title: Delineating the transcriptional network of prognostic gene signatures refines treatment recommendations for lymph node negative breast cancer patients

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

institute: Trinity College Dublin

summary: To define proliferative and senescent cell transcriptional profiles, we performed genome-wide expression analyses of growing and senescent mouse embryonic fibroblasts (MEFs)

overall_design: MEFs were passaged from P1 (growing) to P7 (replicative senescence) and RNA was harvested from 3 independent MEF lines at P2 and P7. This RNA was used for genome-wide expression analyses.

first: Adrian

last: Bracken

first: Gerard

last: Brien


title: Comparison of the expression profiles of the 630E JIR8094 strain and a prdR mutant in the presence of proline in TY

status: Public on Oct 01 2015

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

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

overall_design: Refer to individual Series


title: MicroRNA expression analysis of livers of F1 male offspring fathered from control mice or stressed mice

status: Public on Sep 29 2015

city: Shanghai

first: Yan

last: Lu

address: 180 Fenglin Road

department: Department of Endocrinology and Metabolism

country: China

institute: Zhongshan Hospital, Fudan University

summary: Psychological stress is highly prevalent in modern society. Both epidemiologic and experimental animal studies demonstrate that chronic psychological stress exerts adverse effects on the initiation and/or progression of many diseases. Here, using a mouse model of restraint stress, we report the discovery of a novel signaling pathway linking paternal stress exposure to the reprogram of hepatic gluconeogenesis in the offspring. Offspring fathered by stressed males (Stress-F1) exhibits hyperglycemia as a result of enhanced hepatic gluconeogenesis, conpared to offspring from control fathers (Control-F1). Mechanistically, protein levels of PEPCK, a key gluconeogenic enzyme, were significantly increased, while its mRNA levels were unaffected in the stress-F1 mice, pointing to a posttranscriptional regulatory mechanism. Because MicroRNAs often play an important role in regulating gene expression at the posttranscriptional level, we investigated the expression profile of MicroRNAs in livers from Control-F1 and Stress-F1 mice.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Liver tissues were collected from 12-week-old male control-F1 and stress-F1 mice (n=3 for each group). After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0). Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.

first: Ling

last: Wu


title: miRNA profiling of MYCN-amplified Neuroblastoma cell lines

status: Public on Sep 24 2015

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: miRNA expression levels have been profiled on 13 MYCN-amplified Neuroblastoma cell lines

overall_design: Extracted miRNA for each cell lines have been hybridized on Agilent Human miRNA Microarray v2

first: Viktoryia

last: Sidarovich

first: Paola

last: Scaruffi

first: Gianpaolo

last: Tonini

first: Alessandro

last: Quattrone


title: Use of toxicogenomics for screening of estrogenic activity

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Due to its high throughput nature, toxicogenomics can provide a broad picture of a toxic response, offering the ideal functional platform for grouping chemicals according to mechanistic similarity. In this way, toxicogenomics has found its way into predictive toxicology. However, so far, the predictive potential of toxicogenomics in an endocrine disruptive screening context has not been extensively examined. The aim of this study was to combine a toxicogenomics approach with an estrogen-sensitive MCF-7 cell system.  In total, 18 compounds with endocrine disruptive potential were selected, of which 11 are listed as ICCVAM reference compounds for validation of estrogen receptor (ER) binding and transactivation assays. In this way, the grouping and classification potential of the gene expression profiles could be directly compared to the more classical estrogenicity screens, such as ER binding, ER transactivation and MCF-7 cell proliferation assays. Results indicated that this toxicogenomics approach was clearly capable of grouping compounds into strong, weak and non estrogenic groups. This demonstrates the value of toxicogenomics for evaluating gradual differences in related modes of action, in addition to the more common search for opposite modes of action.  The chemical groups were represented by interesting marker genes such as PGR, ERBB2, CXCL12, AREG and EGR3, including some early-responsive (4h) potential biomarkers. These results open the discussion on the added value of a broader endpoint evaluation in estrogenicity screens provided by omics-techniques compared to the classical single endpoint based assays.

overall_design:
The samples are hybridized in 12 loop designs that can be connected in the analysis via a reference sample that all loop designs have in common.

The 11 ICCVAM reference compounds are: 17beta-estradiol, 2,3,7,8 Tetrachloro-dibenzo-p-dioxin, Atrazine, Genistein, Nonylphenol, Kepone, Testosterone, Methoxychlor, Lindane, p,p'-DDT, Diethylhexylphthalate.

first: Caroline

last: Vanparys

first: Marleen

last: Maras

first: Koen

last: Van Leemput

first: Karlijn

last: van der ven

first: Joke

last: Allemeersch

first: Jurgen

last: Del Favero

first: Paul

last: Van Hummelen

first: Ronny

last: Blust

first: Wim

last: De Coen


title: Expression data for effect of p300 knockdown and Doxorubicin treatment in cardiac myocytes

city: Miami

first: Sumit

last: Jain

state: Florida

address: 1600 NW 10th Avenue RMSB 6041

department: Molecular and Cellular Pharmacology

country: USA

institute: University of Miami

summary:
Role of p300 in regulation of stress-response genes in heart is not clear. Treatment with anti-cancer drug Doxorubicin causes cardiotoxicity through generation of oxidative stress in cardiac myocytes. Loss of p300 enhances cell death and apoptosis in response to Doxorubicin. The objective of this study was to determine if expression of genes regulated by oxidative stress is dependent of presence of p300. Further we investigated if protective effect of p300 against Doxorubicin was due to gene expression effects of p300.
We used microarray to compare the transcriptomes of cardiac myocytes transfected with anti-p300 or non-silencing siRNA beforebefore and after exposure to Doxorubicin.

overall_design: p300 was knocked down (p300kd) in primary culture of rat neonatal cardiac myocytes by using siRNA (Dharmacon). Cardiac myocytes transfected with non-siliencing siRNA (NS) were used as control. p300kd was confirmed by western blotting and real time PCR. Both NS and p300kd cells were treated for either 0 or 8 hrs with 1 micromolar Doxorubicin (Dox). Samples include p300kd and nonsilencing cells (0 and 8 hr Dox) from three different experiments.

first: Nanette

middle: H

last: Bishopric


title: Clostridium difficile C630E: growth in TY with 30 mM proline vs. growth in TY alone

first: Monot

last: Marc

summary:
Clostridium difficile, a proteolytic Gram-positive anaerobe, has emerged as a significant nosocomial pathogen. Stickland fermentation reactions are thought to be important for growth of C. difficile. In Stickland reactions, pairs of amino acids donate and accept electrons, generating ATP and reducing power in the process. Reduction of the electron acceptors proline and glycine requires the D-proline reductase (PR) and the glycine reductase (GR) enzyme complexes, respectively. PrdR, a sigma54-dependent regulator, activates transcription of the PR-encoding genes in the presence of proline and negatively regulates the GR-encoding genes, suggesting that PrdR is a central metabolism regulator that controls preferential utilization of proline and glycine to produce energy via the Stickland reactions.

Here, transcriptional profiling of C. difficile comparing growth in TY medium supplemented with 30 mM L-proline to growth in TY medium alone is performed.

overall_design: Two-condition experiment: TY with excess of proline vs. TY alone. 2 biological replicates for each condition, including a dye-swap.

first: Laurent

last: Bouillaut

first: Thomas

last: Dubois

first: Marc

last: Monot


title: Nucleosome Repositioning: Nicotine- and Cocaine-induced Changes

status: Public on Aug 07 2015

city: Tallahassee

first: Cynthia

last: Vied

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

type: Genome binding/occupancy profiling by array

summary: SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Drugs of abuse modify behavior by altering gene expression in the brain.  Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug-naive positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.

overall_design: SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Two independently grown biological replicates for each time point and condition, and two controls were processed.

first: Amber

middle: N

last: Brown

first: Jonathan

last: Dennis

first: Pradeep

middle: G

last: Bhide


title: Characterization of Pneumococcal Genes Involved in Bloodstream Invasion in a Mouse Model

status: Public on Sep 19 2015

city: Adelaide

first: Mark

middle: B

last: Van der Hoek

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Streptococcus pneumoniae (the pneumococcus) account for significant morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteremia and meningitis. In this study, we used microarray analysis to compare gene expression patterns of either serotype 4 or serotype 6A pneumococci in the nasopharynx and blood of mice, as a model to identify genes involved in invasion of blood in the context of occult bacteremia in humans.

overall_design: Microarray experiments were performed on whole genome S. pneumoniae PCR arrays obtained from the Bacterial Microarray Group at St George's Hospital Medical School, London (http://bugs.sghms.ac.uk/). The array was designed using TIGR4 base strain annotation and extra target genes from strain R6. Pair-wise comparisons were made between the nasopharynx and blood RNA samples labeled with either Alexa Fluor 546 or Alexa Fluor 647 dye from the 48, 72 and 96 h time points.

first: Abiodun

last: Ogunniyi


title: Identification of genes responsible for RelA-dependent proliferation arrest in HMEC conditionally expressing RelA

status: Public on Sep 26 2015

city: Boston

first: Bose

middle: Skaria

last: Kochupurakkal

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Immuno-histochemistry for RelA in breast tumors revealed a range of staining intensity and negative correlation between RelA levels and proliferation-index in estrogen receptor-positive tumors. Conditional expression of RelA arrested proliferation in primary mammary and fallopian tube epithelial cells. RelA dependent CDK4 downregulation was responsible for activating the G1/S checkpoint and cell cycle arrest. RelA target genes, including Interferon Response Factors (IRF), were up-regulated in the arrested cells. Among the IRFs, IRF1 expression correlates with RelA expression. Suppressing IRF1 restored CDK4 levels and rescued RelA-dependent proliferation arrest analogous to abrogating the G1/S checkpoint or restoring CDK4 levels. Apart from cyclins, regulation of CDK4 by the RelA-IRF1 transcriptional network controls proliferation of breast tumors and predicts sensitivity to a CDK4/6 inhibitor.

