title: Gene expression in the peripheral whole blood of established Type 1 diabetes patients

status: Public on Nov 15 2016

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

country: USA

institute: Stanford University

summary: This study was performed to measure gene expression in peripheral whole blood RNA samples of established Type 1 diabetics.

overall_design: Whole blood RNA samples of 10 established Type 1 diabetes patients were provided by TrialNet.  Samples were collected in Tempus tubes (Applied Biosystems) and RNA was extracted using the Kingfisher Purification system (Thermo Scientific). Total RNA concentrations were determined and RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Reagent Kit (Agilent).  One color microarray analysis was performed using the SurePrint G3 Human Gene expression 8×60K one-color microarray kit (Agilent Technologies) and the Low input QuickAmp Labeling Kit (Agilent) according to manufacturer's instructions.


title: Amplification of KRAS in a low grade glioma

status: Public on Nov 18 2016

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

type: Genome variation profiling by genome tiling array

summary: We describe the case of a low grade glioma in a 37 year old male patient showing an amplification of KRAS

overall_design: Sample was analysed by arrayCGH method using Agilent recommendations. Sample was labeled in Cy5 and co-hybridized with control DNA cy3 labeled.

first: Zoé

last: Pedeutour-Braccini

first: Fabien

last: Almairac

first: Esma

last: Saada-Bouzid

first: Valérie

last: Duranton-Tanneur

last: Kubiniek

first: Florence

last: Pedeutour

first: Fanny

last: Burel-Vandenbos


title: Transcriptional profiling of mouse ovarian surface epithelial cells during in vitro spontaneous transformation

status: Public on Nov 16 2016

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary: Mouse ovarian surface epithelial (MOSE) cells were isolated from adult C57BL6 female mice and cultured during 28 passages in a standard medium. Total RNA was analyzed with NIA-15K microarrays.

overall_design: Common reference, single biological repeats, 4 technical repeated dye-swap replicates. Test samples: culture passages 2, 5, 7, 10, 14, 18, 23, 25 and 28. Reference sample: whole newborn male.

first: David

middle: J

last: Munroe


title: Expression data from soybean after soybean mosaic virus inoculation

status: Public on Nov 23 2016

city: changchun

first: he

middle: hong

last: li

state: jilin

address: remin street 5268

country: China

institute: northeast normal university

summary:
Chinese soybean (Glycine max (L.) Merr.) cultivars Rsmv1 and Ssmv1 were used for soybean mosaic virus (SMV) resistance genes screening. The Rsmv1 cultivar was highly-resistant to SMV but the Ssmv1 cultivar was highly-susceptible.
We used microarrays to detail the global programme of gene expression underlying SMV inoculation and identified distinct expression genes between Rsmv1 and Ssmv1.

overall_design: The four sets RNA samples, i.e., SMV inoculated Ssmv1 and Rsmv1, mock inoculated Ssmv1and Rsmv1 for RNA extraction and hybridization on Affymetrix microarrays.

first: Hongli

last: He

first: Bao

last: Liu


title: Expression data of clinical Pseudomonas aeruginosa isolates grown in vitro in glucose minimal medium

status: Public on Nov 20 2016

city: Kgs. Lynbgy

first: Juliane

middle: Charlotte

last: Thøgersen

address: Matematiktorvet build. 301

department: Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: How opportunistic pathogens undergo adaptation during the complex transition from growth in their natural environment to chronic host colonization is not well understood. Successful bacterial pathogens must satisfy specific metabolic requirements constrained by the host environment to cause infection. Evolution has optimized the structure and regulation of metabolism in primary pathogens to operate within host constraints; a systematic evaluation of this process may identify novel targets for therapeutic intervention. An ideal model system for this investigation is the long-term evolution of Pseudomonas aeruginosa within the lungs of cystic fibrosis patients. Using this model, we experimentally determined activity in central metabolism of patient isolates using growth profiling and isotope-labeling experiments. We developed isolate-specific genome-scale metabolic models through integration of transcriptomic and genomic data; these models contextualize our experimental findings from a systems perspective and elucidate specific metabolic adaptations during chronic infection.  We find strong experimental evidence for a shift in metabolism towards fixation of carbon dioxide through reversal of the glycine cleavage system, which may operate as an alternative redox recycling reaction as supported by our computational modeling. This particular metabolic shift may be necessary for the bacteria to survive the oxidative stresses in the human lung environment; we provide support for this hypothesis with computational predictions of isolate-specific essential genes and altered redox pathway activity. Redox-related metabolic adaptation merits greater consideration as an important enabler of pathogen persistence and potential therapeutic target in Pseudomonas and other emergent pathogens.

overall_design: In total 9 samples: Triplicate analysis of three different P. aeruginosa isolates (DK2-WT, DK2-91 and DK2-07). Gene expression profiles are compared between the three P. aeruginosa strains representing different stages of adaptation to the cystic fibrosis lung environment. Two of them, DK2-91 and DK2-07, are late-stage clinical isolates isolated from the same patient in 1991 and 2007, respectively. The third isolate, DK2-WT resembles a non-adapted isolate. All strains share the same clone type (Pseudomonas aeruginosa DK2).

middle: C


title: FRT thyroid cells: 2D monolayers vs. 3D follicles

status: Public on Nov 24 2016

city: Madrid

first: Petrina

last: Koumarianou

state: Madrid

address: 4th Arturo Duperier st.

department: Departamento de Fisiopatología Endocrina y del Sistema Nervioso

country: Spain

institute: Instituto de Investigaciones Biomédicas "Alberto Sols"

summary: Transcriptional profiling of the Fischer Rat Thyroid (FRT) cells comparing polarizing cells grown as a confluent two-dimensional monolayer (2D culture system) with cells grown in matrigel where they acquire a three-dimensional follicular structure (3D culture system).The goal was to identify regulators of 3D epithelial thyroid polarization and follicle formation.

overall_design: Two condition experiment, 3D vs. 2D FRT cell cultures. Biological replicates: 4 for both conditions. A pool of the 2D replicates was compared with each 3D replicate. One dyeswap replicate comparing 2D pool with 3D pool.

first: Pilar

last: Santisteban

first: Gonzalo

last: Gómez-López


title: DNA copy number changes in fragile regions 3p21 and 16p13.3 in malignant mesothelioma

status: Public on Nov 13 2016

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

summary: Malignant mesothelioma (MM) is an asbestos-related malignancy. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor. We applied a copy-number analysis to the identification of new fragile genes in regions 3p21 and 16p13.3 in MM.

overall_design: Array-based comparative genomic hybridization analysis was performed on malignant mesothelioma (MM) primary cell cultures, tumor and matched peripheral blood.

first: Mitsuru

last: Emi


title: Metabolomic profiling of Bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures

status: Public on Nov 28 2016

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary:
Metabolomics and transcriptomics of Bradyrhizobium diazoefficiens-induced root nodules
Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection -time of flight mass spectrometry analysis the metabolome of i) nodules and roots from four different B. diazoefficiens host plants, ii) soybean nodules harvested at different time points during nodule development, and iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by transcriptomics data that was generated for the two mutant strains and were helpful to separate for some examples the respective bacterial and plant contributions to the metabolic profile. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.

overall_design:
Metabolomics by flow injection -time of flight mass spectrometry analysis of i) nodules and roots from four different B. diazoefficiens host plants, ii) soybean nodules obtained from different time points in nodule development, and iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Transcriptomics of nodules induced by the two strains mutated in key genes for nitrogen fixation .
For comparison with the two mutant strain data, the existing wild-type nodules data (GSM210242- GSM210245) were used"

first: Martina

last: Lardi

last: Murset

first: Hans-Martin

last: Fischer

first: Socorro

last: Mesa

first: Christian

middle: H

last: Ahrens

first: Nicola

last: Zamboni


title: Genomic imbalances of lung cancer

status: Public on Nov 17 2016

city: Guangzhou

first: Lei

last: Yang

address: Xinzao, Panyu District,

institute: Guangzhou medical university

summary: The array comparative genomic hybridization (aCGH) was perform to identify regions with genomic imbalance in lung cancer.The aCGH analysis detected a total of 325 regions with genomic imbalance in all 8 lung cancer samples, ranging from focal rearrangements (70 kb–5 Mb) to chromosome-arm alterations with chromosomal segments amplification or deletion. Among these mutations, a total of 115 genomic imbalances were discovered occurring at high frequency varying from 25% to 50%.

overall_design: Genomic imbalances of lung cancer was tested in 8 randomly-selected pairs of lung cancer tissue and adjacent normal tissues using the Agilent SurePrint G3 human CGH 4×180K array by a commercial company

first: Jiachun

last: Lu


title: Seasonal expression analysis of Japanese cedar in cambium region and differentiation xylem

status: Public on Nov 26 2016

city: Hitachi

first: Kentaro

last: Mishima

state: Ibaraki

address: 3809-1 Juochoishi

department: Breeding Department

institute: Forest Tree Breeding Center

summary: A custom cDNA microarray analysis was designed based on a proprietary cDNA library and EST data to investigate seasonal gene expression in Japanese cedar cambial region.

overall_design: The expression analyzed in this study are further described in K. Mishima, T.Fujiwara, T.Iki, K.Kuroda, K. Yamashita, M.Tamura, Y.Fujisawa and A.Watanabe. Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)

first: Atsushi

last: Watanabe


title: Differential microRNA expression along with progression of diet-induced atherosclerotic plaque using Microarray

city: Bangalore

first: Vrushali

middle: Umakant

last: Deshpande

state: Karnataka

address: No. 258/A, Bommasandra Industrial Area,

department: Molecular Immunology

country: India

institute: Thrombosis Research Institute

summary: To understand the changes in microRNA expression regulating specific genes at different stages of diet-induced atherosclerotic development, double knock out Apobtm2Sgy/Ldltm1Her mice were fed with either high-fat or normal chow diet. The microarray was performed using total RNA extracted from ascending aorta of the animals.

overall_design: Double knockout mice fed with rich cholesterol diet and a normal diet were sacrificed after 0, 6, 1, 8 and 30 weeks and RNA was extracted for Microarray analysis

first: Lakshmi

last: Mundkur

first: Rameshkumar

last: Krishnan


title: Expression data from differentiating primary culture of equine satellite cells (ESC) β-hydroxy-β-methylbutyrate  (HMB)

