status: Public on Mar 31 2016

city: Singapore

first: Paul

middle: Michael

last: Yen

address: 8 College Road

department: Cardiovascular & Metabolic disorder Program

country: Singapore

institute: Duke-NUS Graduate Medical School Singapore

summary: Transcriptional regulation of genes in AML12 cells treated with Palmitic acid, LXR lingand (GW3965) and Ulk1 siRNA shows differential effect of Ulk1 KD on LXr responsive genes

overall_design: AML-12 cells co-treated with 0.75mM PA+/- 10µM GW3965 for 24 h +/- Ulk1 SiRNA

middle: M

first: Sujoy

last: Ghosh

first: Rohit

last: Sinha


title: EWAT transcriptomic analysis in male rat offspring of HF-fed dams treated with GSPE or vehicle during pregnancy and lactation

status: Public on Mar 26 2016

city: Reus

first: Antonio

last: Caimari

state: Tarragona

address: Avinguda Universitat, 1

country: Spain

institute: Centre Tecnològic de Nuctrició i Salut

summary: Objective: Procyanidins are polyphenolic bioactive compounds that exert beneficial effects against obesity and its related diseases. The aim of this study was to evaluate whether the supplementation with low doses of a grape seed procyanidin extract (GSPE) to dams during pre and postnatal periods has biological effects on their offspring at youth.  Design: The metabolic imprinting effect of GSPE was evaluated in 30 days-old male offspring of four groups of rats that were fed either a standard diet (STD) or a high-fat diet (HFD) and supplemented with either GSPE at 25 mg per kg of body weight/day or vehicle during pregnancy and lactation.   Results: A significant increase in the adiposity index and in the weight of all the white adipose tissue depots studied (retroperitoneal –RWAT-, mesenteric –MWAT-, epididymal –EWAT- and inguinal –IWAT-) was observed in offspring of dams fed with a HFD and treated with GSPE (HFT group), compared to the offspring of dams fed with the same diet and that do not received procyanidins (HF group). HFT animals also showed a higher number of cells in the EWAT, a sharply decrease of the circulating levels of monocyte chemoattractant protein-1 (MCP-1) as well as a moderate, but significant, decrease of plasma glycerol levels. The transcriptomic analysis performed in the EWAT showed 238 genes differentially expressed between HF and HFT animals, covering an entire range of processes related with the immune function and the inflammatory response (the metabolic pathway mainly reflected in the EWAT), adipose tissue remodeling and function, lipid and glucose homeostasis and metabolism of methyl groups.  Conclusion: GSPE treatment to dams fed a HFD during pregnancy and lactation increases adiposity, decreases the circulating levels of MCP-1 and modulates the expression of key genes involved in the adipose tissue metabolism of their offspring.

overall_design: The microarray study was performed with the EWAT RNA samples of rats from the HF and the HFT groups (n=8 animals each).

first: Antoni

first: Josep

last: del Bas

first: Anna

last: Crescenti

first: Lluís

last: Arola

last: Arola-Arnal


title: Posttranscriptional Control of Flocculation, Surface Adhesion and Invasive Growth by the Pumilio gene pfr1+ in Schizosaccharomyces pombe

status: Public on Mar 24 2016

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

country: Canada

institute: University of Calgary

summary: The regulation of flocculation, surface adhesion and invasive growth in the fission yeast Schizosaccharomyces pombe has focused primarily at the transcriptional level, but little is known with regards to posttranscriptional control. Here, we identified the Pumilio protein Pfr1 as a novel posttranscriptional regulator of these processes. Deletion of pfr1+ prevented flocculation, surface adhesion and invasive growth under inducing conditions, while overexpression of pfr1+ was sufficient to trigger flocculation. The flocculent phenotype of pfr1+ overexpression was dependent on the presence of the Gsf2 flocculin, but not on the Mbx2, Cbf12 and Adn3 transcription factors. In addition, we used RNA immunoprecipitation and expression microarrays to identify pvg1+ and SPBPB7E8.01, which encode a galactose pyruvyltransferase and glycophosphatidylinositol membrane protein, respectively, as putative mRNA targets potentially degraded by Pfr1. The mRNAs of these genes were upregulated and downregulated in the pfr1 deletion and overexpression strains, respectively, and contained putative binding sites in the 3’-untranslated region. We also discovered that ccr4+ and ste13+, which encode components of the mRNA decay machinery, were required for these processes, but did not suppress the pfr1+ overexpression flocculent phenotype when deleted. This data suggest that these processes in S. pombe involve multiple posttranscriptional-regulatory pathways of which one requires Pfr1.