overall_design: Stable HMEC harboring the two plasmid Tetracycline inducible system (Clontech). HRA cells are stable pooled clones of HMEC cells that express RelA in a Doxycycline (Dox) dependent manner. Triplicate samples for gene expression analysis were generated by plating HRA cells at low density and harvested after subjecting them to four conditions 24 hours post plating (time 0 of the experiment): i) Uninduced (No Dox sample), harvested on successive days i.e. 24, 48 and 72 hours after time 0; ii) Induced with Dox for 24 hours (24+ sample) at time 0, 24 and 48, and harvested 24 hours later; iii) Induced with Dox at time 0 and harvested 72 hours later (72+ sample) and iv) Induced with Dox at time 0, Dox withdrawn at time 24 and harvested at 72 hours. Dox+/Dox- media in all plates were changed every 24 hours as required. See supplementary Figure S5 for a schematic representation of the protocol.

middle: S


title: Clinical and prognostic relevance of squalene epoxidase in breast cancer

status: Public on Jul 28 2015

city: Genova

first: Patrizio

last: Castagnola

state: GE

address: Largo Rosanna Benzi 10

institute: IRCCS AOU San Martino - IST

type: Genome variation profiling by genome tiling array

summary: All cell lines were purchased from ATCC (LGC Standards S.r.l., Milan, Italy), except T-47D and MDA-MB-468 that were obtained from the National Cancer Institute Developmental Therapeutics Program (Frederick, MD).

overall_design: Six untreated breast cancer cell lines grown according to the growth protocol reported below

first: David

first: Irene

last: Caffa

first: Gabriella

last: Cirmena

first: Daniela

last: Piras

first: Anna

last: Garuti

first: Maurizio

last: Gallo

first: Alessio

last: Nencioni

first: Alberto

last: Ballestrero

first: Gabriele

last: Zoppoli


title: ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary:
Investigation of parasite (T. annulata) gene expression over the course of the life-cycle (sporozoite->macroschizont->merozoite->piroplasm).
The study focused on the expression of known and putative transcription factors, in particular members of the ApiAP2 gene family. Up-stream motifs associated with stage-specifically expressed genes were identified during the course of the analysis.

platform_organism:
Theileria annulata
Bos taurus

overall_design: The experiment investigates Theileria annulata gene expression over a differentiation time-course - sporozoite through to piroplasm. 20 samples were analyzed - 4 x sporozoite (replicates), 3 x macroschizont (replicates), 3 x day 4, 3 x day 7, 3 x day 9 (replicates) and 4 x piroplasm (replicates)

first: Marta

last: Pieszko

first: Ian

last: Goodhead

first: Jane

last: Kinnaird

first: Brian

last: Shiels


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Altered SRY Genomic Binding During Gonadal Sex Determination

status: Public on Aug 28 2015

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Genome binding/occupancy profiling by genome tiling array

summary: A critical transcription factor required for mammalian male sex determination is SRY (sex determining region on the Y chromosome).  The expression of SRY in precursor Sertoli cells is one of the initial events in testis development. The current study was designed to determine the impact of environmentally induced epigenetic transgenerational inheritance on SRY during gonadal sex determination in the male. The agricultural fungicide vinclozolin and vehicle control (DMSO) exposed gestating females (F0 generation) during gonadal sex determination promoted the transgenerational inheritance of differential DNA methylation in sperm of the F3 generation (great grand-offspring). The fetal gonads in F3 generation males were used to identify potential alterations in SRY binding sites in the developing Sertoli cells. Chromatin immunoprecipitation with an SRY antibody followed by genome-wide promoter tiling array (ChIP-Chip) was used to identify alterations in SRY binding. A total of 81 adjacent oligonucleotide sites and 173 single oligo SRY binding sites were identified to be altered transgenerationally in the Sertoli cell vinclozolin lineage F3 generation males. Observations demonstrate the majority of the previously identified normal SRY binding sites were not altered and the altered SRY binding sites were novel and new additional sites. The chromosomal locations, gene associations and potentially modified cellular pathways were investigated. In summary, environmentally induces epigenetic transgenerational inheritance of germline epimutations appears to alter the cellular differentiation and development of the precursor Sertoli cell SRY binding during gonadal sex determination that influence the developmental origins of adult onset testis disease.

overall_design: The experimental design involved the intraperitoneal exposure of gestating female rats to vinclozolin or a vehicle control (dimethyl sulfoxide, DMSO) transiently from embryonic days E8-E14. Sister littermates were divided into control and vinclozolin treatment groups and mated to similar males to minimize the genetic variation between the control and vinclozolin lineages.   Sufficient females were used so no inbreeding (sibling or cousin) occurred in any generation.  The F1 generation was bred within the lineage to generate the F2 generation and these F2 generation bred to generate the F3 generation.  The only exposure was the F0 generation female.  The F3 generation control and vinclozolin lineage embryonic day 13 (E13) embryos were collected and the gonads micro-dissected and then sexed with an SRY PCR protocol.  The male gonads were pooled from a minimum of three different litters and the pools used to collect DNA.  Three different experiments were performed to collect 3 control and vinclozolin E13 F3 generation testis pools, each with different animals (n=25 gonads/pool).  The chromatin DNA (not denatured) from each pool was fragmented and used in an SRY chromatin immunoprecipitation (ChIP) procedure for each pool separately.  The control and vinclozolin SRY ChIP DNA were paired for a competitive hybridization on a genome-wide promoter tiling array (ChIP-Chip) assay. The hybridization data obtained was used to identify the SRY binding sites that were different in the F3 generation vinclozolin versus control lineage in E13 testis.

first: Ramji

last: Bhandari

first: M

middle: M

last: Haque

first: Eric

middle: E

last: Nilsson


title: microRNA expression in thymic epithelial cells

city: San Francisco

first: Imran

last: Khan

state: CA

address: 513 Parnassus Ave, HSW 1102

department: Diabetes Center

institute: University of California, San Francisco

summary: Thymic epithelial cells (TECs) support T cell development in the thymus. Cortical thymic epithelial cells (cTECs) facilitate positive selection of developing thymocytes whereas medullary thymic epithelial cells (mTECs) facilitate the deletion of self-reactive thymocytes in order to prevent autoimmunity. The mTEC compartment is highly dynamic with continuous maturation and turnover, but the genetic regulation of these processes remains poorly understood. MicroRNAs (miRNAs) are important regulators of TEC genetic programs since miRNA-deficient TECs are severely defective. However, the individual miRNAs important for TEC maintenance and function and their mechanisms of action remain unknown. Here, we demonstrate that miR-205 is highly and preferentially expressed in mTECs during both thymic ontogeny and in the postnatal thymus. This distinct expression is suggestive of functional importance for TEC biology. Genetic ablation of miR-205 in TECs, however, neither revealed a role for miR-205 in TEC function during homeostatic conditions nor during recovery from thymic stress conditions. Thus, despite its distinct expression, miR-205 on its own is largely dispensable for mTEC biology.

overall_design: In order to identify miRNAs differentially expressed in mTECs, we purified cortical thymic epithelial cells (cTECs), mTECs and CD45+ cells as three distinct populations and prepared RNA for microarray analysis. Thymic subsets were FACS-purified from 4-week old NOD wildtype mice. Thymi from 10-12 female mice were pooled together for stromal cell isolation for a total of 3 CD45+, 2 cTEC and 3 mTEC biologic replicates.

first: Lukas

last: Jeker

first: Mark

last: Anderson

first: David

last: Erle

first: Joshua

last: Pollack

first: Andrea

last: Barczak


title: Transcriptome characterization of genotype-dependent effects of CaCl2 treatment on drought adaptation in barley (Hordeum vulgare L.).

status: Public on Sep 30 2015

city: Poznań

first: Małgorzata

last: Kaczmarek

address: Strzeszyńska 34

department: Department of Environmental Stress Biology

country: Poland

institute: Institute of Plant Genetics

summary:
The hypothesis whether CaCl2 seed treatment prior to sowing (osmopriming) can enhance drought stress tolerance, and/or alleviate the effect on plant growth was tested.
Here we elucidate whether seed treatment prior to sowing (osmopriming) with CaCl2 can improve the drought stress tolerance, as it was previously reported for salt stress on wheat. Thus the effect of 50 mM CaCl2, previously chosen based on pilot experiment, versus water-treated control exposed to drought stress was investigated.

overall_design: The experiment was carried out with two spring barley genotypes differing in the response to drought stress: Sebastian and Georgia.  A pot experiment was arranged with two seeds treatments (50 mM CaCl2 versus water), two plants treatments at the stage of three-week old plants (drought stress and control) and three replications (10 plants/replication) under controlled conditions in a growth chamber, with the following parameters maintained: 22/18°C day/night, 30% RH and the photoperiod of 16h. The youngest leaves were taken at three selected time points, corresponding to field water capacity (pF) of 3.2, 3.6, and 4.2 in the following days, for RNA extraction and hybridization with Affymetrix microarrays.

first: Malgorzata

first: Paweł

last: Krajewski

first: Grzegorz

last: Koczyk

first: Olga

last: Fedorowicz-Strońska

first: Katarzyna

last: Głowacka

first: Jan

last: Sadowski


title: aCGH profiling of MYCN-amplified Neuroblastoma cell lines

first: Erik

last: Dassi

summary: Genome copy-number status has been profiled on 13 MYCN-amplified Neuroblastoma cell lines

overall_design: Extracted DNA for each cell lines has been hybridized on Agilent Human Genome CGH Microarray 244A

first: Viktoryia

last: Sidarovich

first: Paola

last: Scaruffi

first: Gianpaolo

last: Tonini

first: Alessandro

last: Quattrone


title: Histone dosage and gene expression changes in Halobacterium salinarum

status: Public on Aug 31 2015

city: Durham

first: Keely

last: Dulmage

state: NC

address: FFSC3242, 124 Science Drive

department: Biology

institute: Duke University

summary: We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent.  To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

overall_design: The histone deletion mutant and parent strain, at log and stationary phase, were compared to the common reference strain NRC-1 (log). There are three biological replicates each, plus dye-flips, for a total of 24 arrays

middle: A

first: Amy

last: Schmid


title: The effects of permethrin on the transcriptome of an endangered fish, the delta smelt (Hypomesus transpacificus)

status: Public on Sep 01 2015

city: Davis

first: Ken

last: Jeffries

address: One Shields Avenue

institute: UC Davis

summary: Research on the effects of contaminants on fishes is often conducted on well-studied model test species, whose responses may be different than those of species of conservation concern. We used an oligonucleotide microarray to examine the effects of permethrin, a widely used pyrethroid pesticide, on a critically endangered fish species endemic to Northern California, the delta smelt (Hypomesus transpacificus). These results demonstrate the effects of a widely used pesticide on a sensitive fish species at concentrations below those that affect model test species.