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of β-hydroxy-β-methylbutyrate-treated (24h) differentiating equine satellite cells (3rd day of differentiation) compared to control HMB-untreated cells. Goal was to determine the effects of HMB influence on gene expression in equine satellite cells during in vitro myogenesis

overall_design: Two-condition experiment, HMB-treated (24h) differentiating equine satellite cells (3rd day of differentiation) vs. differentiating equine satellite cells without HMB treatment (control). Biological replicates: 4 reps of examined condition (Cy5), 4 control replicates (Cy3)

first: Anna

last: Ciecierska

first: Katarzyna

middle: A

last: Szcześniak


title: Genome-wide epigenetic profiling of CD4+ T cells, CD8+ T cells, CD56+ NK cells and Neutrophils in healthy individuals by CHARM.

city: Solna

first: David

last: Gomez-Cabrero

state: Stockholm

address: Karolinska University Hospital Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: Study of cell type specific DNA Methylation profiles for 4 cell types.

overall_design: CD4+ T cells, CD8+ T cells, CD56 NK cells and Neutrophils isolated from 5 individuals.

first: Tomas

last: Ekstrom


title: Yeast (Saccharomyces cerevisiae) synchronized meiotic timecourse II

city: Stony Brook

first: Bruce

last: Futcher

state: NY

address: STONY BROOK UNIVERSITY

department: Molecular Genetics & Microbiology

institute: Stony Brook University

summary: transcriptional profiling of yeast meiotic culture

overall_design: generate synchronized meiotic time course after Ndt80 block and take samples at certain times. Several timepoints before NDT80 block releasing is also included. RNA expression is measured by microarray

first: Yifeng

last: Xu


title: Gene expression in matched samples of peripheral whole blood collected and processed using the PAXgene vs Tempus system

first: Linda

last: Yip

summary: To compare gene expression in whole blood samples collected in PAXgene RNA or Tempus collection tubes, and processed using  the PAXgene Blood RNA Kit or Tempus Spin RNA isolation Kit, respectively.

overall_design: Whole blood samples of 9 healthy individuals were collected into one PAXgene and one Tempus tube, and total RNA was extracted using the PAXgene Blood RNA Kit and the Tempus Spin RNA Isolation Kit, respectively. Total RNA concentrations were determined and RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Reagent Kit (Agilent).  One color microarray analysis was performed using the SurePrint G3 Human Gene expression 8×60K one-color microarray kit (Agilent Technologies) and the Low input QuickAmp Labeling Kit (Agilent) according to manufacturer's instructions.


title: Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues.

city: Bethesda

first: Christopher

last: Hourigan

address: 10 Center Drive

institute: NHLBI

summary: We analyzed using quantitative real-time PCR (qRT-PCR), gene expression of 65 potential leukemia associated antigens in de-identified, clinically annotated samples from ficoll purified peripheral blood samples from 30 newly diagnosed untreated AML patients collected under IRB-approved protocols from three NCCN cancer centers.

overall_design: qPCR gene expression profiling

middle: S

first: Meg

last: Goswami


title: A genome-wide analysis of MDS and MDS/MPN patients

status: Public on Nov 21 2016

city: Salamanca

first: María

last: Abáigar

state: Salamanca

address: Campus Miguel de Unamuno

institute: Centro de Investigación del Cáncer

summary: To characterize the molecular changes in myelodysplastic syndromes (MDS) and to explore novel genetic abnormalities occurring in these disorders through a genome-wide study in a series of MDS and MDS/MPN patients. A total of 285 abnormalities were identified in 71 patients. Three high-risk MDS cases displayed chromothripsis. In addition, cryptic deletions were identified in genomic regions where MDS-related genes, such as DNMT3A (2p23.3), TET2 (4q24), RUNX1 (21q22) and BCOR (Xp11.4), are located.

overall_design: A genome-wide analysis of molecular changes in a series of 301 MDS and MDS/MPN patients

first: Jesús

middle: M

last: Hernández-Rivas


title: Phenotypic, genomic and transcriptional analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance

status: Public on Nov 19 2016

city: MEXICO DISTRITO FEDERAL

first: Rosa Maria

middle: Gutierrez

last: Rios

state: DISTRITO FEDERAL

address: AV. UNIVERSIDAD 3000, UNAM, CU

department: Molecular Microbiology

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

summary:
Background: Growth in the global population and industrial activities has increased world energy consumption. Bioethanol is considered as an alternative renewable energy source. Among various ethanol-producing microbes, Zymomonas mobilis ZM4 has received special attention due to its higher ethanol yield and tolerance. Advances in genetic engineering are particularly important for developing microorganisms with improved ethanol production. However, the variety of factors involved in the response to high concentrations of ethanol makes it difficult to devise genetic engineering strategies to generate alcohol tolerant strains. For a better understanding of the ethanol tolerance phenomenon, we obtained and characterized two Z. mobilis ZM4 mutants (ER79ap and ER79ag) with increased ethanol tolerance.
Results: Mutants were obtained using a strain adaptive evolution method in mini-fermentors and sequential transfers to higher ethanol concentrations. Mutations were identified by Illumina genomic sequencing. Strain ER79ap possesses three point mutations in the following genes: SpoT/RelA, which synthesizes and degrades the alarmone ppGpp; clpB, encoding a disgregase; and clpP, a component of the Clp protease. In contrast, strain ER79ag has four mutations in the subsequent genes: spoT/relA; rimO; clpP; and in a gene encoding a hypothetical protein with a CBS domain. Transcript profiles of ZM4 and ER79ap were obtained with microarray analysis and identified 126 genes in ZM4 and 148 genes in ER79ap that were differentially expressed in response to ethanol.
Conclusions: Both mutants carry mutations in clpP and relA/spoT genes, suggesting that these genes are responsible of their enhanced ethanol tolerance. Transcript profile analysis of the ZM4 and ER79ap showed that they share a set of forty genes that are differentially expressed under ethanol stress and this set may correspond to those that are crucial for the ethanol response.  The expression profiles indicate that ethanol induces a major reprograming of transcription that involves changes in the cell membrane, protein synthesis, and in some metabolic pathways, especially those involved in the amino acid metabolism. Our data suggest that clpP and in particular the relA/spoT gene can be targets for bioengineering ethanol tolerance.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Two-condition experiment, ZM4 in the presence or absence of  ethanol and the mutant ER79ap in the presence or absence of ethanol. For both experimets we reported three biological replicates and three thecnical replicates

first: Ofelia

last: Carreon

first: Alfredo

last: Martinez

first: José

last: Acosta

first: Rosa

last: Gutierrez

first: Miguel

last: Cevallos


title: Gene expression signatures for Hib conjugate vaccine

city: Kunming

first: Ying

last: Zhang

state: Yunnan

address: 935 Jiaoling Rd.

institute: Institute of Medical Biology, Chinese Academy of Medicine Science

summary: To development of our gene expression, we have employed whole rhesus monkey genome microarray expression profiling as a discovery platform to identify genes with the potential to induce immune response. The peripheral blood from rhesus macaques, who were immunized in groups of three with the capsular polysaccharide (CPS antigen), carrier protein tetanus toxoid (TT) or conjugate vaccine via intramuscular injection (i.m.) in the anterolateral thigh on days 0, 30 and 60 using the formulations, were obtained on days 0, 30, 60 and 90. PBMCs were collected for microarray assays. Dynamic expression variations of eight genes (KLRC1, LGALS13, LTB4DH, NUAK1, VNN2, GALNT3, LOC710050 and LOC716305) were maintained in Hib conjugate vaccine group throughout experiment comparing with the CPS antigen group and carrier protein TT group.

overall_design: Hib conjugate vaccine, Hib capsular polysaccharide (CPS) and carrier protein tetanus toxoid (TT) induced gene expression in macaque blood was measured at 0, 30, 60 days after immunized to doses of 0.5 ml. 0.5ml Hib conjugate vaccine contains 10 μg polyribosyl ribitol phosphate (PRP) and 30 μg TT, 0.5 ml Hib capsular polysaccharide (CPS) contains 10 μg PRP, and 0.5 ml carrier protein tetanus toxoid (TT) contains 30 μg TT. Two independent macaques were performed in each group.


title: Age-associated Changes in the Respiratory Epithelial Response to Influenza Infection [hNEC]

city: Chapel Hill

first: William

middle: A.

last: Fischer

state: NC

address: 104 Mason Farm Road

department: Division of Pulmonary and Critical Care Medicine

institute: The University of North Carolina School of Medicine

summary: This study evaluates how aging impacts the interaction between influenza viruses and human respiratory epithelial cells.  Our results indicate that aging is associated with a decrease in the gene expression of key antiviral mediators, IFITM1 and MX1, and a decrease in the expression of MHC-I and TAP mRNA and proteins responsible for antigen processing and presentation.  Importantly however epithelial cells from older individuals produce similar, and in some cases greater, levels of chemokines as compared with hNECs from younger individuals.  Taken together a defect in antigen processing and presentation could result in impaired clearance of infected epithelial cells allowing them to continue to produce inflammatory cytokines and chemokines resulting in prolonged inflammation and perhaps increased severity of disease.

overall_design: Primary human nasal epithelial cells (hNECs) were cultured, and differentiated at air-liquid-interface (ALI). hNECs were cultured from nasal epithelial biopsies obtained from two groups of healthy volunteers between the ages of 20-25 (Young; N=5) and over 50 years of age (Old; N=7). Cultures were infected with 10 TCID50/cell Influenza A H3N2 virus (Influenza A/Washington/897/90) or media alone (Mock) and maintained in culture for 24 hours.

