kelen

last: Malmegrim de Farias

first: Alessandra

last: Sousa

first: Osvaldo

last: Takayanagui

first: Yuetsu

last: Tanaka

first: Dimas

last: Covas

first: Simone

last: Kashima


title: Exression profiling of 9-cisRA in adrenocortical carcinoma cell line

status: Public on Feb 10 2013

city: Budapest

middle: Rita

last: Szabo

address: Szentkirályi u. 46

country: Hungary

institute: Semmelweis University

summary: Adrenocortical carcinoma is a rare tumour with a poor prognosis. The currently available medical treatment options of adrenocortical cancer are limited. In the present study we examine the potential antitumoral effects of 9-cis-retinoic acid (9-cisRA) on the adrenocortical cancer cell line NCI-H295R.

overall_design: For the gene expression profiling, H295R cells were treated for 24h with 9cisRA at a final concentration of 2.5*10-5, 5*10-5 and 7.5*10-5 M and for the contol with the same amount of ethanol.

first: D

first: P

middle: M

first: K

last: Eder

first: A

last: Falus

last: Racz

last: Igaz


title: Gene expression profiling of dsDNA90 or ssDNA90 stimulated Mouse Embryonic Fibroblasts

status: Public on Jan 15 2013

city: Miami

first: Tianli

last: Xia

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

summary: Gene expression analysis of wild type, STING knock-out and STAT1 knock-out Mouse Embryonic Fibroblasts (MEFs) stimulated with 90-mer dsDNA or 90-mer ssDNA. Genes whose expression that are affected by cytosolic DNA in a STING dependent manner will be identified and signaling pathways regulated by STING will be elucidated.

overall_design: Primary MEFs were mock treated or transfected with dsDNA90 or ssDNA90 for 3 hours. Total RNA was then extracted for array analysis.

first: Glen

last: Barber


title: Expression of genes in the spleen of WT and MUC1.Tg mice immunized with dendritic cells loaded with MUC1 peptide

status: Public on Jan 16 2013

city: New York

first: Adam

last: Farkas

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Goal of study: To determine differentially expressed genes with potential roles in tolerance and immunity in MUC1-immunized WT and MUC1.Tg mice

overall_design: WT (C57Bl/6) and MUC1.Tg mice were immunized (i.v.) with dendritic cells loaded with sythetic, human MUC1 peptide. At 24h and 72h splenic RNA from vaccination groups (n=3) was pooled and microarray performed.

first: Olivera

last: Finn