overall_design: Twenty samples were run on twenty arrays, there were four replicates for each of four permethrin exposure concentrations and a control group.

first: Lisa

last: Komoroske

first: Jennifer

last: Truong

first: Inge

last: Werner

first: Matthias

last: Hasenbein

first: Simone

first: Nann

last: Fangue

first: Richard

last: Connon


title: Inhibition of 13-cis retinoic acid-induced gene expression of reactive-resistance genes by thalidomide in glioblastoma tumours in vivo

status: Public on Jul 23 2015

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: The cell differentiation potential of 13-cis retinoic acid (RA) has not succeeded in the clinical treatment of glioblastoma (GBM) so far. However, RA may also induce the expression of disistance genes such as HOXB7 which can be suppressed by Thalidomide (THAL). Therefore, we tested if combined treatment with RA+THAL may inhibit growth of glioblastoma in vivo. Treatment with RA+THAL but not RA or THAL alone significantly inhibited tumour growth. The synergistic effect of RA and THAL was corroborated by the effect on proliferation of glioblastoma cell lines in vitro. HOXB7 was not upregulated but microarray analysis validated by real-time PCR identified four potential resistance genes (IL-8, HILDPA, IGFBPA, and ANGPTL4) whose upregulation by RA was suppressed by THAL. Furthermore, genes coding for small nucleolar RNAs (snoRNA) were identified as a target for RA for the first time, and their upregulation was maintained after combined treatment. Pathway analysis showed upregulation of the Ribosome pathway and downregulation of pathways associated with proliferation and inflammation. Combined treatment with RA + THAL delayed growth of GBM xenografts and suppressed putative resistance genes associated with hypoxia and angiogenesis. This encourages further pre-clinical and clinical studies of this drug combination in GBM.

overall_design: The purpose was to study differential gene expression in glioblastoma xenografts after treatment with 13-cis retinoic acid (RA), thalidomide (Thal) or a combination of both drugs.

first: Dusan

last: Milanovic

last: Herskind


title: MiRNA expression arrays from esophageal squamous cell carcinomas with different neoadjuvant chemoradiotherapy response

status: Public on Jul 27 2015

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
Preoperative chemoradiotherapy (CRT)  followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patients’ survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response.
We aim to identify miRNA markers for ESCC CRT-response prediction through miRNA expression analyses.

overall_design: MiRNA expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery using Agilent human miRNA microarrays based on miRBase (release 18.0) GeneChip®.

first: Jianhua

last: Fu


title: Human Fibroblast cells immortalised cells: Control vs DNA damage

city: Bethesda

first: Vivek

last: Sharma

state: MD

address: 41 Library Drive

department: CCR

institute: NCI

summary:
Transcriptional profiling of human fibroblast cells after DNA damage with Camptothecin or Etoposide or Neocarzinostatin
Upon DNA damage, the DNA damage response (DDR) elicits a complex signaling cascade, which includes the induction of multiple non-coding RNA species. Recently long non-coding RNAs (lncRNAs) have been shown to contribute to DDR by regulating gene expression. However, very little is known about the role that lncRNAs play in regulating DNA Repair. Using a genome-wide microarray screen we identified a novel ubiquitously expressed lncRNA, DDSR1 (DNA damage-sensitive RNA 1), which is induced upon DNA damage by several DNA double-strand break (DSB) agents.

overall_design: Two-condition experiment, Control vs. DNA damage human fibroblast cells. No Replicates, DNA damage was induced with either Camptothecin or Etoposide or Neocarzinostatin, Total RNA or Nuclear RNA was profiled.

first: Tom

last: Misteli


title: Diagnosis of Early-Stage Parkinson's Disease Using Autoantibodies as Blood-based Biomarkers

city: Stratford

first: Robert

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Human serum samples from early-stage Parkinson's disease and non-diseased controls were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators.  Other neurodegenerative and non-neurodegenerative diseases were also used to help measure the specificity of the selected biomarkers.

overall_design: In the study presented here, 103 Early-stage Parkinson's disease and 156 control human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies.  Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant differences in group prevelance were selected as potential biomarkers of disease.  Prediction classification analysis using Invitrogen's Prospector v5.2.1 and Random Forest tested the diagnostic efficacy of the identified biomarkers.  Differentiation of early-stage PD samples from other neurodegenerative and non-neurodegenerative controls (Alzheimer's disease, multiple sclerosis, and breast cancer) assessed the specificity of the selected biomarkers, while comparison with mild-moderate Parkinson's disease samples assessed their utility for use in disease staging.

first: Cassandra

last: DeMarshall

first: Min

last: Han

first: Eric

middle: P

first: Abhirup

last: Sarkar

first: Nimish

last: Acharya

first: George

last: Godsey

middle: L

last: Goldwaser

first: Mary

last: Kosciuk

first: Umashanger

last: Thayasivam

first: Benjamin

last: Belinka


title: High-density deletion bin map of wheat D genome

status: Public on Jul 22 2015

city: Albany

first: Yi

last: Wang

address: 800 Buchanan Street

institute: USDA, ARS, WRRC

summary: A NimbleGen array containing both gene-based and RJM repeat junction probe sequences derived from Ae. Tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes.

overall_design: The NimbleGen array was hybridized in duplicate with Cy3 labeled seven nullisomic-tetrasomic lines, deletion bin lines for D genome chromosomes, and control reference Chinese Spring; as well as Cy5 labeled reference line Chinese Spring.

first: Yong

middle: Q

last: Gu


title: Transcriptional profile comparing Hep3B transfected with miR-19b inhibitor with Hep3B transfected with control

city: ChaiYi county

first: Chung-Lin

last: Hung

address: No.2, Minsheng Rd., Dalin Township,

department: Division of Oncology and Hematology, Department of Internal Medicine,

country: Taiwan

institute: Buddhist Dalin Tzu Chi General Hospital

summary: miR-19b was up-regulated with hepatocellular carcinoma. We compared the transcriptional profile of Hep 3B transfected with miR-19b inhibitor with Hep3B transfected with control to identify genes affected by miR-19b knockdown.

overall_design: Hep 3B_miR-19b transfected vs Hep 3B_control transfected

first: Chia-Jui

last: Yen


title: Real-time quantitative PCR analysis for validation of miRNAs expressed during osteogenic differentiation of bone marrow MSCs versus healthy donors MSCs

status: Public on Jul 14 2015

city: Madrid

first: José Ramón

middle: Lamas

last: Lamas

state: MADRID

address: Calle Profesor Martín Lagos s/n. Hospital Clínico san Carlos

department: Rheumatology

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC)

summary: Total small RNA was isolated from BM-MSCs obtained from OA diagnosed patients (n=10) and non-OA (n=10 after osteogenic induction for 1, 10 and 21 days. miRNAs, were initially screened and those with consistent differential expression were selected for further validation by qRT-PCR analysis.

overall_design: From an initial screening of 246 differentially expressed miRNAs (fold change ≥± 2, P ≤0.05) between OA and non-OA BM-MSC samples 21 were selected and validated by qRT-PCR

first: Pilar

last: Tornero-Esteban

first: Luis

last: Rodríguez-Rodríguez

first: Lydia

last: Abásolo

first: María

last: Tomé

first: Pedro

last: López-Romero

first: Eva

last: Herranz

first: Manuel

last: González

first: Fernando

last: Marco

first: Enrique

last: Moro

first: Benjamín

last: Fernández-Gutiérrez

first: José


title: ATM deficiency in the absence of T cells promotes the development of NF-kB-dependent B cell lymphomas [aCGH]

status: Public on Jul 18 2015

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

summary:
Our model removes T cells as targets for lymphomagenesis as well as eliminating T cell-dependent immune surveillance. These mice  exclusively develop early onset IgM+ B cell lymphomas that histologically and genetically resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL).
This dataset includes the array CGH  of B-cell lymphomas (tumors) from ATMKO.CD3eKO mice.

overall_design: A total of 23 ATMKO.CD3εKO B cell lymphoma cell lines were established from tumor-bearing spleen cells. DNA was extracted and labeled according to manufacturer's protocols. DNA from normal spleens was used as a reference DNA for these experiments.

first: Karen

last: Hathcock

first: Hesed

last: Padilla-Nash

first: Dong-Mi

last: Shin

first: Daniel

last: Triner

first: Robert

middle: W

last: Maul

first: Seth

last: Steinberg

first: Patricia

middle: J

last: Gearhart

first: Herbert

middle: C

last: Morse III

first: Thomas

last: Ried

first: Richard

last: Hodes


title: The effect of mitochondrial uncoupling in murine skin samples using Keratin 5-UCP3 trangenic model

city: Austin

first: Edward

last: Mills

state: Texas

address: 107 W. Dean Keeton, BME 3.510D

department: Pharmacology/Toxicology

institute: University of Texas at Austin

summary: Uncoupling protein 3 (UCP3) is a nuclear encoded, member of the mitochondrial solute carrier family which localizes to the inner mitochondrial membrane and dissipates the proton gradient used to drive ATP synthesis. UCP3 is expressed at low levels in skin and our lab has demonstrated that overexpression of UCP3 in epidermis (K5-UCP3 mice) provides marked resistance to two-stage chemical carcinogenesis protocols in skin.  To further understand the mechanisms by which UCP3 promotes this cancer resistant phenotype, we performed a microarray analysis of dorsal skin biopsies from wild type FVB/N and K5-UCP3 mice.  The results of this array indicate that UCP3 overexpression in skin enhances keratinocytes differentiation and fatty acid oxidation in skin, and taken together with other data we have provided a mechanistic link between fatty acid oxidation and Akt inhibition in UCP3-mediated cancer resistance.