first: Ilona

last: Jaspers

first: Kelly

last: Chason

first: Joel

last: Parker

first: Subashini

last: Sellers


title: Role of differential microRNA 378 expression in increased pro-angiogenic activity of mobilized CD34+ progenitor cells of patients with acute ST-elevation myocardial infarction:

status: Public on Nov 11 2016

city: Hannover

first: Julia

last: Osipova

address: Carl-Neuberg Str. 1

department: IMTTS

country: Germany

institute: MHH

summary:
Rationale: Pro-angiogenic effects of mobilised bone-marrow-derived stem/progenitor cells are essential for cardiac repair after myocardial infarction. MicroRNAs (miRNA/miR) are key regulators of angiogenesis.
Objective: To determine the differential regulation of angiomiRs, i.e microRNAs regulating neovascularisation, in mobilised CD34+ progenitor cells obtained from patients with an acute ST-segment elevation myocardial infarction (STEMI) as compared to those with stable coronary artery disease (sCAD) or healthy subjects.
Methods and Results: CD34+ progenitor cells were isolated from patients with STEMI (on day 0 and day 5), sCAD and healthy subjects (n=27). CD34+ progenitor cells of patients with STEMI exhibited increased pro-angiogenic activity as compared to CD34+ cells from the other groups. Using a PCR-based miRNA-array and Real-Time PCR validation we identified a profound up-regulation of two known angio-miRs, i.e. miR-378 and let-7b, in CD34+ cells of patients with STEMI. Especially, we demonstrate that miR-378 is a critical regulator of the pro-angiogenic capacity of CD34+ progenitor cells and its stimulatory effects on endothelial cells in-vitro and in-vivo, whereas let-7b up-regulation in CD34+ cells failed to proof its effect on endothelial cells in-vivo.
Conclusion: The present study demonstrates for the first time a significant upregulation of the angiomiRs miR-378 and let-7b in mobilised CD34+ progenitor cells of patients with STEMI. The increased pro-angiogenic activity of these cells in patients with STEMI and the observation that in particular miR-378 regulates the angiogenic capacity of CD34+ progenitor cells in-vivo suggest that this unique microRNA expression pattern represents a novel endogenous repair mechanism activated in acute myocardial infarction.

overall_design: CD34+ progenitor cells from patients with acute STEMI, patients with stable CAD and healthy subjects were isolated from 60 ml of anticoagulated peripheral blood (BD Vacutainer, K2EDTA 18.0 mg) using the CD34-MicroBead-Kit (Miltenyi Biotec) according to the manufacturer’s protocol. Total RNA was isolated from CD34+ cells according to the Mini Kit (Qiagen) manufacturer’s instructions. Differential miR-expression in CD34+ cells was analysed using PCR-based miRNA profiling on Human panel I plates from Exiqon and validated using real-time PCR analysis according to miRCURY LNA™ Universal RT microRNA PCR protocol (Exiqon)

first: Ulf

last: Landmesser

first: Christian

last: Templin

first: Thomas

middle: F

last: Lüscher

last: Thum

first: Simon

middle: P

last: Hoerstrup

first: Maximilian

middle: Y

last: Emmert

first: Roland

last: Klingenberg

last: Matter

first: Sylvie

last: Briand

first: Jelena

middle: R

last: Ghadri

first: Maja

last: Müller

first: Martin

last: Meyer

first: Pavani

last: Mocharla


title: Combined transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions [C. albicans]

city: Jena

first: Ilse

middle: Denise

last: Jacobsen

address: Beutenbergstr. 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The opportunistic fungal pathogen Candida albicans is a common cause of life-threatening nosocomial bloodstream infections. In the murine model of systemic candidiasis the kidney is the primary target organ while the fungal load declines over time in liver and spleen. To get a better understanding of the organ-specific differences in host-pathogen interaction during systemic murine candidiasis, we performed a time-course gene expression profiling to investigate the differential responses of murine kidney, liver and spleen and determined the fungal transcriptome in liver and kidney. We clearly demonstrate a delayed immune response on the transcriptional level in kidney accompanied by late induction of fungal stress response genes in this organ. In contrast, early upregulation of the proinflammatory response in the liver was associated with a fungal transcriptional profile resembling that of phagocytosed cells, suggesting that the resident phagocytic system contributes significantly to fungal control in the liver. Although no visible filamentation occurred in the liver, C. albicans hypha-associated genes were upregulated, indicating an uncoupling of gene expression and morphology during infection of this organ. In vitro the induction of hypha-associated gene expression in yeast cells led to altered interaction with macrophages, suggesting that the observed transcriptional changes affect host-pathogen interaction in vivo. Consistently, the combination of host and pathogen transcriptional data in an inference network model implied that C. albicans cell wall remodeling and metabolism were connected to the immune responses in kidney and liver. Furthermore, the network suggested links between fungal iron acquisition and amino acid metabolism in the kidney and host organ homeostasis. Thus, this work provides novel insights into the organ-specific host-pathogen interactions during systemic C. albicans infection.

overall_design: Candida albicans, 17 samples, organs: kideny, liver; time points: 8h, 12h, 24h post infection

first: Betty

last: Hebecker

first: Sebastian

last: Vlaic

first: Michael

last: Bauer

first: Sascha

middle: O

last: Brunke

first: Theresia

last: Conrad

first: Jörg

last: Linde

first: Bernhard

last: Hube

middle: D


title: Age-associated Changes in the Respiratory Epithelial Response to Influenza Infection

first: William

last: Fischer

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

overall_design: Refer to individual Series


title: Yeast (Saccharomyces cerevisiae) synchronized meiotic timecourse I

first: Bruce

last: Futcher

overall_design: generate synchronized meiotic time course after Ndt80 block and take samples at certain times. RNA expression is measured by microarray

first: Yifeng

last: Xu


title: Endometrial transcriptome profile of cows affected by subclinical or clinical endometritis

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

summary:
Clinical or subclinical endometritis could affect the cow fertility by disturbing the molecular milieu of the uterine environment.
We used a global gene expression approach to understand the effect of clinical and subclinical endometritis on endometrial transcriptome profiles of cows

overall_design: Holstein Friesian cows at 42-60 days postpartum were classified as healthy (HE), subclinical endometritis (SE) or clinical endometritis (CE) based on clinical examination of the animals and histological evaluation of the corresponding endometrial biopsies. Endometrial transcriptome profile changes and associated molecular pathways induced by subclinical or clinical endometritis were then investigated using GeneChip® Bovine Genome Array.

first: Sally

last: Ibrahim

first: Samuel

last: Gebremedhn

first: Dawit

last: Tesfaye

first: Maike

last: Heppelmann

first: Heinerich

last: Bollwein

first: Christiane

last: Pfarrer

first: Ernst

last: Tholen

last: Neuhoff

first: Karl

last: Schellander

last: Hoelker


title: Age-associated Changes in the Respiratory Epithelial Response to Influenza Infection [biopsy]

overall_design: Nasal biopsies from young (N=6) and older (N=5) subjects were collected and expression profiled.

first: Ilona

last: Jaspers

first: Kelly

last: Chason

first: Joel

last: Parker

first: Subashini

last: Sellers


title: Nucleolin-aptamer therapy in retinoblastoma: molecular changes and mass spectrometry–based imaging

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: Retinoblastoma (RB) is an intraocular childhood tumor which, if left untreated, leads to blindness and mortality. Nucleolin (NCL) protein which is differentially expressed on the tumor cell surface, binds ligands and regulates carcinogenesis and angiogenesis. We found that NCL is over expressed in RB tumor tissues and cell lines compared to normal retina. We studied the effect of nucleolin-aptamer (NCL-APT) to reduce proliferation in RB tumor cells. Aptamer treatment on the RB cell lines (Y79 and WERI-Rb1) led to significant inhibition of cell proliferation. Locked nucleic acid (LNA) modified NCL-APT administered subcutaneously (s.c.) near tumor or intraperitoneally (i.p.) in Y79 xenografted nude mice resulted in 26 and 65% of tumor growth inhibition, respectively. Downregulation of inhibitor of apoptosis proteins, tumor miRNA-18a, altered serum cytokines, and serum miRNA-18a levels were observed upon NCL-APT treatment. Desorption electrospray ionization mass spectrometry (DESI MS)-based imaging of cell lines and tumor tissues revealed changes in phosphatidylcholines levels upon treatment. Thus, our study provides proof of concept illustrating NCL-APT-based targeted therapeutic strategy and use of DESI MS-based lipid imaging in monitoring therapeutic responses in RB.

overall_design: Four Samples, two controls and two treated.

first: Nithya

last: Subramanian

first: Amitava

last: Srimany

first: Jagat

last: Kanwar

first: Rupinder

middle: K

first: Balachandran

last: Akilandeswari

first: Pukhraj

last: Rishi

first: Vikas

last: Khetan

first: Madavan

last: Vasudevan

first: Thalappil

last: Pradeep

first: Subramanian

last: Krishnakumar


title: Transcriptome analysis of the pfkB1 deletion mutant cultivated with glucose or fructose

city: Kizugawa

first: Satoshi

last: Hasegawa

state: Kyoto

address: 9-2, Kizugawadai

department: molecular microbiology and biotechnology group

institute: Research Institute of Innovative Technology for the Earth

summary: In the analysis of a carbohydrate metabolite pathway, we found that a mutant strain of Corynebacterium glutamicum deficient in pfkB1, which encodes fructose-1-phosphate kinase, showed interesting characteristics. After aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced lactate more than 2-fold as compared with the wild-type under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of the pfkB1 deletion and fructose cultivation. On the basis of the metabolome and transcriptome analyses, we identified marked intracellular accumulation of fructose-1-phosphate and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis in this strain. Therefore, the considerably enhanced glucose consumption and organic acid production presumably resulted from a relief of transcriptional repression driven by global regulator SugR owing to the accumulated fructose-1-phosphate. Furthermore, we demonstrated that engineered strains overexpressing the above upregulated genes showed enhanced glucose consumption and organic acid production. The ppc deletion mutant of the engineered strain consumed 1,250 mM glucose and produced 2,390 mM lactate in 48 h under oxygen deprivation, which are 2.6- and 2.7-fold higher than the corresponding parameters of the ppc-deleted wild-type.

overall_design: Gene expression profile of the wild type cultivated with glucose in the early log phase (at 4 h) was compared with those of the wild type cultivated with glucose in the stationary phase (at 12 h), the wild type cultivated with fructose in the early log phase (at 4 h) and stationary phase (at 12 h), and the pfkB1 deletion mutant cultivated with glucose or fructose in the early log phase (at 4 h) and in late log/stationary phases (at 12 h).