overall_design: We generated 2 overexpression microarrays with dye swap that were biological replicates, 2 deletion microarrys with dye swap. Mutants samples were compared to empty vector control or wild type. 1 RIP-chip array was generated with IP rna compared to total RNA from the sample.

first: Darren

last: Henry


title: Matrix metalloproteinase-9 in chronic lymphocytic leukemia

status: Public on Mar 21 2016

city: MADRID

first: M Ángeles

last: García-Pardo

state: MADRID

address: RAMIRO DE MAEZTU, 9

institute: CENTRO DE INVESTIGACIONES BIOLÓGICAS, CSIC

summary:
Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of malignant CD5+ B lymphocytes (CLL cells) in the peripheral blood, and their progressive infiltration in lymphoid organs.
MMP-9 plays an important role in cell migration and survival, contributes to CLL pathogenesis by proteolytic and non-proteolytic mechanisms and may constitutive a therapeutic target.
We used Affimetrix microarray technology to characterize the global gene expression profile of chronic lymphocytic leukemia (CLL) cells upon MMP-9 transfection. The aim was to establish whether MMP-9 regulates gene expression and to identify new therapeutic targets in CLL.

overall_design: MEC-1 cells (CLL-derived) were genetically modified using a GFP lentiviral vector with (MMP-9 cells) or without (Mock cells) a proMMP-9 DNA construct; upon  2 h starvation, total RNA was extracted and used for hybridization

first: A

first: E

last: Bailón


title: Genome-wide analysis of the impact of NeuroAiD MLC901 on H9 hESC-derived human neural progenitor cells (NPC) undergoing neural differentiation.

status: Public on Mar 19 2016

first: Lawrence

middle: W

last: Stanton

address: 60 Biopolis Street, Genome

institute: Genome Institute of Singapore

summary: Comparing the gene expression profile of human NPC undergoing neural differentiation in the presence and absence of NeuroAid MLC901.

overall_design: Total RNA obtained from human NPC undergoing neural differentiation in the presence of NeuroAid MLC901 compared to those undergoing neural differentiation in the absence of NeuroAid MLC901 at timepoints 0, 4, 8, 12, 24 hours.


title: Engineering of Corynebacterium glutamicum for growth and succinate production from levoglucosan as a pyrolytic sugar substrate

status: Public on Mar 17 2016

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

summary: We deveolped the C. glutamicum strains that is able to utilize levoglucoan as sole carbon and produce succinate. To understand the cellular metabolism in a levoglucosan-utilizing strain, we compared the mRNA profiling of a levoglucosan-utilizing strains grown in either glucose or levoglucosan.

overall_design: Comparision of the transcriptome from a levoglucosan-utilizing strain & succinate-producing strain (BL-1-LGK) grown in either glucose (as a control) or levoglucosan (as an experiment) at 5 h

first: Eun-Mi

last: Kim

first: Youngsoon

last: Um


title: Analysis of the effects of ZNF16 on gene expression in k562 cells.