overall_design: Whole skin biopsies were taken from dorsal skin of 7 week old male wild type FVB/N (n=3) and K5-UCP3 mice (n=3) and RNA was isolated using Trizol Reagent followed by clean up using the Qiagen Rneasy Kit.  Samples were amplified from 100ng RNA using the Illumina RNA Amplification Kit. Biotin-16-UTP was used to label transcripts which were then hybridized (700ng per array) to the Illumina Mouse-6 v1.0 BeadChip.  Arrays were scanned with an Illumina bead array reader confocal scanner.  Array data processing was performed using the Illumina BeadStudio software.

first: Sara

last: Nowinski

first: Ashley

last: Solmonson

first: Cory

last: Lago


title: Allergic contact dermatitis to nickel is characterized by a specific microRNA signature [KCs]

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

summary: We found that keratinocytes (KCs) (from healthy subjects) stimulated with nickel were characterized by a specific miRNA signature that were different from vehicle-stimulated KCs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition experiment, nickel vs. vehicle challenged keratinocytes (KCs). Biological replicates: 3 healthy subjects. One replicate per array.  Sample 1-6 (A28-A33)

first: Beatrice

last: Dyring-Andersen

first: Marie

middle: T

last: Vennegaard

first: Anders

last: Clemmensen

first: Charlotte

last: Bonefeld

first: Mads

last: Røpke

first: Lone

last: Skov


title: Prediction of the Mechanism of Action of Fusaricidin on Bacillus subtilis

status: Public on Jul 15 2015

city: shanghai

first: wenbang

last: yu

address: meilong road 130, east china university of science and technology, shanghai, china

summary: Transcriptome analysis of B.subtilis in response to cyclic lipopeptide antibiotic (fusaricidin)

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Transcriptional changes between fusaricidin-exposed and untreated B.subtilis.

first: Wen-Bang

last: Yu

first: Chun-Yun

last: Yin

first: Ying

last: Zhou

first: Bang-Ce

last: Ye


title: Rosette-forming glioneuronal tumour arising in the spinal cord: a case report and molecular profiling

status: Public on Jul 13 2015

city: Barretos

first: Rui

middle: Manuel

last: Reis

state: SP

address: R. Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

summary: Rosette-forming glioneuronal tumour (RGNT) of the IV ventricle is a very recent entity, recognized in the latest WHO classification of Central Nervous System Tumors. It is composed by two distinct features: a glial component, with typical characteristics of pilocytic astrocytoma, and a component forming neurocytic rosettes, with eosinophilic regions positive for synaptofisin and/or perivascular rosettes. Herein, we describe a 33-year-old man with RGNT arising in a peculiar location, namely the spinal cord. We further performed an extensive immunohistochemistry and molecular analysis, using array-CGH (aCGH), whole exome and cancer-related hotspot sequencing, in order to better understand its underlying biology. The histology revealed a WHO grade I RGNT typically found in the fourth-ventricle. Immunoreactivity for synaptophysin and neurofilament protein was noted in the neurocytic component, whereas the glial component exhibited positivity for GFAP and S-100. Neurocytic component was found negative for GFAP. Mitoses were rare, and there was no necrosis present.  Across all mutational analyses, there were detected somatic mutations in 4 genes: MLL2, CNNM3, PCDHGC4 and SCN1A. The tumor exhibited a microsatellite stable (MSS) phenotype. Array-CGH (aCGH) showed loss in 1p and gain of 1q, as well as gain of the whole chromosomes 7, 9 and 16. Moreover, we observed focal gains/losses in the chromosomes 1, 2, 3, 6, 7, 11, 14, 17, 22 and 23. Local amplifications in 9q34.2 (region with no genes mapped) and 19p13.3 (region encompassing the gene SBNO2) were identified. Additionally, we verified the KIAA1549-BRAF fusion, typically found in pilocytic astrocytomas, through aCGH, RT-PCR and FISH. Our comprehensive molecular profiling of a RGNT case suggests the existence of a unique genetic pathway for the development of these tumors: KIAA1549-BRAF fusion is a possible driver by constitutively activating MAPK pathway, and MLL2 mutation may lead to profound changes in the methylome. Taken together, these mechanisms may increase survival and/or tumorigenic capacity of cells, leading to the development of this rare entity.

overall_design: Two-color Agilent 8x60K array CGH (aCGH) was performed in the rosette-forming glioneuronal tumour (CY3) and reference DNA (CY5 - DNA extracted from leucocytes of the patient).

first: Lucas

last: Bidinotto

first: Cristovam

last: Neto

first: Alan

last: MacKay

first: Gisele

last: Almeida

first: Bernd

last: Scheithauer

first: Gustavo

middle: N

last: Berardinelli

first: Raul

last: Torrieri

first: Carlos

last: Clara

first: Leonir

last: Feltrin

first: Marta

last: Viana-Pereira

first: Marileila

last: Garcia Varella

first: Chris

last: Jones


title: Expression analysis of draculin (drl) expressing cells in embryonic zebrafish

city: Boston

first: Gabriel

last: Musso

address: 75 Francis St, Thorn 1123

department: Medicine

institute: Harvard Medical School

summary:
drl expression initiates during gastrulation and condenses as a band of cells at the prospective lateral embryo margin. In late epiboly, drl:EGFP is detectable as a band of scattered EGFP-fluorescent cells; after gastrulation, drl:EGFP-positive cells coalesce at the embryo margin that then in somitogenesis break down into the anterior and posterior lateral plate with subsequent cell migrations that form the posterior vascular/hematopoietic stripes and the anterior cardiovascular and myeloid precursors.
Data is as published in Mosimann & Panakova et al (Nature Communications, 2015)

overall_design: The same pool of homozygous drl:EGFP transgenic zebrafish were mass-mated 3 times and embryos collected at 2ss. Embryos were de-chorionated, homogenized, and sorted, then subject to mRNA isolation and expression analysis.

first: Leonard

last: Zon

first: Christian

last: Mosimann


title: Transcription Profiling of Malaria-Naïve and Semi-Immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge [RT-PCR]

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

summary: Whole blood gene expression was monitored in 85 samples using a Fluidigm nanoscale RT-qPCR array targeting 96 genes that we refer to as “blood informative transcripts” (BIT). There was no evidence for transcriptional changes prior to the appearance of blood stage parasite at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity. This samples are related with the samples with accession number GSE67184

overall_design: Reverse Transcription followed by quantitative PCR (RT-qPCR) was performed using Fluidigm 96×96 nanofluidic arrays targeting a set of 96 transcripts that are broadly informative of the major axes of variation for peripheral blood gene expression from Preininger et al. (2013) at six time-points (Pre-challenge, day 5, day 7, day 9, Diagnosis (Dx) and month 4).

first: Andres

last: Vallejo

first: Sócrates

last: Herrera

first: Greg

last: Gibson

first: Myriam

last: Arévalo-Herrera


title: In-vivo Gene Signatures of Mycobacterium tuberculosis In C3HeB/FeJ Mice

status: Public on Jul 11 2015

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: In this experiment we have compared Mtb transcriptomics in-vivo, using samples derived from chronically infected C3HeB/FeJ mice, which produce human like caseating lesions, unlike other murine species, to Mtb cultured in-vitro. Similarly, the genome-wide expression of MtbdeldosR, MtbdeldosS and MtbdeldosT mutants is also compared between lungs from C3HeB/FeJ mice and in-vitro culturing.

first: Uma

middle: S

last: Gautam


title: Expression data from cold treatment between WT and tcf1-1

status: Public on Jul 10 2015

city: shijiazhuang

first: hongtao

last: Ji

state: hebei

address: 286 huaizhong rode

department: Centor for agricultural resources Research

institute: Institute of genetics and developmental biology,Chinese academy of sciences

summary: Cell water permeability and cell wall properties are critical to survival of plant cells during freezing, however the underlying molecular mechanisms remain elusive. Here, we report that a specifically cold-induced nuclear protein, Tolerant to Chilling and Freezing 1 (TCF1), interacts with histones H3 and H4, and associates with chromatin containing a target gene, BLUE-COPPER-BINDING PROTEIN (BCB), encoding a glycosylphosphatidylinositol-anchored protein that regulates lignin biosynthesis. Loss of TCF1 function leads to reduced BCB transcription through affecting H3K4me2 and H3K27me3 levels within the BCB gene, resulting in reduced lignin content and enhanced freezing tolerance. Furthermore, plants with knocked-down BCB expression (amiRNA-BCB) under cold acclimation had reduced lignin accumulation, and increased freezing tolerance. The pal1pal2 double mutant (lignin content reduced by 30% compared with WT) also showed the freezing tolerant phenotype, and TCF1 and BCB act upstream of PALs to regulate lignin content. In addition, TCF1 acts independently of the CBF (C-repeat binding factor) pathway. Our findings delineate a novel molecular pathway linking the TCF1-mediated cold-specific transcriptional program to lignin biosynthesis, thus achieving cell wall remodeling with increased water permeability and consequent freezing tolerance.

overall_design: Total RNA of three week old Arabidopsis seedlings was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip at CapitalBio Corporation (Beijing, China).

first: Hongtao

first: Xia

last: Li


title: Gene expression in experimental aortic coarctation and repair: candidate genes for therapeutic intervention?

city: Milwaukee

first: John

last: LaDisa

state: Wisconsin

address: 1637 West Wisconsin Ave

department: Biomedical Engineering

institute: Marquette University

summary:
The objective of the current investigation was to use microarray techniques to quantify differentially expressed genes (DEGs) in the upstream aorta subjected to high arterial BP after surgical induction of CoA, and restoration of normal arterial BP after its correction.
DEGs may offer additional insight into potential mechanisms of persistent CV morbidity despite successful surgical repair.