first: Yuya

last: Tanaka

first: Masako

last: Suda

first: Toru

last: Jojima

first: Masayuki

last: Inui


title: Regulatory Landscape and Clinical Implication of MBD3 in Human Malignant Glioma [low-grade glioma and glioblastoma screening]

status: Public on Nov 08 2016

city: West Lafayette

first: Yi

last: Cui

state: Indiana

address: 1203 W. State Street

department: Agricultural and Biological Engineering

institute: Purdue University

summary: A comprehensive study is conducted to inspect the role and function of methyl-CpG-binding domain protein 3 (MBD3) in human malignant glioma, as well as to test its potential as a novel prognostic biomarker. Using whole-genome microarray for transcriptome, the MBD3-mediated epigenetic regulation in glioma was profiled.

overall_design: A negative correlation between the glioma WHO grade and the MBD3 protein level was first revealed in our collected patient biopsies. Therefore,  the differentiated expressed genes between low-grade glioma (WHO grade II) and glioblastoma (GBM, WHO grade IV) were screened. Four patients with characterized glioma grade were enrolled in each group.

first: Jian

last: Li

first: Sara

middle: E

last: Wirbisky

first: Jennifer

middle: L

last: Freeman

first: Joseph

last: Irudayaraj


title: The microbial functional diversity in response to warming incubation at Alaska as characterized by GeoChip

status: Public on Nov 09 2016

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

summary: Microbial decomposition of soil organic carbon (SOC) in Arctic permafrost is one of the most important, but poorly understood, factors in determining the greenhouse gas feedback of tundra ecosystems to climate. Here, we examine changes in the structure of microbial communities in an anoxic incubation experiment at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC and geochemistry, and GeoChips 5.0 were used to determine microbial community structure and functional genes associated with C availability and Fe(III) reduction.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: 30 samples were collected under 10 conditions from Barrow, Alaska, with 3 replicates in each treatment

first: Baohua

last: Gu

first: Yunfeng

last: Yang

first: Ziming

first: Sihang


title: Regulatory Landscape and Clinical Implication of MBD3 in Human Malignant Glioma


title: Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics [Tumor]

city: Belfast

first: Jaine

last: Blayney

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queen's University

summary: An expert-pathologist-reviewed epithelial ovarian cancer reference library (n = 50) used to assign the histopathology of epithelial ovarian cell lines using compositional statistics and random gene-sets

overall_design: In the study presented here, we applied Gene Expression Compositional Assignment (GECA) to epithelial ovarian cell lines (GSE73637), using first a reference library of solid tumors (expO [http://www.intgen.org/expo/]) and then a second library of expert pathologically-reviewed epithelial ovarian cancer samples


title: XY female mice develop severe abdominal aortic aneurysms

status: Public on Nov 07 2016

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Abdominal aortic aneurysms (AAAs) are a prevalent and deadly human pathology with strong sexual dimorphism.  Research demonstrates that sex hormones influence, but do not fully explain, male versus female AAA pathology.  In addition to sex hormones, the X and Y sex chromosomes, and their unique complements of genes, may contribute to sexually dimorphic AAA pathology.  Here, for the first time, we defined the effect of female (XX) versus male (XY) chromosome complement on AAA formation and rupture in phenotypically female mice using an established murine model.  Abdominal aortas from female mice bearing the XY chromosome selectively expressed Y chromosome genes, while genes known to escape X-inactivation were higher in XX females.  The majority of gene differences in XY females fell within inflammatory pathways.  When XY females were infused with AngII, AAA incidences doubled and aneurysms ruptured.  AAAs from XY females exhibited significant inflammation.  Moreover, infusion of AngII to XY females augmented aortic activity of matrix metalloproteinases.  Finally, testosterone exposure applied chronically, or as a single bolus at postnatal day 1, markedly worsened AAA outcomes in XY compared to XX females.  These results demonstrate that an XY sex chromosome complement profoundly influences aortic gene expression profiles and promotes AAA severity.

overall_design: Phenotypically female Ldlr-/- mice with an XX or an XY sex chromosome complement were used. XY animals were made phenotypically female as follows: male sires had the Sry gene responsible for testes development knocked out of the Y chromosome and knocked in to automal chormosomes. During sexual reproduction, XY progeny that did not receive the autosomal Sry gene developed into phenotypical and reproductively intact females. At 8 weeks of age; XX (n = 10) and XY (n = 10) subjects underwent sham surgery or ovariectomy (OXV), yielding four treatment groups- XX Sham (n = 5); XX OVX (n = 5); XY Sham (n = 4); and XY OVX (n = 6). After two weeks of recovery, mice were fed the Western high fat diet for one week.  Animals were then killed and aortas were dissected under a dissecting microscope and placed in RNA later solution (Ambion, cat#AM7021).  Abdominal aortas (diaphragm to the ileac bifurcation) were used for RNA extraction. RNA was extracted using the Rneasy fibrous tissue mini kit (Qiagen, cat#74704), and the RNA concentration and quality was quantified by Agilent 2100 bioanalyzer using RNA 6000 Nano labchip kit (Agilent Technologies, Cat# 5067-151).  Harvested abdominal aortic RNA samples (n = 20) were of sufficient quantity and quality that did not differ significantly among treatment groups (Agilent Bioanalyzer RNA Integrity Number [RIN]: 9.51 ± 0.07 – p = 0.25; [RNA] (ng/ul): 39.5 ± 3.4 – p = 0.93; 28s:18s ratio: 2.83 ± 0.89 – p = 0.33-; all statistical tests by ANOVA). Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Assay 1.0 arrays (one array per subject/ aorta).  Signal intensities were calculated using the RMA algorithm at the transcript level in Genomics Suite (Partek, St Louis).  Data were transferred to flat files in Excel and associated with vendor-provided April 2015 annotation data.  Pre-statistical filtering retained unique, annotated probe sets with adequate signal intensity (signal intensity ≥ 4.2 on at least 4 arrays in the study). Filtered signal intensities were analyzed by two-way ANOVA to identify significant main effects of genotype (XX versus XY), surgery (Sham vs OVX), as well as interaction.  The False Discovery Rate (FDR) procedure was used to estimate the error of multiple testing.

first: Yasir

last: Alsiraj

first: Sean

last: Thatcher

first: Richard

last: Charnigo

first: Kuey-Chu

last: Chen

first: Alan

last: Daugherty

first: Lisa

last: Cassis


title: Gene expression profiling of resistance genes to low temperature in leaves of peanut (Arachis hypogaea L.)

city: Qingdao

address: wannianquan road

institute: Shandong Peanut Research Institute

summary:
Investigation of  resistance genes from 36,158 peanut ESTs after cold stress treatment, compared with untreated peanut.
Yield some useful insights into cold-mediated signal transduction pathways in peanut.

overall_design: A six chip study using total RNA recovered from three separate untreated peanut leaves and three separate cold-treated peanut leaves.  Each chip measures the expression level of 36,158 ESTs.

first: Shanlin

last: Yu


title: Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics


title: KYSE (450, 520, 890, 960) cell lines

status: Public on Nov 06 2016

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

summary: microRNA profiles in human esophageal squamous cell carcinoma cell lines

overall_design: KYSE cell lines were maintained in Ham’s F-12/RPMI 1640 (Invitrogen, San Diego, CA) containing 5% fetal bovine serum at 37 ˚C in a fully-humidified 5% CO2 atmosphere. Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method. According to manufacture’s instructions, 500 ng of total RNA was labeled with Hy5 and was hybridized on the Human miRNA Oligo chip for 16 hour at 32˚C. A Human miRNA Oligo chip was scanned using ProScanArray (PerkinElmer).


title: Differential gene expressions in the hypertensive heart using pressure-overload model

status: Public on Nov 04 2016

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Differential gene expressions were constructed through expression profiling of a total of 26,423 genes in the hypertrophic heart followed by pressure-overload model, then 537 significant differential genes were filtered based on the criteria (p<0.05 and fold change >1.5).

overall_design: In the study presented here, the mice were performed the transverse aortic constriction (n=3) or sham operation (n=2) for 28 days. The hearts were collected and performed transcriptome analysis by microarray. The 537 significant differential genes were identified through expression profiling of a total of 26,423 genes.

first: Yulin

last: Li

first: Congcong

last: Zhang


title: Regulatory Landscape and Clinical Implication of MBD3 in Human Malignant Glioma [MBD3 knockdown in SF767]

first: Yi

last: Cui

overall_design: siRNAs targeting MBD3 were introduced into SF767 GBM cells and the knockdown efficiency was confirmed by qRT-PCR, western blot, and immunofluorescence staining. Then the genome-wide changes of transcriptome were determined by Agilent one-color microarray (Design ID: 028004).

first: Jian

first: Sara

last: Wirbisky

first: Jennifer

last: Freeman

first: Joseph

last: Irudayaraj


title: Gene expression signature in Lactococcus lactis after ethanol, butanol or hexanol exposure

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

department: DTU Systems Biology

institute: Technical University of Denmark

summary:
Reference samples: Strain MG1363 was grown balanced in SAL medium supplemented with 1% glucose.
Stressed samples: Strain MG1363 was exposed to either ethanol (55 mg/ml), butanol (10 ml/mg) or hexanol (2 mg/ml) in GSAL medium after balanced growth

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: Each condition (reference, ethanol, butanol and hexanol stressed) were performed in minimal two biological replicas. Samples from the reference culture were taken at OD450 ~ 0.4, following which alcohol stress were added. Samples from the alcohol stressed conditions were substracted 5 and 60  min after the addition of set stress

first: Anne-Mette

last: Hviid


title: TRAF6, a master activator of p53 transactivation, suppresses mitochondrial p53 and apoptosis

city: New York

first: Xian

address: 580 main st apt 138

institute: MSKCC

summary:
TRAF6 -/- thymi display defects in IR-induced p53 target gene expression and attenuate further enhancement of apoptosis upon IR treatment.
TRAF6-mediated K63-linked ubiquitination of p53 at K24

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2.5 week WT and TRAF6 null mice were IR (15Gy) treated for 10h, thymi were then isolated and RNA was extracted by standard Trizol methods.  H1299 cells were transfected with p53 wt and K24R mutant, RNA was extracted by standard Trizol methods.

first: Hui-kuan

last: Lin


title: Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics [Cell lines]

first: Jaine

last: Blayney

summary: Compositional statistics and random gene-sets were used to assign the tumor site of origin and histopathology of 18 epithelial ovarian cancer cell lines

overall_design: In the study presented here, we applied Gene Expression Compositional Assignment (GECA) to epithelial ovarian cell lines, using first a reference library of solid tumors (expO [http://www.intgen.org/expo/]) and then a second library of expert pathologically-reviewed epithelial ovarian cancer samples (GSE73551)


title: N-acetylgalactosamine Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae

status: Public on Nov 02 2016

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

summary:
Three Microarray comparisons have been preformed in this study.
1-  Transcriptome comparison of the Streptococcus pneumoniae D39 wild type grown in M17 medium + 0.5 % (w/v) NAGa (NAGaM17) to  M17 medium + 0.5 % (w/v) glucose (GM17) (GSM2372597 and GSM2372598).
2- Transcriptome comparison of the Streptococcus pneumoniae D39 ΔagaR to D39 wild type grown in M17 medium + 0.5 % (w/v) glucose (GM17) (GSM2372599 and GSM2372600).
3- Transcriptome comparison of the Streptococcus pneumoniae D39 ΔccpA to D39 wild type grown in M17 medium + 0.5 % (w/v) NAGa (NAGaM17) (GSM2290636 and GSM2290637).

overall_design:
- Two conditions design comparison of one strain including a dye swap or Microarray comparisons 1.
- One condition design comparision of two strains including a dye swap for Microarray comparisons 2 and 3.

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Gene Expression Profile In Presence of p53 alone, p47 alone, or both

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

summary: H1299 cells (p53-/-) were transfected with plasmid constructs expressing p53 alone, p47 alone or both, and gene expression profile was probed

overall_design: Agilent one-color experiment,Organism: Homo sapiens, Agilent 8x60k Human Whole Genome Microarray Gene expression  (AMADID: 039494) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Saumitra

last: Das

first: Ananda

last: Guha Majumdar


title: Limited Fluid Resuscitation Significantly Alters the Hepatic Gene Profiles in Rats with Uncontrolled Hemorrhagic Shock

city: chengdu

first: ping

middle: shi

last: liu

state: sichuan

address: guoxue road

department: Emergency Department

institute: West China Hospital of Sichuan University

summary: The study aimed to investigate the effect of limited fluid resuscitation on gene profiles of rat hepatic tissue. Limited fluid resuscitation can reduce mortality resulting from traumatic hemorrhagic shock. However, the protective mechanism of limited fluid resuscitation is not very clear. The rats were subjected to uncontrolled hemorrhagic shock and resuscitated with limited fluid resuscitation or aggressive fluid resuscitation. Following 5 h of resuscitation, hepatic RNA was isolated, and gene expression profiles were measured using a NimbleGen microarray. Gene ontology (GO) and pathway analyses were performed. Real-time reverse transcription polymerase chain reaction was used to verify the microarray findings. A total of 449 differentially expressed genes between aggressive fluid resuscitation and limited fluid resuscitation groups were found. The GO analysis of differential gene expression predicted a significant downregulation of response to stress, alcohol biosynthetic process, response to wounding, gluconeogenesis, hexose biosynthetic process, acute inflammatory response, inflammatory response, response to oxygen levels, glucose metabolic process, acute-phase response, and so forth, and upregulation of steroid biosynthetic process, sterol metabolic process, steroid metabolic process, alcohol metabolic process, lipid metabolic process, cholesterol metabolic process, glycogen catabolic process, glucan catabolic process, cellular polysaccharide catabolic process, monocarboxylic acid metabolic process, and so on. This study showed that limited fluid resuscitation can downregulate the expression of injury-associated differentially expressed genes and upregulate the expression of metabolism-associated differentially expressed genes, which may account for the attenuation of the deleterious effects and overall prosurvival effects of limited fluid resuscitation on uncontrolled hemorrhagic shock.

overall_design: the rats were randomly assigned to three groups of six rats each: group A (limited fluid resuscitation group): Ringer’s solution infusion to reach and maintain MAP at 50–60 mmHg, beginning immediately after the tail amputation; group B (aggressive fluid resuscitation group): Ringer’s solution infusion, with an attempt to maintain MAP over 80 mmHg; and group C (control group): without induction of hemorrhagic shock, suffering euthanasia shortly after the postoperative stabilization period. At 330 min,the rats were immediately sacrificed by exsanguination under anesthesia. The liver was taken out quickly and saved in liquid nitrogen container for gene expression profile analysis.Thirty milligrams of liver tissue from groups A and B was homogenized, and RNA was extracted using an RNeasy mini kit (Qiagen, CA, USA). RNA from each sample (three samples from each group)  was for  NimbleGen microarray analysis

first: Shiping

last: Liu

first: Zhi

last: Zeng

first: Yao

last: Chen

first: Xiaodong

last: Du


title: Gene expression in medaka (Oryzias latipes) ovarian follicles at late vitellogenesis, oocyte maturation and pre-ovulation stages

status: Public on Nov 01 2016

city: Seattle

first: Yasushi

last: Shibata

state: Washington

address: 1122 NE Boat Street

department: SAFS

institute: University of Washington

summary: Investigation of gene expression level changes in Oryzias latipes ovarian follicles with comparing seven developmental stages; late vitellogenic (-47 hr, -35 hr and -32 hr) , maturation (-23 hr and -14 hr) and pre-ovulation (-8 hr and -2 hr) stages.

overall_design: A seven chip study using total RNA extracted from the isolated ovarian follicles which were collected at 47 hr, 35 hr, 32 hr, 23 hr, 14 hr, 8 hr and 2 hr before spawning stages.

first: Takeshi

last: Usami

first: Yoshitaka

last: Nagahama


title: Differential Gene expression anslysis between Paromomycin sensitive and resistat Leishmania donovani.

summary: Gene expression analysis was carried out between experimental Paromomycin resistant Leishmania donovani (adapted to 100 µM paromomycin drug pressure) and it's corresponding wild type paromomycin sensitive parasite.

overall_design: Organism : Leishmania , Agilent Custom Leishmania  Gene Expression  8x15k Array (AMADID: 027511) designed  by Genotypic Technology Private Limited.

first: A

last: Verma

first: V

last: Bhandari

first: M

last: Ouellette

first: R

last: Singh

first: P

last: Salotra


title: Protein expression of women with varying BMI [Custom Antibody Array]

first: Paul

last: Lampe

state: WA

address: 1100 Fairview Ave. N., Mail Stop M5-C800

institute: Fred Hutchinson Cancer Research Center

summary: Protein expression was analyzed by antibody array for differences between women of varying BMI.

overall_design: Protein was extracted from plasma of women with no prior history of any type of cancer. Albumin and IgG were depleted from the plasma.

first: C

middle: B

last: Garrison


title: Phenotypically-anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish

status: Public on Oct 31 2016

city: Corvallis

first: Robert

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: We employed whole-genome microarray expression profiling in 48 hpf zebrafish to better understand the mechanism of action of the antimicrobial agent, triclosan (TCS)

overall_design: TCS-induced transcriptional changes was measured in 48 hpf embryos exposed to 0 or 7.37 uM TCS from 6-48 hpf. Four biological replicates of 8 pooled whole embryos were used for each treatment

first: Derik

last: Haggard


title: Expression data of epithelial organoid cultures generated from intestinal mucosa of non-IBD controls and patients with ulcerative colitis

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

summary:
The transcriptional signature of mucosa of patients with ulcerative colitis (UC) in remission reveals long-lasting changes in the epithelial barrier which persist once the inflammatory response has resolved. In order to investigate if these changes are caused by primary defects in the epithelial cells, we generated in vitro epithelial organoid cultures (EpOCs) from colon samples of non-IBD controls and UC patients.
After induction of differentiation, total RNA was extracted from both EpOCs and differentiated EpOCs (d-EpOCs) and used for hybridization on Affymetrix microarray.

overall_design: Colon samples from non-IBD controls and UC patients were collected. Both surgical and biopsy samples for non-IBD controls, and only biopsy samples for UC patients, were considered. Non-IBD controls were those subjects undergoing surgery for colorectal cancer, colonoscopy for mild gastrointestinal symptoms, or a screening for CRC and who presented no lesions during examination.  Inclusion criteria for UC patients at the time of colonoscopy were: age between 18 and 80, diagnosis at least 5 years before inclusion, and exclusion of colitis-associated dysplasia or neoplasia. Endoscopic activity of UC at the time of colonoscopy was categorized according to the Mayo endoscopy subscore. Active disease was defined as Mayo endoscopic subscore of ≥1; quiescent disease was defined as a Mayo score of 0. Only samples from UC patients with inactive or mildly active disease were included in the generation of epithelial organoid cultures (EpOCs). Once expanded, EpOCs were  induced to differentiate into the different epithelial lineages (d-EpOCs). Finally, a total of 19 human samples were analysed: 11 from non-IBD controls and 8 from UC patients. From these samples 19 EpOCs and 17 d-EpOCs were generated. RNA was then extracted and used for hybridization on Affymetrix microarrays.

first: Isabella

last: Dotti


title: The identification of key genes for the internaliztion of peroxiredoixin protein by macrophage-like cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
Msr1 and Mafb were identified as essential genes for the internalization of peroxiredoxin protein by this microarray analysis.
We found that Msr1 and Mafb were deficient in mutant RAW lines. Overexpression of Msr1 or Mafb in mutant RAW cells regained the activity for the efficient internalization of peroxiredoxin protein.

overall_design: RAW cell internalized peroxiredoxin protein. Mutant RAW lines were generated by random mutagenesis with ENU treatment, which lost ability to internalize peroxiredoxin. We compared gene expression pattern between parental and mutant RAW cell line.

first: Takashi

last: Shichita

first: Akihiko

last: Yoshimura


title: A new model for long-range chromatin reorganization linked to enhancer activation [Agilent_ChIP]