overall_design: Male New Zealand white rabbits ~10 weeks old and weighing ~1.0 kg randomly underwent proximal dAo CoA. A 20 mmHg BP gradient was imposed using silk (permanent) or Vicryl (degradable) suture to mimic untreated CoA and surgically corrected CoA, respectively. Rabbits develop a pronounced stenosis and accompanying elevated BP as a stimulus for arterial remodeling within one week. Degradation of Vicryl suture in the corrected group restores aortic diameter close to normal, but with modest residual narrowing. Non-experimental rabbits were designated as a control group. This results in a statistically significant increase in mean, systolic and pulse BP proximal to the coarctation for CoA as compared to both control and corrected rabbits. A ~4 mm circumferential region from the proximal aorta between the coarctation site and left subclavian artery was excised at harvest (32 weeks of age) and frozen. Frozen samples (n=4/group) were shipped overnight to Arraystar, Inc (Rockville, MD) for microarray analysis.

middle: F

first: Thomas

last: Eddinger

first: Serdar

last: Bozdag

first: Jessica

last: Olson

first: Ramani

last: Ramchandran

first: Judy

last: Kersten


title: Chromosomal origin utilisation in Haloferax meiditerranei wild type and mutant strains

status: Public on Jul 08 2015

city: Beijing

first: Haibo

last: Yang

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: We have comprehensively explored the origin utilisation in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated.

overall_design: Genomic DNA was extracted from the H. mediterranei cultures at specific time points(12h,18h,24h,36h,42h and stationary phase 66h), or during the exponential phase (OD600≈0.5) and stationary phase (OD600≈4.0)for the origin deletion strains. After being lablled, Genomic DNA from exponential phase and stationary phase were hybridized to Haloferax mediterranei genome array genechips.

first: Zhenfang

last: Wu

first: Jingfang

last: Liu

first: Lei

last: Wang

first: Xiaoqing

first: Hua

last: Xiang


title: Comparison of C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells after 12 h

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

summary:
The aim of this study was to identify differently expressed genes between C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells. To elucidate the unresolved mechanism behind the promoting effect of C3156-181 on PNR we cultured primary rat neonatal SCs and treated them for up to 72 h with C3 or C3156-181. We then performed gene expression microarray analysis
Results from two loops of two different treatment times are summarized in this study. The samples were taken from two C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cell cultures. Microarrays were hybridized in a loop approach.

overall_design: Results from two loops that map to two different sampling times (loop1: after 12 hours, loop2: after 72) are compared in this study. The data in this file represents loop1. The samples were taken from untreated, C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells.

first: Patrick

last: Lindner


title: Comparison of C3 or C3156-181-peptide treated Isolated primary rat neonatal Sschwann Cells after 72 h

summary:
The aim of this study was to identify differently expressed genes between C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells. To elucidate the unresolved mechanism behind the promoting effect of C3156-181 on PNR we cultured primary rat neonatal SCs and treated them for up to 72 h with C3 or C3156-181. We then performed gene expression microarray analysis
Results from two loops of two different treatment times are summarized in this study. The samples were taken from two C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cell cultures. Microarrays were hybriszed in a loop approach.

overall_design: Results from two loops that map to two different sampling times (loop1: after 12 hours, loop2: after 72) are compared in this study. The data in this file represents loop2. The samples were taken from The samples were taken from untreated, C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells.


title: Comparison of C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells

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

overall_design: Refer to individual Series


title: A Novel, Dynamic Pattern-based Analysis of NF-kappaB Binding During the Priming Phase of Liver Regeneration Reveals Switch-Like Functional Regulation

status: Public on Jul 07 2015

city: Newark

first: Daniel

last: Cook

state: DE

address: 104 Academy St.

department: Chemical and Biomolecular Engineering

institute: University of Delaware

summary: Following partial hepatectomy, a coordinated series of molecular events occurs to regulate hepatocyte entry into the cell cycle to recover lost mass. In rats during the first six hours following resection, hepatocytes are primed by a tightly controlled cytokine response to prepare hepatocytes to begin replication. Although it appears to be a critical element driving regeneration, the cytokine response to resection has not yet been fully characterized. Specifically, the role of one of the key response elements to cytokine signaling (NF-κB) remains incompletely characterized. In this study, we present a novel, genome-wide, pattern-based analysis characterizing NF-κB binding during the priming phase of liver regeneration. We interrogated the dynamic regulation of priming by NF-κB through categorizing NF-κB binding in different temporal profiles: immediate sustained response, early transient response, and delayed response to partial hepatectomy. We then identified functional regulation of NF-κB binding by relating the temporal response profile to differential gene expression. We found that NF-κB bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. NF-κB also transiently regulates genes responsible for lipid biosynthesis and transport as well as induction of apoptosis following hepatectomy. By the end of the priming phase, NF-κB regulation of genes involved in inflammatory response, negative regulation of cell death, and extracellular structure organization became prominent. These results suggest that the immediate, transient, and delayed NF-κB signaling serve different functional transitions that drive the onset of regeneration.

overall_design: Adult (8-10 week old) Sprague-Dawley rats were given ad-libitum access to food (Chow) and water. When their weight reached 275-350 g, they were anesthetized and subjected to 70% partial hepatecomy by surgical removal of medial and left lateral lobes as per standard procedure. The medial and left lateral lobes were flash frozen using liquid nitrogen-cooled aluminum clamps to serve as within-animal, 0 hour controls. At 1 hour, 2 hours, 4 hours, and 6 hours post-PHx, rats (three biological replicates per time) were again anesthetized and the remnant liver tissue was excised and flash-frozen as before. Following excision of the remaining liver mass, rats were sacrificed by cervical dislocation. Liver tissue from 0h, 1h, 2h, 4h, and 6h post-PHx was subjected to chromatin immunoprecipitation. Immunoprecipitated samples (ChIP) from 0h, 1h, and 6h post-PHx were used to identifiy genome-wide NF-κB binding sites using microarrays (ChIP-chip). Immunoprecipitated samples from 0h, 1h, 2h, 4h, and 6h post-PHx were used for validation and extension of ChIP-chip results using qPCR.

first: Biswanath

last: Patra

first: Lakshmi

last: Kuttippurathu

first: Jan

middle: B

last: Hoek

first: Rajanikanth

last: Vadigepalli


title: BDF1 wild type mice vs F33 (HIV-1 Tat-Tg- mice) - Differential thymic microRNA Expression

status: Public on Jul 06 2015

city: Catanzaro

first: Giuseppe

last: Fiume

address: Viale Europa - Germaneto

department: Department of Experimental and Clinical Medicine

institute: University of Catanzaro "Magna Graecia"

summary:
Thymic microRNA expression profiles of wild type vs Tat-Transgenic  mice
Wild type vs HIV-1 Tat Transgenic mice - microRNA Expression: 3 Biological Replicates

overall_design: The overall experiment included 3 Chip: 1) Wild -type BDF-1 (Cy3) vs F33-Tat-Tg mice (Cy5); 2) F33-Tat-Tg mice (Cy3) vs Wild -type BDF-1 (Cy5); 3) Wild -type BDF-1 (Cy3) vs F33-Tat-Tg mice (Cy5)

first: Annalisa

last: Rossi


title: Gene expression in the kidneys of two spontaneously hypertensive rat strains at 3 and 6 weeks of age

status: Public on Jul 03 2015

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: We examined gene expression profiles in the rat kidneys using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.

overall_design: The rat kidneys derived from normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP) were　examined. Each strain was run in triplicate.

first: Yuko

last: Watanabe

first: Momoko

last: Yoshida

first: Kazunori

last: Shimada

first: Hiroshi

last: Nojima

first: Hiromichi

last: Yamanishi


title: Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

status: Public on Jul 12 2015

city: Guangzhou

first: zhangying

last: wang

state: Guangdong

address: Jinying West 2nd Street 18#, Wushan Tianhe

department: Crops Research Institute

institute: Guangdong Academy of Agricultural Sciences

summary:
Investigation of whole transcriptome gene expression level during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87
Identification of transcription factors (TFs) during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87

overall_design: A total of 7 samples were analyzed using RNA isolated from sweetpotato roots at 10, 15, 20, 30, 60, 90, 120days after transplanting. Each sample had two biological replicates.

first: Zhangying

last: Wang

first: Boping

last: Fang


title: Sigma factor WhiGch positively regulates natamycin production in Streptomyces chattanoogensis L10

status: Public on Jul 02 2015

city: Hangzhou

first: Shui

middle: Ping

last: Liu

state: Zhejiang

address: 866, Yuhangtang road

department: Biohemistry and moleculer biology

institute: Zhejiang University

summary: In LG01 there were a total of 861 genes displaying at least a two-fold change (P<0.05), including 470 genes with lower and 391 genes with higher expressions

overall_design: In this study, RNA isolated from LG01 or wild type Streptomyces chattanoogensis L10, was used to acquire expression profiles of a total of 8,117 protein-coding genes in S.  chattanoogensis L10, leading to the successful construction of different expression profiles between  whiGch deletion mutant and wild type S.  chattanoogensis L10.

first: Shuiping

first: Yongquan

last: Li


title: Spinal cord of male wistar rats exposed to repeated psychological stress

status: Public on Jul 01 2015

city: Los Angeles

first: Sylvie

last: Bradesi

address: 10833 Le Conte Avenue

department: Digestive Diseases

institute: UCLA

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


title: Spinal gene expression signature in male wistar rats exposed to repeated psychological stress

summary: To test the effect of chronic water avoidance stress on spinal gene expression profile in male wistar rats.

overall_design: Lumbar spinal cord samples were freshly isolated from rats exposed to daily water avoidance stress for 10 consecutive days. Samples were collected 24 hours after the last stressors.

first: Iordanes

last: Karagiannides


title: Spinal microRNA expression signature in male wistar rats exposed to repeated psychological stress

summary: To test the effect of chronic water avoidance stress on spinal microRNA expression profile in male wistar rats.


title: Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition [miRNA]

city: Rome

first: Giulia

last: Fontemaggi

address: Via Elio Chianesi, 53

institute: Italian National Cancer Institute Regina Elena

summary:
Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination
In this dataset, we include the microRNA expression data obtained from the profiling of ribosome/polysome-associated miRNAs and mRNAs in proliferating HL60 cells and in cells induced to differentiate by 1,25-dihydroxyvitamin D3 (VitD3) treatment

overall_design: 18 total samples, 9 from control proliferating HL60 cells and 9 from VitD3-treated HL60 cells

first: Francesco

last: Fazi

first: Giovanni

last: Blandino


title: Gene expression profiling of mouse liver regeneration after PHx

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary:
Genome-wide expression analysis revealed that 3653 mRNAs and 465 putative lncRNAs were differentially expressed compared to transcripts isolated from livers of control sham operated mice.
Analysis was done using the NCode Mouse Non-coding RNA Microarray (Invitrogen), which contains 25,179 coding featues and 10,802 noncoding features.

overall_design:
To identify lncRNAs that regulate cell proliferation during liver regeneration, we analysed lncRNA expression profiles in mouse liver tissue collected at 4, 12, 36, and 72 hours after PHx, using Sham operated mouse livers as control.
--------------------------
submitter cannot locate original raw data files

first: Lulu

last: Huang

first: Shuling

last: Guo


title: Gene expression analysis of EpH4 cell monolayers following TGF-β3 treatment

status: Public on Oct 01 2015

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary:
EpH4 cell monolayers were treated with 1 ng/ml TGF-β3 or vehicle for 24 hours. The experiment was performed three independent times, with 3 wells per condition in each experiment.