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

type: Genome binding/occupancy profiling by genome tiling array

summary:
The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding bteween Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1.  This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models.
ChIP-on-chip for H3K27me3 on the Shh regulatory region on ESCs and transfected ESCs and NPC showed no loss of Polycomb marks upon Shh activation.

overall_design: Comparison of different Tale-Vp64 transfected ESCs and NPC H3K27me3 profiles on Shh region

first: Iain

last: Williamson

last: Illingworth

first: Shelagh

last: Boyle

first: Graeme

last: Grimes

first: Pierre

last: Therizols

first: Wendy

middle: A

last: Bickmore


title: Autoantigen-Autoantibody expression of women with varying BMI [Custom Antibody Array]

summary: Autoantigen-Autoantibody expression was analyzed by antibody array for differences between women of varying BMI.

overall_design: Autoantigen-Autoantibody was measured from plasma of women with no prior history of any type of cancer.


title: Indole signaling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: Vibrio campbellii BAA-1116 was used as a Harveyi clade model organism to determine the impact of indole signaling on virulence. Gene expression analysis of V. campbellii grown in LB35 broth with or without 100 μM indole revealed that indole decreased: (1) V. campbellii virulence in shrimp and prawn challenge assays, (2) exopolysaccharide production, and (3) swimming motility. The results also indicated that indole inhibits quorum sensing-regulated bioluminescence and blocks the three-channel quorum sensing system by interfering with quorum sensing signal transduction.

platform_organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

overall_design: Five biological replicates of V. campbellii were grown in LB35 broth (24 h, 200 rpm, 28°C) with and without 100 μM indole and total RNA was extracted from 5.0E+8 cells. Messenger RNA was isolated from the total RNA extracts, treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarrays (520694F, Affymetrix).

first: Qian

last: Yang

first: Gde

last: Sasmita Julyantoro Pande

first: Zheng

last: Wang

last: Rubin

first: Gary

middle: J

last: Vora

first: Tom

last: Defoirdt


title: Protein and Autoantigen-Autoantibody expression of women with varying BMI

first: Paul

last: Lampe

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

overall_design: Refer to individual Series


title: Expression analysis of chinese cabbage (B.rapa ssp. pekinensis) : cold stress conditions

city: Jeonju

first: Chang-Kug

last: Kim

address: 370, Nongsaengmyeong-ro

department: Genomics Division

country: South Korea

institute: National Institute of Agricultural Sciences (NAS)

summary: Using 300K′-high density microarray covering the chinese cabbage whole genome, genome-wide expression analyses of cold stress conditions.

overall_design: A total of 10 chips were used for microarray. Total RNAs were extracted from cold stress conditions.

first: ChangKug


title: Gene expression in Aspergillus fumigatus at different developmental stages

city: Higashihiroshima

first: Ken

last: Oda

state: Hiroshima

address: 3-7-1 Kagamiyama

department: Fundamental research division

institute: National research institute of brewing

summary: Microarray analysis was used to compare different divelopmental stages of the filamentous fungi Aspergillus fumigatus af293. Cells were grone for various times and comparisons made between: 1. Dormant conidia (0 hours) and isotropically expanding cells (1hr). 2. Dormant conidia (0 hours) and isotropically expanding cells (2hr) . 3. Dormant conidia (0 hours) and isotropically expanding cells (4hr).  4.  Isotropically expanding cells (4hr) and polarity extending cells (6hr). 4.  Isotropically expanding cells (4hr) and germ tube (8hr).

overall_design:
A total of 6 hybridizations were performed for each microarray experiment described in summary. The following replicates were carried out: 1. Three biological replicates were performed using cultures grown in parallel. 2. Technical 'dye swap' replicates were carried out for each biological replicate.
Please note that [1] each array slide has two spots of same probes, and thus, data was merged and analyzed as described in the sample data processing field.
[2] The normalized data derived from each raw data file 'before the intensities across two technical repeats are averaged' are provided in the *normalized_MDS.mev file and sample data tables include the averaged data of two technical repeats.
[3] For the value in each sample data table, we have performed dye-swapped two slides and normalized at same time. Each slide have two spots for one gene, so we performed In-slide replicate analysis (averaged) and statistic analysis. At final step, fold change ratio (FC) was calculated as 1hr/0hr, 2hr/0hr, 4hr/0hr, 6hr/4hr, 8hr/4hr in each experiment as and then Log2-treansformed (log2 FC).

first: Michelle

last: Momany


title: Overexpression of OsERF71, an AP2/ERF Transcription Factor, Alters Rice Root Structure That Confers Drought Resistance

status: Public on Sep 30 2016

city: Pyeongchang

first: Dong-Keun

last: Lee

address: Pyeongchang Dae-ro, Daehwa-myeon

department: GBST

institute: Seoul National University

summary: Plant responses to drought stress require the regulation of transcriptional networks via drought responsive transcription factors, which mediate a range of morphological and physiological changes. AP2/ERF transcription factors are known to act as key regulators of drought resistance transcriptional networks; however, little is known about the associated molecular mechanisms that give rise to specific morphological and physiological adaptations. In this study, we functionally characterized the rice (Oryza sativa) drought responsive AP2/ERF transcription factor, OsERF71, which is predominantly expressed in the root meristem, pericycle, and endodermis. Overexpression of OsERF71 either throughout the entire plant or specifically in roots, resulted in a drought resistance phenotype at the vegetative growth stage, indicating that overexpression in roots was sufficient to confer drought resistance. The root specific overexpression was more effective in conferring drought resistance at the reproductive stage, such that grain yield was increased by 23-42% over wild type plants or whole-body overexpressing transgenic lines under drought conditions. OsERF71 overexpression in roots elevated the expression levels of genes related to cell wall loosening and lignin biosynthetic genes, which correlated with changes in root structure, the formation of enlarged aerenchyma and high lignification levels. Furthermore, OsERF71 was found to directly bind to the promoter of OsCCR1, a key gene in lignin biosynthesis. These results indicate that the OsERF71-mediated drought resistance pathway recruits factors involved in cell wall modification to enable root morphological adaptations, thereby providing a mechanism for enhancing drought resistance.

overall_design: A six microarray study using total RNA recovered from two separate wild-type roots Nipponbare, two separate GOS2::OsERF71 roots, and  two separate RCc3::OsERF71 roots.This microarray chip contains 27,448 genes deposited at the International Rice Genome Sequencing Project Rice Annotation Project 1 database (http://rapdb.lab.nig.ac.jp).

first: Ju-Kon


title: Whole genome gene expression analysis of evolved polyploid Saccharomyces cerevisiae cell lines at 36 degrees Celsius

status: Public on Oct 11 2016

city: Taipei

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

country: Taiwan

institute: Institute of Molecular Biology

summary: Transcriptional change by profiling yeast cells, comparing polyploid S. cerevisiae cells at 1000 generations with ancestral cells. Transcriptional change by profiling yeast cells, comparing both ancestral and evolved cells with diploid cells, stands for control.

overall_design: Evolved vs. ancestral cell, independently grown and harvested. Technical triplicates for RNA isolation.

first: Jun


title: Karyotype analysis of polyploid Saccharomyces cerevisiae cell lines

summary: The polyploid S. cerevisiae karyotypes were analyzed by array-CGH to identify the deletion or duplication of gene or chromosome during the strain construction and after experimental evolution.

overall_design: Polyploid vs. haploid cells. Biological replicates, independently grown and harvested.


title: Differential expression of lncRNAs during the HIV replication cycle

city: Gent

first: Wim

last: Trypsteen

state: East-Flanders

address: Corneel Heymanslaan 10

department: Internal Medicine

country: Belgium

institute: UGent

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

summary:
Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell’s molecular network and are highly involved in the regulation of molecular processes, including gene expression. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay.
Many lncRNAs were shown to play a role in mechanisms relying on proteasomal and ubiquitinylation pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated from each other. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis (HIV linked co-expression) with possible cis regulatory lncRNAs that control the nearby mRNA expression and function.
Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication.

overall_design: HIV time-course experiment at 4 time points post HIV infection: 2h, 6h, 18h, 30h. Each timepoint has an uninfected and infected condition. Time course experiment was performed in duplicate resulting in a total of 16 samples.

first: Mohammadi

last: Pejman

first: Clarisa

last: Van Hecke

first: Pieter

last: Mestdagh

first: Steve

last: Levefer

first: Yvan

last: Saeys

last: De Bleser

first: Jo

last: Vandesompele

first: Angela

last: Ciuffi

first: Linos

last: Vandekerckhove

first: Ward

last: De Spiegelaere


title: Gene profiling of v-Src transformed primary chicken embryo fibroblasts (CEFs) under the condition of AP-1 repression

status: Public on Oct 10 2016

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

state: Ontario

address: 1280 Main St. West

department: Biology

country: Canada

institute: McMaster University

summary: To investigate the role of AP-1 in Src-mediated transformation, we undertook a gene profiling study to characterize the transcriptomes of v-Src-transformed CEF expressing either the c-Jun dominant-negative mutant TAM67 or JunD shRNA.

overall_design:
CEFs were transfected with B-type RSV viral vectors expressing JunD shRNA, GFP control, or the c-Jun TAM67 dominant negative mutant. Transfected CEFs were superinfected with the temperature sensitive A-type NY72-4 RSV. Infected CEFs were cultured at the non-permissive temperature until such time when temperature shift was performed to induce v-Src activation. All experimental groups consisted of three biological replicates except for NY72-4/RCAS(B)-JunD shRNA permissive which was conducted in sextuplicate.
[Type] viral transformation of primary cells, transformation, AP-1 inhibition, temperature sensitive mutant, v-Src, apoptosis

middle: M

last: Maślikowski

first: Lizhen

last: Wang

first: Ying

last: Wu

first: Ben

last: Fielding

first: Pierre-André

last: Bédard


title: The Gene Expression Profile of Lung Tissue Following Sulfur Mustard Inhalation Exposure in Large Anesthetized Swine

status: Public on Sep 01 2016

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

country: USA

institute: USAMRICD

summary:
Sulfur mustard (HD) is a vesicating agent that targets the eyes, skin, and lungs, producing skin burns, conjunctivitis, and compromised respiratory function.
Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures.
This study utilized mRNA analysis to evaluate molecular effects of HD on lung tissue from anesthetized swine inhalationally exposed to HD

overall_design:
Anesthetized large swine were exposed for 10 minutes to either air, 60 ug/kg (low), or 100ug/kg (medium) HD vapor. At 12 hours, animals were euthanized, lungs removed and dissected by lobe, and stabilized in RNAlater.
Total RNA was isolated and processed for hybridization to Affymetrix Porcine GeneChip.

first: Alfred

last: Sciuto

first: Bronwen

last: Jugg

first: Cristin

last: Rothwell

first: James

middle: F

last: Dillman

first: Jonathon

last: David

first: John

last: Jenner


title: MicroRNAs as diagnostic biomarkers for major depression

status: Public on Aug 31 2016

city: Cork

first: Anand

last: Gururajan

address: Western Road

department: Anatomy & Neuroscience

country: Ireland

institute: University College Cork

summary: Blood samples taken from healthy controls and patients with major depression were analyzed for differences in microRNA expression.  Patients were treated with either electroconvulsive therapy or ketamine and samples were again analyzed to determine if these treatments affected microRNA expression.  Baseline microRNA expression profiles were studied to see if they could predict treatment response.

overall_design: Heatly controls (19), MDD patients (31)


title: Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

institute: Memorial University of Newfoundland

summary: This study was conduct to identify the virus-responsive transcripts in Atlantic cod, using viral mimic, polyriboinosinic polyribocytidylic acid (pIC)

overall_design:
Six individual Atlantic cod (1.087 ± 0.73 kg) were used for identification of antiviral (i.e. pIC-responsive) macrophage transcripts. The fish were kept in a 21 m^3 tank and optimum conditions (5.2-6.4˚C, 95-110% oxygen saturation and under an ambient photoperiod) in the Dr. Joe Brown Aquatic Research Building (JBARB) of the Ocean Sciences Centre (OSC).
Atlantic cod head kidney cells were isolated from 6 fish. The cells were allowed to adhere overnight (16 h) at 10˚C, and then the non-adherent cells were removed. Thereafter, macrophages (adherent cells) from each individual were exposed to either viral mimic using 50 ug/ml pIC or PBS (control). Macrophages were lysed at 24 HPS using TRIzol, and RNAs were extracted. A common reference design was used for the microarray experiment. For each group (pIC or control), 6 biological replicates (pIC and control from 6 fish) were used for microarray experiment. The common reference consisted of a pool of 12 RNA samples. All test samples were labeled with Cy5, whereas common reference was labeled with Cy3. Each individual test sample was co-hybridized with the common reference sample on an array (20K Atlantic cod microarray platform); therefore, 12 arrays were used for this experiment.
[variable] other: pIC: Fish_1_pIC, Fish_2_pIC, Fish_3_pIC, Fish_4_pIC, Fish_5_pIC, Fish_6_pIC,
[variable] other: Control: Fish_1_Control, Fish_2_Control, Fish_3_Control, Fish_4_Control, Fish_5_Control, Fish_6_Control,
[repeat] biological replicate:  Fish_1_pIC, Fish_2_pIC, Fish_3_pIC, Fish_4_pIC, Fish_5_pIC, Fish_6_pIC,
[repeat] biological replicate:  Fish_1_Control, Fish_2_Control, Fish_3_Control, Fish_4_Control, Fish_5_Control, Fish_6_Control,

first: Xi

last: Xue

first: Marije

last: Booman

first: Matthew

last: Rise


title: Global transcriptomic analysis of the response of Corynebacterium glutamicum to vanillin

city: Yangling

first: Can

last: Chen

address: No.3 Taicheng Road

country: China

institute: Northwest A&F University

summary:
Lignocellulosic biomass is an abundant and renewable resource for biofuels and bio-based chemicals. Vanillin is one of the major phenolic inhibitors in biomass production using lignocellulose.
To assess the response of Corynebacterium glutamicum to vanillin stress,  a global transcriptional response analysis was performed by using microarray.

overall_design: Samples were collected during the mid-logarithmic growth phase in minimal medium with added glucose (control sample 100mM) or vanillin as the sole carbon source (3mM), respectively. Two-condition experiment, glucose vs. vanillin. Biological replicates: 4 control replicates, 4 treatment replicates.

first: C

first: J

last: Pan

first: X

last: Yang

last: Guo

first: W

last: Ding

first: M

last: Si

last: Shen

first: Y


title: MiROvaR, a microRNA-based predictor of early relapse for ovarian cancer patients [training set; OC179]

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Despite a pathological complete response, risk-of-relapse remains a challenge for most of epithelial ovarian cancer (EOC) patients and an ad-hoc predictor can be a valuable clinical tool. We developed a 35 miRNAs-based predictor of Risk of Ovarian Cancer Relapse (MiROvaR) using a training set of patients from MITO-2 (Multicentre Italian Trials in Ovarian Cancer-2; Pignata S et al. J Clin Oncol. 2011 Sep 20). MiROvaR performance was confirmed in two independent validation cohorts.

overall_design: The training set OC179 was derived from MITO2 clinical trial. Paraffin blocks from primary tumors of 549 patients out of the 820 enrolled for the MITO2 trial were collected from 17 out of 43 centers participating to the trial: 305 were excluded for lack of materials for RNA extraction, 18 for poor quality of extracted RNA, 10 since tumor derived from metastatic lesions, 30 because not chemo-naive and 1 for hybridization failure. After profiling on Agilent SurePrint 8x60K human miRNA arrays, 179 cases were eligible for data analysis. Ethical Statement: Samples collection for translational research purpose was done following the approval of study amendments (Prot. CEI/98/11).                                                                                Clinical codes:  Age (years)  Histology: according to International Federation of Gynecological and Obstetrics guidelines ( 1: Serous; 2: Mucinous; 3: Endometrioid; 4: Undifferentiated; 5: Clear cell; 6: Mixed or other; NA:  Missing information)  Stage: according to International Federation of Gynecological and Obstetrics guidelines  Grading: according to WHO guidelines (BL: border line; G1: well differentiated; G2: moderately differentiated; G3: poorly differentiated; undiff: undifferentiated; NA: missing information)  Debulking: NED: not evident disease; mRD: minimal residual disease (<1cm) ; GRD: gross residual disease (>1cm); NO: not operated; NA: missing information  Time to relapse (TTR, months) code: 0=no relapse; 1=relapse  Overall survival (OS, months) code: 0=alive; 1=dead


title: Genowide expression analysis of HCT116, HL60 and SNU398 cells after 5-Aza-CdR and combination treatment

status: Public on Aug 30 2016

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Comparing gene expression after combination treatment of 5-Aza-CdR and vitamin C to 5-Aza-CdR treatment alone in HCT116, HL60 and SNU398 cells

first: Minmin

last: Liu

first: Gangning

last: Liang


title: Karyotype analysis and whole genome gene expression analysis of evolved polyploid Saccharomyces cerevisiae cell lines

first: Jun-Yi

last: Leu

type:
Genome variation profiling by array
Expression profiling by array


title: A genomic classifier predicting metastatic disease progression in men with biochemical recurrence after prostatectomy

status: Public on Sep 19 2016

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary:
BACKGROUND: Due to their varied outcomes, men with biochemical recurrence (BCR) following radical prostatectomy (RP) present a management dilemma. Here, we evaluate Decipher, a genomic classifier (GC), for its ability to predict metastasis following BCR.

METHODS: The study population included 85 clinically high-risk patients who developed BCR after RP. Time-dependent receiver operating characteristic (ROC) curves, weighted Cox proportional hazard models, and decision curves were used to compare GC scores to Gleason score (GS), PSA doubling time (PSAdT), time to BCR (ttBCR), the Stephenson nomogram, and CAPRA-S for predicting metastatic disease progression. All tests were two-sided with a type I error probability of 5%.

RESULTS: GC scores stratified men with BCR into those who would or would not develop metastasis (8% of patients with low versus 40% with high scores developed metastasis, p<0.001). The area under the curve for predicting metastasis after BCR was 0.82 (95% CI, 0.76-0.86) for GC, compared to GS 0.64 (0.58-0.70), PSAdT 0.69 (0.61-0.77) and ttBCR 0.52 (0.46-0.59). Decision curve analysis showed that GC scores had a higher overall net benefit compared to models based solely on clinicopathologic features. In multivariable modeling with clinicopathologic variables, GC score was the only significant predictor of metastasis (p=0.003).

CONCLUSIONS: When compared to clinicopathologic variables, GC better predicted metastatic progression among this cohort of men with BCR following RP. While confirmatory studies are needed, these results suggest that use of GC may allow for better selection of men requiring earlier initiation of treatment at the time of BCR.

overall_design: 85 formalin-fixed paraffin-embedded (FFPE) tissue samples from primary prostate cancer obtained from Radical Prostatectomy.

first: Ashley

last: Ross

first: Felix

last: Feng

first: Mercedeh

last: Ghadessi

first: Nicholas

last: Erho

first: Anamaria

last: Crisan

first: Christine

last: Buerki

first: Debasish

last: Sundi

first: Anirban

middle: P

last: Mitra

first: Ismael

last: Vergara

first: Darby

last: Thompson

first: Timothy

last: Triche

first: Eric

last: Bergstralh

first: Robert

last: Jenkins

first: R

last: Karnes

first: Edward

last: Schaeffer


title: HuMiChip2 for Strain Level Identification and Functional Profiling of Human Microbiomes

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

summary: HuMiChip2 was applied to analyze perform both strain-level identification and the functional profiling of human gut microbiomes from alcoholic cirrhosis patients and healthy individuals with alcohol abuse.

overall_design: A total of 18 individuals were recruited for the study, among whom 9 were diagnosed with alcoholic cirrhosis and 9 were healthy individuals with alcohol abuse.

first: Zhili

last: He

first: Lanjuan

last: Li


title: Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.)