Keywords: Expression profiling by array

overall_design: Each sample represents pooled RNA from three wells of a single experiments. N=3 experiments. Gene expression was analyzed using Affymetrix Mouse Gene 1.1 ST Array Strips and the GeneAtlas System.

first: Aik

first: Pepper

last: Schedin

first: Jaime

last: Fornetti


title: Identification of Dysregulated Long Noncoding RNAs in the Midbrain of Human Cocaine Abusers

status: Public on Jul 04 2015

city: Detroit

first: Michael

last: Bannon

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University School of Medicine

summary: Maintenance of the drug-addicted state involves changes in gene expression in different neuronal cell types and neural circuits. Midbrain dopamine neurons in particular mediate numerous responses to drugs of abuse. Long noncoding RNAs (lncRNAs) regulate CNS gene expression through a variety of mechanisms, but very little is known about their role in drug abuse. The proportion of lncRNAs that are primate-specific provides a strong rationale for their study in human drug abusers. We examined the profile of lncRNA expression in postmortem human midbrain specimens from chronic cocaine abusers and well-matched control subjects (n=11 subject pairs) using a custom lncRNA microarray. Differential expression was validated by quantitative PCR, and cellular localization investigated by in situ hybridization histochemistry.A profile of lncRNAs significantly dysregulated in chronic cocaine abusers was determined. LncRNAs with dopamine cell-specific expression, differential subcellular distribution, covariance with protein-coding genes, and tissue-specific drug-responsiveness were identified. Dysregulation of midbrain lncRNA expression may reflect pathophysiological processes associated with chronic cocaine abuse. LncRNAs may be central mediators of cellular responses to drug abuse.

overall_design: cRNAs were generated from postmortem human midbrain specimens from chronic cocaine abusers and well-matched control subjects and hybridized to a custom Agilent 4 x 44,000-feature high-density oligonucleotide microarray platform using 60-mer probes. Cocaine control pairs were run together in a dye-flip two-color design, meaning each sample was run in quadruplicate, twice with each dye (Alexa-647 and Alexa-555; Invitrogen, Carlsbad, CA). Microarray slides were scanned with the default Agilent protocol and the intensity of fluorescence between dyes was normalized using a Loess correction. There are 7 probes per gene. Data across all cases and quadruplicates were quantile-normalized.

first: Candace

last: Savonen

first: Hui

last: Jia

first: Fabien

last: Dachet

first: Steven

middle: D

last: Halter

first: Carl

last: Schmidt

first: Leonard

last: Lipovich

first: Gregory

last: Kapatos


title: Expression data from different tissues (shoots and roots) of Medicago truncatula exposed to three different types of biosolids amended soil

city: Lexington

first: Chun

last: Chen

state: Kentucky

address: 1100 Nicholasville Road, University of Kentucky

department: Plant and Soil Science

institute: University of Kentucky

summary:
Little progress has been made in studying the toxicity of realistic 'non-pristine' forms of nanoparticles that presents in real soil environment. It is presently unkown whether the transformed nanoparticles in realistic environment exerts an adverse effect to rhizobium-legume symbiosis on molecular level.
We used microarray to investigate the toxicogenomic responses of the model legume Medicago truncatula following 30 days exposure to three different types of biosolids (control biosolids (control BS), a mixture of Ag, ZnO and TiO2 manufactured nanomaterials added biosolids (Nano BS) and a corresponding bulk metals added biosolids (Bulk BS) ) amended soil that were aged for 6 months prior to exposure in pot experiment.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Our Genechip® Medicago Genome Array is designed specially to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. For our study, RNA were extracted from shoots and roots of Medicago truncatula that exposure to control, Bulk and Nano BS treatments for 30 days, and used for all hybridization on Affymetrix microarray. The objective of our study is to investigate the molecular mechanisms of toxicity of Nano BS in comparison with their counterpart Bulk BS treatment, using a commercial Medicago truncatula microarrays.

first: Olga

last: Tsyusko

first: Jason

last: Unrine

first: Jonathan

last: Judy

first: Ricky

last: Lewis

first: Jing

first: David

last: McNear Jr


title: Immune Gene Profiling in Healthy and HBV-exposed Cord Blood Immune Cells

status: Public on Jun 30 2015

city: Singapore

first: Antonio

last: Bertoletti

address: 8 College Road

department: Emerging Infectious Diseases

country: Singapore

institute: Duke-NUS Graduate Medical School

summary: The newborn immune system is characterized by an impaired Th1-associated immune response. Hepatitis B virus (HBV) transmitted from infected mothers to newborns is thought to exploit the newborns’ immune system immaturity by inducing a state of immune tolerance that facilitates HBV persistence. Contrary to this hypothesis, we demonstrate here that HBV exposure in utero triggers a state of trained immunity, characterized by innate immune cell maturation and Th1 development, which in turn enhances the ability of cord blood immune cells to respond to bacterial infection in vitro. These training effects are associated with an alteration of the cytokine environment characterized by low IL-10 and, in most cases, high IL-12p40 and IFN-α2. Our data uncover a  potentially symbiotic relationship between HBV and its natural host and highlight the plasticity of the fetal immune system following viral exposure in utero.

overall_design: RNA was extracted from 15 cord blood samples comprising of healthy cord blood monocytes (n=4), HBV-exposed cord blood monocytes (n=3), healthy cord blood plasmacytoid dendritic cells (n=4), and HBV-exposed cord blood plasmacytoid dendritic cells (n=4). Healthy adult peripheral blood monocytes (n=3) were included for comparison. The immune profile was analyzed using Nanostring and nCounter® GX Human Immunology Kit v1, comprising probes for a total of 511 immune genes.

first: Michelle

last: Hong


title: Expression data of  leaves from transgenic barley expressing wheat Lr34 gene

city: Roorkee

first: Harsh

last: Chauhan

state: Uttaranchal

address: Old Biotechnology Building

department: Department of Biotechnology

country: India

institute: Indian Institute of Technology Roorkee

summary:
The wheat gene Lr34 (Yr18/Pm38/Sr57/Ltn1) encodes a putative ABCG-type of transporter and is a unique source of disease resistance providing durable and partial resistance against multiple fungal pathogens. Lr34 has been found to be functional as a transgene in barley.
We used microarrays to decipher the changes in global gene expression goverened by Lr34 expression in barley.

overall_design: Leaves from two indipendent lines of transgenic barley plants were selected at seedling (Two weeks old plants) and mature (six weeks old plants) stages of  development for RNA extraction and hybridization on Affymetrix microarrays. We used three biological replicates for expression profiles. Wild type plants served as controls.

first: Keller

last: Beat

first: Chauhan

last: Harsh


title: Transgenic Ah24-OE vs Wild type Col 0 Arabidopsis plants

status: Public on Jun 26 2015

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

summary: Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing Ah24 gene from Amaranthus hypochondriacus.

overall_design: One-condition experiment WT vs Ah24 OE plant leaves.

first: Julio

middle: A

last: Massange-Sanchez

first: A

last: Tiessen

first: John

middle: P


title: Human lung adenocarcinoma NCI-H1975 cells: parental vs cell lines resistant to the EGFR-TK inhibitor CNX-2006

city: Amsterdam

first: Elena

last: Galvani

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: VU University Medical Center

summary: Genome variation profiling of lung adenocarcinoma cells comparing untreated NCI-H1975 cells with CNX-2006-resistant untreated cells. Goal was to determine the potential mechanism of resistance to mutant EGFR-TKIs and rationally design novel strategies for the treatment of EGFR-mutant lung cancer patients.

overall_design: Two-condition experiment: NCI-H1975 parental cells vs CNX-2006-resistant cells. Pooled DNA from healthy volunteers was used as reference.

first: Elisa

last: Giovannetti


title: Transcriptomics of rat born to dams fed a diet deficient in methyl group donors

status: Public on Jun 22 2015

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

summary: It is clearly established that the maternal diet during pregnancy can induce physiological and metabolic adaptations in the developing fetus which determine its susceptibility later in life to develop diabetes, obesity... The molecular and genomic mechanisms underlying the programming of the metabolic syndrome remain largely unknown but may involve resetting of epigenetic marks and fetal gene expression. We analyzed the profile of the liver transcriptome in 21-day-old rats born to mothers fed with a standard diet or a diet lacking methyl donor nutrients (Vitamin B12 and folates) during gestation and lactation. From a total of 44,000 probes for 26,456 genes, we found two gene clusters whose expression levels had statistically significant differences between control and deficient rats: 3,269 up-regulated and 2,841 down-regulated genes.  Bioinformatics analysis revealed that these genes are mainly involved in glucose and lipid metabolism, nervous system, coagulation, endoplasmic reticulum (ER) stress and mitochondrial function.