status: Public on Aug 28 2016

city: Wuhan

first: Jihong

last: Hu

state: Hubei

address: Ba-Yi Road

department: Department of Genetics

institute: College of life sciences, Wuhan University

summary: Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expression genes (DEGs) in each of the three CMS lines. GO and Mapman analysis indicated that these DEGs were mainly involved in lipid metabolic and cell wall organization. Comprised with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were differentially expressed and 56 of them were down-regulated in all the CMS lines. Co-expression network analysis suggested that many genes were significantly differentially expressed in the CMS lines. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. The present study will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide some candidate genes for pollen development in rice.

overall_design: Examine gene expression profiles of young panicles of three male sterile lines and their maitainer line.

first: Guanglong

last: Chen

first: Hongyuan

last: Zhang

first: Qian

last: Qian

first: Yi

last: Ding


title: MH002: FoxO6 is required for Plxna4-mediated neuronal migration during cortical development

status: Public on Nov 11 2016

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The forkhead transcription factor FoxO6 is prominently expressed during development of the murine neocortex. However, its function in cortical development is as yet unknown. We now demonstrate that cortical development is altered in FoxO6+/- and FoxO6-/- mice, showing migrating neurons halted in the intermediate zone. Using a FoxO6-directed siRNA approach, we substantiate the requirement of FoxO6 for a correct radial migration in the developing neocortex. Subsequent genome-wide transcriptome analysis reveals altered expression of genes involved in cell adhesion, axon guidance, and gliogenesis upon silencing of FoxO6 We then show that FoxO6 binds to DAF-16-binding elements in the Plexin A4 (Plxna4) promoter region and affects Plxna4 expression. Finally, ectopic Plxna4 expression restores radial migration in FoxO6+/- and siRNA-mediated knockdown models. In conclusion, the presented data provide insights into the molecular mechanisms whereby transcriptional programs drive cortical development.

overall_design: In utero knockdown of FoxO6 was done on C57/BL6 mice embryos at E14.5 with either siFoxO6-2 or siFoxO6-3 both targeting FoxO6 specifically or the control siRNA Scrambled. All cortices were co-transfected with GFP. At E16.5, embryos were harvested, cortex was isolated and dissociated followed by FAC sorting. Sorted cells were subjected to RNA isolation, cortices were pooled into 4 independent pools per FoxO6 si-RNA, and 1 reference pool for the non-targeting control siRNA to minimize effects due to electroporation differences. Per si-RNA, 2 samples were labeled normal and 2 in dye swap against the common reference, and hybridized on a mouse expression microarray.

first: Ricardo

last: Paap

first: Saskia

last: Oosterbroek

first: Lars

last: von Oerthel

first: Raymond

last: Schellevis

first: Annemarie

last: Vastenhouw-van der Linden

first: Marco

last: Hoekman

first: Marten

last: Smidt


title: Comprehensive gene expression changes by the expression levels of Dicer protein

status: Public on Aug 23 2016

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: MicroRNA regulates gene expression. In this experiment, we determined the gene expression changes by the microRNA expression status using Dicer protein nulll. Wildtype, and intermediate expression.

overall_design: Dicer gene disrupted HCT116 colon cancer cells were transduced with tetracycline regulated Dicer protein expression. To determine the gene expression changes dependent on the Dicer protein levels, we used Dicer disrupted cells, Dicer wild-type cells, and cells with intermediate expression level of Dicer protein for the cDNA microarrya analyses.

first: Takeshi

last: Yoshikawa

first: Motoyuki

last: Otsuka

first: Kazuhiko

last: Koike.


title: Slug-dependent UVR induction of cytokines and chemokines

status: Public on Aug 27 2016

city: Albuquerque

first: Donna

middle: Frances

last: Kuseiwtt

state: NM

address: Reginald Heber Fitz Hall, Room 335;  915 Camino de Salud

department: Pathology

institute: University of New Mexico School of Medicine

summary: Studies of the zinc finger transcription factors Slug and Snail have largely focused on their important role in modulating epithelial-mesenchymal transition during embryonic development and tumor progression. However, these transcription factors also appear to regulate local inflammation. In previous studies, we showed that Slug knockout mice were resistant to sunburn, an acute cutaneous inflammatory response, compared to wild type mice. In the present studies, we used Slug knockout, chimeric Slug knockout/wild type, conditional Slug knockout, and Slug transgenic mice to study the role of Slug in ultraviolet radiation (UVR)-induced cutaneous inflammation. We demonstrated, using immunohistochemistry, in vivo imaging, and neutrophil migration studies, that it was Slug expression in the epidermis rather than in neutrophils that modulated the UVR response. Microarray analysis indicated that this modulation was effected by the production of epidermal cytokines, including CCL3, CCL4, oncostatin, and interleukin-1β, that recruited neutrophils to UVR-exposed skin. The pattern of pro-inflammatory gene regulation by Slug suggested a central role for NF-κB in mediating gene induction. Immunohistochemical analysis of UVR-induced NF-κB activation demonstrated reduced activation in Slug knockout and enhanced activation in Slug transgenic epidermis. Slug thus appears to modulate NF-κB activation in response to UVR.

overall_design: Shaved Slug knockout and wild type mice were exposed to ~3 MED of UVR or left untreated. 24 hours later, mice were sacrificed and skin samples were frozen. Epidermal RNA was isolated from frozen skin samples using Trizol. Several replicates of each exposure condition were performed. RNA isolation was completed as recommended by the TRIzol supplier and RNA quality was assessed using Agilent’s RNA 6000 Nano kit. No RNA was used if the RIN value was less than 7.5. A total of 1000 ng of RNA was used to synthesize cDNA using the High Capacity cDNA RT Kit from Applied Biosystems. SABiosciences PAMM-3803Z RT-PCR array was used to quantify mRNA expression. Equal amounts of cDNA were added to each well, cDNA was mixed with iTAQ SYBR Green Supermix with ROX from Bio-Rad Laboratories, and each plate was run using the Applied Biosystems Prism 7900 HT qPCR protocol as follows: one cycle at 95° C for 10 minutes; 40 cycles at 95° C for 0.15 seconds and at 60° C for 60 seconds; and a final cycle of 15 seconds each at 95° C, 60° C, and 95° C. Analyses of each plate was performed using the SDS 2.3 program from Applied Biosciences, using the same threshold and baseline for all samples.

last: Kusewitt


title: Identification of genes that play a role in menstrual breakdown and repair

status: Public on Aug 25 2016

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

department: Microbiology

country: Australia

institute: Monash University

summary: We examined the molecular profile of human endometrium on days 2, 3 and 4 of menstruation to identify genes and pathways that play a role in the menstrual process.  Endometrial samples were collected by Pipelle biopsy on days 2 (n=9), 3 (n=9) or 4 (n=6) of menstruation and arrayed.  We identified key gene pathways involved in menstruation and identified a number of genes not previously associated with the process (Paiva et al. 2016. Mol Hum Reprod. In press).

overall_design: Total RNA obtained from endometrial biopsies collected from women on days 2 (n=9), 3 (n=9) or 4 (n=6) of menstruation.

first: Premila

last: Paiva

first: Michelle

middle: G

last: Lockhart

first: Jane

last: Girling

first: Nicole

last: Woodrow

first: Jennifer

last: Marino

first: Martha

last: Hickey

first: Peter

middle: W

last: Rogers


title: Design, characterization, and use of a novel amyloid β-protein control for assembly, neurotoxicity, and gene expression studies

status: Public on Aug 24 2016

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: A key pathogenic agent in Alzheimer’s disease (AD) is the amyloid β-protein (Aβ), which self-assembles into a variety of neurotoxic structures. Establishing structure-activity relationships for these assemblies is critical for proper therapeutic target identification and design. We examined the effects of Aβ monomers, dimers, higher-order oligomers, and fibrils on gene expression in primary rat hippocampal neurons. As opposed to “reverse” Aβ or non-Aβ peptides typically used as controls in such studies, we designed novel scrambled Aβ peptides predicted to behave distinctly from native Aβ. Significant changes in gene expression were observed for all peptide assemblies, but fibrils induced the largest changes. Significant changes in gene expression were observed for all peptide assemblies, but fibrils induced the largest changes. Weighted gene co-expression network analysis (WGCNA) revealed two predominant gene modules related to Aβ treatment. Many genes within these modules were associated with inflammatory signaling pathways

overall_design:
We examined the effects of Aβ monomers, dimers, higher-order oligomers, and fibrils on gene expression in primary rat hippocampal neurons. Novel scrambled Aβ peptides, as opposed to  “reverse” Aβ or non-Aβ peptides, were used as controls.

Please note that the 'XL42_1' sample was excluded from data processing as an outlier (resulting total 23 sample records). However the  'XL42_1' raw data is provided in the 'non_normalized.txt' (total 24 data columns).

first: Ghiam

last: Yamin

first: David

last: Teplow


title: Pericyte-fibroblast transition promotes tumor growth and metastasis

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

summary: Vascular pericytes, an important cellular component, in the tumor microenvironment, are often associated with tumor vasculatures and their functions in cancer invasion and metastasis are poorly understood. Here we show that PDGF-BB induces pericyte fibroblast transition (designated as PFT), which significantly contributes to tumor invasion and metastasis. Gain- and loss-of-function experiments demonstrate that the PDGF-BB-PDGFRβ signaling promotes PFT in vitro and in in vivo tumors. Genome-wide expression analysis indicates that PDGF-BB-activated pericytes acquire mesenchymal progenitor features. Pharmacological inhibition and genetic deletion of PDGFRβ ablate the PDGF-BB-induced PFT. Genetic tracing of pericytes with two independent mouse strains, i.e., TN-AP-CreERT2:R26R-tdTomato and NG2:R26R-tdTomato, shows that PFT cells gains stromal fibroblast and myofibroblast markers in tumors. Importantly, co-implantation of PFT cells with less-invasive tumor cells in mice markedly promotes tumor dissemination and invasion, leading to an increased number of circulating tumor cells (CTCs) and metastasis. Our findings reveal a novel mechanism of vascular pericytes in PDGF-BB-promoted cancer invasion and metastasis by inducing PFT and thus targeting PFT may offer a new treatment option of cancer metastasis.

overall_design: Pericytes were isolated and treated with PDGF-BB or control for 1 or 5 days