overall_design: Modifications of gene expression in rat liver were measured in 21-day-old rats born to mothers fed with a standard diet or a diet lacking methyl donor nutrients (Vitamin B12 and folates). Eight independent experiments were performed (4 Controls versus 4 Methyl Donor Deficiency - MDD).

first: Gaili

first: Rémi

last: Houlgatte

first: Sébastien


title: Transcriptomics and epigenomics of rat born to dams fed a diet deficient in methyl group donors

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene Expression Profiles of Chicken Embryo Fibroblasts in Response to Salmonella Enteritidis Infection

status: Public on Jun 12 2015

city: Budapest

first: Ama

last: Szmolka

address: Hungária krt. 21.

department: Enteric Bacteriology and Foodborne Zoonoses

country: Hungary

institute: Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences

summary: The response of chicken to non-typhoidal Salmonella infection is becoming well characterised but the role of particular cell types in this response is still far from being understood. Therefore, in this study we characterised the response of chicken embryo fibroblasts (CEFs) to infection with two different S. Enteritidis strains by microarray analysis. The expression of chicken genes identified as significantly up- or down-regulated (≥3-fold) by microarray analysis was verified by real-time PCR followed by functional classification of the genes and prediction of interactions between the proteins using Gene Ontology and STRING Database. Finally the expression of the newly identified genes was tested in HD11 macrophages and in vivo in chickens. Altogether 19 genes were induced in CEFs after S. Enteritidis infection. Twelve of them were also induced in HD11 macrophages and thirteen in the caecum of orally infected chickens. The majority of these genes were assigned different functions in the immune response, however five of them (LOC101750351, K123, BU460569, MOBKL2C and G0S2) have not been associated with the response of chicken to Salmonella infection so far. K123 and G0S2 were the only 'non-immune' genes inducible by S. Enteritidis in fibroblasts, HD11 macrophages and in the caecum after oral infection. The function of K123 is unknown but G0S2 is involved in lipid metabolism and in β-oxidation of fatty acids in mitochondria. Increased levels of G0S2 might decrease the availability of fatty acids to mitochondria. In non-professional phagocytes such as CEFs, this may lead to the dysfunction of mitochondria, apoptosis of CEFs and release of intracellular Salmonella. In professional phagocytes, G0S2 might be involved in the control of mitochondrial respiration, resulting in a decrease of reactive oxygen species as respiration by-products and lower damage to tissue.

overall_design: In this study we were interested whether chicken embryo fibroblast (CEFs) respond to S. Enteritidis infection and to what extent their response differs from that of other cells and caecal tissue. To address this, we characterised the gene expression of CEFs after infection with two different wild-type S. Enteritidis strains of poultry origin - SE 147 and SE 11 - using Agilen custom 8×15K microarrays. In total, 13,681 probes were designed to characterise the expression of ~9,000 transcripts of Gallus gallus.

first: Zoltán

last: Wiener

first: Marta

middle: E

last: Matulova

first: Karolina

last: Varmuzova

first: Ivan

last: Rychlik


title: Systems Toxicology Identifies Mechanistic Impacts of 2-amino-4,6-dinitrotoluene (2-ADNT) Exposure in Northern Bobwhite

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to pursue a holistic understanding of the effects of the explosives degradation product 2-amino-4,6-dinitrotoluene (2A-DNT) dosing on the health of the wildlife bird model, Northern bobwhite (Colinus virginianus).  A subchronic 60d toxicology bioassay was leveraged where both sexes were dosed via daily gavage with 0, 3, 14, or 30 mg/kg-d 2-ADNT.  Effects on global transcript expression were investigated in liver and kidney tissue using custom microarrays for C. virginianus in both sexes at all doses, while effects on the proteome expression were investigated in liver for both sexes and kidney in males, all at the 30 mg/kg-d dose.  As expected, transcript expression was not directly indicative of protein expression in response to 2A-DNT.  However, a high degree of correspondence was observed among platforms when investigating higher-order functional responses including statistically enriched gene networks and canonical pathways, especially when connected to toxicological outcomes of 2A-DNT exposure.   Specifically, comparison of gene networks statistically enriched from differentially expressed transcripts and for proteins showed common responses including inhibition of programmed cell death and arrest of cell cycle in liver tissues at 2A-DNT doses that caused liver necrosis and death in females.  Additionally, both transcript and protein expression in liver tissue was indicative of induced phase I and II xenobiotic metabolism potentially as a mechanism to detoxify and excrete 2A-DNT.  Nuclear signaling, transcript expression and protein expression assays each implicated PPAR nuclear signaling as a primary molecular target in the 2A-DNT exposure with significant downstream enrichment of PPAR-regulated pathways including various lipid metabolic pathways and gluconeogenesis suggesting impaired bioenergetic potential.  Although the relative expression of transcripts and proteins within enriched pathways was at times divergent, transcript expression assays identified many critical metabolic pathways involved in 2A-DNT toxicity as well as impaired PPAR signaling, a key molecular initiating event known to be affected in di- and tri-nitrotoluene exposures.

overall_design: The animal exposure design is presented in a study by Quinn et al (2010).  Five treatment groups consisting of 12 male and 12 female bobwhites each were administered 2A-DNT at 0, 0.5, 3, 14, or 30 mg/kg/day via oral gavage for 60 days. Controls received a volume of corn oil equivalent to the mean volume given to birds in the highest dose group without compound. Microarray hybridizations were conducted using completely randomized design experiments including a 2 x 4 factorial treatment arrangement to investigate the conditions:  sex (male and female) and 2A-DNT dose (control, 3, 14,  and 30 mg/kg-d) for both liver and kidney tissues.  All conditions included 4 biological replicates. REFERENCE:  Quinn Jr. MJ, McFarland CA, LaFiandra EM, Bazar MA, Johnson MS (2010) Acute, subacute, and subchronic exposure to 2A-DNT (2-amino-4,6-dinitrotoluene) in the northern bobwhite (Colinus virginianus) Ecotoxicology 19:945-952.

first: Bindu

last: Nanduri

first: Arun

last: Rawat

first: Mitchell

last: Wilbanks

first: Choo

middle: Y

last: Ang

first: David

last: R. Johnson

first: Xianfeng

last: Chen

first: Michael

last: Quinn Jr

first: Mark

last: Johnson

first: Shane

last: Burgess

first: Edward

last: Perkins


title: Identification of a novel insulin receptor-binding protein from Momordica charantia by transcriptomic, proteomic, and docking analyses

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: Momordica charantia (MC) is a common vegetable in tropical areas and has been used for a long time as an alternative therapy for diabetes. Although several constituents of MC have displayed the hypoglycemic effects, the hypoglycemic targets of these constituents remain to be clarified. In this study, we analyzed and elucidated the therapeutic targets contributing to the hypoglycemic effect of aqueous extract of MC seeds (MCSE) by transcriptomic analysis. The protein ingredients aimed at the hypoglycemic target were further identified by proteomic, docking, and receptor-binding assays. Our data showed that MCSE, which was rich in small-molecular weight proteins, displayed hypoglycemic effects in normal and diabetic mice by glucose tolerance assay. MCSE significantly and primarily regulated the insulin signaling pathway in muscles and adipose tissues, suggesting that MCSE might target to insulin receptor (IR), stimulate the IR-downstream pathway, and subsequently display the hypoglycemic activity. We further identified that inhibitor against trypsin (TI) of MC directly docked into IR and activated the kinase activity of IR. In conclusion, our findings suggested that MCSE regulated glucose metabolism mainly via insulin signaling pathway. Moreover, we newly identified that TI was a novel IR-binding protein of MC that triggers the insulin signaling pathway via binding to IR.

overall_design: Mice were fasted for 4 h and MCSE or PBS was then orally given 15 min before intraperitoneal administration of glucose solution (1 g/kg body weight). Blood samples were collected from tails at 15 min before and at 15, 30, 60, 90, 120, 150, 180, and 240 min after glucose challenge. Blood glucose was measured by glucose oxidase method using a glucometer (ACCU-CHEK Advantage, Roche Diagnostics, Basel, Switzerland). Mice were sacrificed 4 h after glucose challenge. Muscles, adipose tissues, and livers were collected for microarray analysis.

first: Hsin-Yi

last: Lo

first: Chian-Cheng

last: Li

first: Tin-Yun

last: Ho


title: Canine Spontaneous Head and Neck Squamous Cell Carcinomas Represent Their Human Counterparts at the Molecular Level.

status: Public on Jun 02 2015

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Spontaneous canine head and neck squamous cell carcinoma (HNSCC) represents an excellent model of human HNSCC but is greatly understudied. To better understand and utilize this valuable resource, we performed a pilot study that represents its first genome-wide characterization by investigating 12 canine HNSCC cases, of which 9 are oral, via high density array comparative genomic hybridization and RNA-seq. The analyses reveal that these canine cancers recapitulate many molecular features of human HNSCC. These include analogous genomic copy number abnormality landscapes and sequence mutation patterns, recurrent alteration of known HNSCC genes and pathways (e.g., cell cycle, PI3K/AKT signaling), and comparably extensive heterogeneity. Amplification or overexpression of protein kinase genes, matrix metalloproteinase genes, and epithelial–mesenchymal transition genes TWIST1 and SNAI1 are also prominent in these canine tumors. This pilot study, along with a rapidly growing body of literature on canine cancer, reemphasizes the potential value of spontaneous canine cancers in HNSCC basic and translational research.

overall_design: Copy Number Abnormalities in Canine Head and Neck Squamous Cell Carcinomas

first: Shaying

last: Zhao


title: Human Splice Junction Arrays of Parkinson's Patients Leukocytes mRNA Pre- and Post-Deep Brain Stimulation

status: Public on May 22 2015

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

summary: Parkinson’s disease (PD) is the second most common neurodegenerative disease worldwide and the first involving motor symptoms. Deep brain stimulation (DBS) neurosurgery treatment through electrodes implanted to the subthalamic nucleus (STN) improves dramatically the debilitating motor symptoms of the disease due to yet unknown molecular mechanisms. Affymetrix human junction prototype microarrays (HJAY) of blood leukocytes mRNA from PD patients prior to, and following DBS neurosurgery treatment on electrical stimulation were compared to these of age- and gender-matched healthy control volunteers. About 95% of all human genes undergo alternative splicing, and alternative splicing is involved in human diseases and specifically in neurodegenerative diseases. Thus, the goal of this study was to detect alternatively spliced genes in PD patients prior to, and following DBS and to predict the effect of these on the functional level of change at the transcript level (such as exon inclusion, intron retention and nonsense-mediated decay events). Understanding the role of alternative splicing in neurodegenerative diseases will open new avenues to future novel approaches for early detection and neuroprotective treatment enabled by the development of future genetic therapeutics targeted at specific modified splice variants.

overall_design: A total of 11 blood leukocytes mRNA samples were analyzed: four from Parkinson's Disease (PD) patients pre-DBS treatment, three from PD patients tested again post-DBS (while being on electrical stimulation), three from age- and gender-matching healthy control (HC) volunteers, and one PD sample  pre-DBS sample was re-stained and rescanned .

first: Hagai

last: Bergman

first: Zvi

last: Israel

first: Hermona


title: Expression data from embryonic chicken feather and scale skins

city: Taipei City

first: Shau-Ping

last: Lin

address: No. 81, Chang-Xing St.

department: Institute of Biotechnology

institute: National Taiwan University

summary:
Epithelial appendages are the product of epithelial – mesenchymal interactions. Tissue recombination experiments showed that in general, the dermis determines the phenotype of the epithelial appendage. Chicken dorsal skin epithelium interacts with its underlying mesenchyme to form feathers beginning at E7 (H&H stage 31), while metatarsal scale epithelium interacts with its mesenchyme to form scales beginning at E9 (H&H stage 35) which stabilize around E12 (H&H stage 38).
We sought to evaluate the molecular differences of tissues with different competence and inductive abilities to form feathers and scales.

overall_design: Chicken embryos were selected to obtain competent E7 and non-competent at E9 feather forming skin from dorsal. The competent E9 and non-competent E11 meta-tarsal scale forming skin from metatarsal were selected for examing the differences in regional specificity. Epithelium and mesenchyme from each skin were prepared separately. Samples were prepared for RNA extraction and hybridization on Affymetrix microarrays. We gathered 8 sets of samples for the analysis: undifferentiated E7 feather skin epithelium (E7fe) and mesenchyme (E7fm); differentiated E9 feather skin epithelium (E9fe) and mesenchyme (E9fm); undifferentiated E9 scale skin epithelium (E9se) and mesenchyme (E9sm); and differentiated E11 scale skin epithelium (E11se) and mesenchyme (E11sm)

middle: W

last: Hughes

first: Chen-Ming

last: Chuong


title: Comprehensive genomic analysis of relapse neuroblastoma [gene expression]

status: Public on Jun 19 2015

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

summary:
Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation.
Here we describe the expression data.

overall_design: Array from tumours at relapse were compared to pretreatment tumours and corresponding normal samples.

first: Matthias

last: Fischer


title: Targets of Pax3 and Zic1 in neural crest and cranial placode progenitors

status: Public on May 06 2015

first: Jean-Pierre

last: Saint-Jeannet

state: NY

address: 345 East 24th Street

department: Basic Science and Craniofacial Biology

institute: New York University

summary: The transcription factors Pax3 and Zic1 are among the earliest genes activated at the neural plate border. Pax3 and Zic1 in combination promote neural crest fate, while Zic1 alone regulate cranial placode progenitor formation.  We used microarrays to identify the global repertoire of genes activated by these facors individually or in combination to gain insights into the molecular mechanisms underlying cell fate decision at the neural plate border.

overall_design: Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding Pax3GR and Zic1GR , the hormone-inducible version of Pax3 and Zic1, alone or in combination. At the blastula stage (stage 9), animal cap explants were dissected and cultured for 8 hours in the presence of dexamethasone. A glucocorticoid receptor (GR) mRNA was also injected as negative control.

first: Chang-Soo

last: Hong

first: John

last: Tobias


title: Age-dependent Response of Isolated Male Germ Cells to Oxidative Stress

status: Public on Apr 30 2015

city: Montreal

first: Johanna

middle: Samantha

last: Selvaratnam

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill

summary:
Male germ cells from young and aged Rats were Isolated and cultured and then treated with pro-oxidant SIN-1 and antioxidant EUK134
Study of the response of isolated male germ cells from young and aged Brown Norway Rats to oxidative stress.

overall_design: Treatment of Isolated and cultured germ cells with pro-oxidant and antioxidant.

first: Bernard

last: Robaire


title: Comprehensive genomic analysis of relapse neuroblastoma [arrayCGH]

summary:
Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation.
This data set contains the aCGH data.


title: Epigenomics of rat born to dams fed a diet deficient in methyl group donors (MDD)

first: Sebastien

last: Hergalant

summary: It is clearly established that the maternal diet during pregnancy can induce physiological and metabolic adaptations in the developing fetus which determine its susceptibility later in life to develop diabetes, obesity... The molecular and genomic mechanisms underlying the programming of the metabolic syndrome remain largely unknown but may involve resetting of epigenetic marks and fetal gene expression. We analyzed the profile of the liver methylome  in 21-day-old rats born to mothers fed with a standard diet or a diet lacking methyl donor nutrients (Vitamin B12 and folates) during gestation and lactation. Modifications of DNA methylation were found in the promoter regions of 1,032 genes out of 14,981 genes. Bioinformatics analysis revealed that these genes are mainly involved in glucose and lipid metabolism, nervous system, coagulation, endoplasmic reticulum (ER) stress and mitochondrial function.

overall_design: MDD induced modifications of methylation in rat liver were measured in 21-day-old rats born to dams fed with standard food or food deficient in methyl group donor. Six independent experiments were performed (3 controls versus 3 MDD).

first: Gaili

last: Chen

first: Rémi

last: Houlgatte

first: Sébastien


title: Time-series of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds

status: Public on Apr 16 2015

city: Wageningen

first: Maria

middle: Cecilia

last: Costa

state: The Netherlands

address: Droevendaalsesteeg, 1

department: Plant Physiology

institute: Wageningen University

summary:
Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose DT while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA).
We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the re-establishment of desiccation tolerance with ABA.

overall_design: Germinated Arabidopsis seeds at the stage of radicle protrusion were incubated in ABA for 0h, 2h, 12h, 24h and 72h for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates represented by pools of seeds bulk-harvested from at least two plants were used.

middle: C

first: Karima

last: Righetti

first: Wilco

last: Ligterink

first: Julia

last: Buitink

first: Henk

last: Hilhorst


title: Estrogen Receptor Alpha Signaling in Cervical Cancer Associated Fibroblasts

status: Public on Apr 03 2015

city: Bangalore

last: Jayshree

state: Karnataka

address: Dr. M.H Marigowda Road, Hombegowda Nagar

department: Department of Microbiology

institute: Kidwai Memorial Institute of Oncology

summary: Cancer Associated Fibroblasts (CAFs) are crucial in the genesis and progression of tumors. Cervical CAFs (C-CAFs) are less well characterized. Estrogen (E2) is considered a cofactor in cervical carcinogenesis. We studied the molecular signature of exvivo cultured C-CAFs from 4 early International Federation of Gynaecology and Obstetrics (FIGO, IB2) and 2 late (IIIA) stage disease using gene expression microarray. We found C-CAFs to be both pro-tumorigenic and moderately inflammatory; late stage C-CAFs were more actively metabolizing, and cycling, but expressed fewer genes related to immune function. We investigated the expression of ERα in exvivo cultured C-CAFs and studied the role of E2 in their biology by gene expression microarray in the presence of two ERα antagonists: ICI 182,780 and Methyl Piperidino Pyrazole (MPP). Both modulated C-CAF function by down regulating genes associated with cell cycle and metabolism, affecting angiogenesis and cancer progression, though their transcriptomes differed. MPP also down regulated genes involved in Epithelial to Mesenchymal Transition. Thus, canonical ERα signaling is vital for C-CAF functioning. Interfering with paracrine signaling through fibroblast ERα may be worth exploiting as a targeted therapy in cervical cancer.

overall_design: Gene expression microarray profiling of 4 early-stage E2 (estrogen) treated, 2 late-stage E2 treated, 2 early-stage ICI (ER-alpha antagonist) treated, 2 late-stage ICI treated and 2 early-stage MPP (ER-alpha antagonist) treated cervical cancer CAFs. E2 treated C-CAFs served as control.

first: M

middle: K

last: Mahesh

first: Sravanthi

last: Davuluri

first: Akhilesh

last: Bajpai

first: Kshitish

last: Acharya

first: Rudrapatna


title: Transcriptomics Analyses of tobacco leaves and roots sample during water-deficit

status: Public on Mar 31 2015

city: Dallas

first: Roel

last: Rabara

state: Texas

address: 17360 Coit Road

country: USA

institute: Texas A&M AgriLife Research

summary: Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblegen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons.  The seeds were sown in sterile petri plates with modified half-strength MS agar medium. The seedlings were then aseptically transferred into sterile polycarbonate container  with half-strength MS liquid medium. Seedlings were grown for 2 weeks in an incubator set at 25 oC with constant light and subjected to dehydration for 20min, 40min, 1hr, 2hrs, and 4hrs.

overall_design: We used a hydrophonics system for the trancriptome profiling of tobacco (cv Burley 21) root and leaves samples to study plant reponses during water- deficit or drought. Plants were grown in controlled growth chamber conditions and subjected to water deficit condition after 2 weeks.The plants were transferred to empty containers without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tissues and hence called 0-min dehydrated tissue. Similarly other time-points were processed( for instance, 20 min of dehydration, plants were dehydrated for 20 min after being taken out from the container and then harvested). Tissues for three biological replicates and 20 plants per biological replicates were collected for each time-point. RNA was isolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.

first: Prateek

last: Tripathi

first: Michael

last: Timko

first: Paul

middle: J

last: Rushton