status: Public on Mar 29 2016

city: Bei Jing

first: Junwu

last: Zhang

address: 5 Dong Dan San Tiao

country: China

institute: National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences,

summary: We previously characterized zinc finger protein gene HZF1 (ZNF16) and demonstrated its important roles in erythroid and megakaryocytic differentiation of K562 cells by loss-function assay. However its effect in erythroid and megakaryocytic differentiation of hematopoietic stem/progenitor cells (HSPCs) and the mechanisms by which it functions have not been understood. In this study, we detected up-regulation of ZNF16 during erythroid and megakaryocytic differentiation of K562 cells and normal CD34+ HSPCs, and demonstrated that ZNF16 promotes erythroid and megakaryocytic differentiation by gain-of-function and loss-of-function experiments. Gene expression profiling by mRNA array and PCR validation in the K562 transforments with ZNF16 over-expression suggested that cell division cycle-associated 7-like gene (JPO2) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog gene (c-KIT) were among the genes regulated possibly by ZNF16. Luciferase reporter assay and Chromatin Immunoprecipitation demonstrated that ZNF16 binds to JPO2 and c-KIT promoters and inhibits their expression in K562 cells. A significant decrease of JPO2 and c-KIT levels was observed during erythroid and megakaryocytic differentiation of K562 and CD34+ cells. The knockdown of either JPO2 or c-KIT partially rescued the differentiation inhibition caused by ZNF16 knockdown. We also found that ZNF16 inhibits c-KIT/c-Raf/MEK/ERK/c-Jun/HEY1 signal pathways, which finally up-regulated expression of GATA1, a central regulator of erthroid and megakaryocyte differentiation. By lentivirus-mediated gene transfer, we demonstrated that enforced expression and knockdown of ZNF16 in HSPCs down-regulated and up-regulated expression of its targets respectively. Our data collectively demonstrate that ZNF16 promotes erythropoiesis and megakaryocytopoiesis via its regulation on JPO2 and c-KIT.

overall_design: 4 samples are analyzed, H4-1 and H4-2 are two stable K562 transductants with ZNF16 over-expression, PC1 and PC2 are stable control K562 transductants. Stable K562 transductants were obtained for RNA extraction and hybridization on an Illumina HumanHT-12 V4.0 expression beadchipe xpression Array platform.

first: Jing

last: Chen


title: Effect of polyphosphates on osteoblast mineralization

status: Public on Mar 15 2016

city: Niigata

first: yoshikazu

last: mikami

address: 1-757 Asahimatidori, Chuo-ku

department: Division of Microscopic Anatomy

country: Japan

institute: Niigata University Graduate School of Medical and Dental Sciences

summary: Rat osteoblasts ROB17/2.8 cells were cultured in the presence of high (1mg/ml) or low (0.01mg/ml) concentration of polyphosphates.

overall_design: Poly(P) induced gene expression in rat osteoblast ROS17/2.8 cells was measured after the treatment with high (1mg/ml) or low (0.01mg/ml) for 24 h.

first: Yoshikazu

last: Mikami


title: Expansion of hepatic tumor progenito cell population in PTEN deficient mice requires liver injury and is reversed by deletion of Akt2

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

country: USA

institute: Penn State College of Medicine

summary: We found that hepatic injury induced by PTEN loss establishes a selection pressure for tumorinitiating cells (TICs) to proliferate and form mixed lineage tumors. The Pten null mice demonstrate escalating levels of hepatic injury prior to proliferation of hepatic progenitors. Attenuation of hepatic injury by deleting Akt2 reduces progenitor cell proliferation and delays tumor development. Treatment of double mutant mice with 3,5-dietoxycarbonyl-1,4  dihydrocollidine (DDC) shows that the primary effect of AKT2 loss is attenuation of hepatic injury and not inhibition of progenitor cell proliferation in response to injury.

overall_design: Pten/Akt2 double mutant (PtenloxP/loxP; Akt2-/-; Alb-Cre+) (Dm) were generated by crossing the PtenloxP/loxP; Alb-Cre+ (Pm)  with the Akt2-/- mice [19]. Control animals are PtenloxP/loxP; Albumin (Alb)-Cre-.

first: Vivian

last: Medina

first: Lina

last: He

first: Ni

last: Zeng

first: Bangyan

last: Stiles


title: Maternal age related changes in transcriptome of bovine granulosa cells of the dominant follicle at the time of selection

city: SASKATOON

first: Muhammad

middle: Irfan-ur-Rehman

last: Khan

state: SASKATCHEWAN

address: 52 Campus drive

department: Veterinary Biomedical Sciences

institute: University of Saskatchewan

summary: The objective was to determine age-associated changes in the transcriptome of granulosa cells recovered from the dominant follicle at the time of selection. Granulosa cells were collected from the dominant follicle of aged and young cows after ovariectomy (15 ±1.5 years, n=3 and 6 ± 1.1 years, n=3), or ultrasound-guided follicle aspiration (16±2.1 years, n=4 and 7±1.2 years, 6 ± 1.1 years, n=4) 3-days after ovulation (Day 0). Messenger-RNA was extracted, amplified, labeled with florescent dyes, and hybridized with bovine-specific microarrays (GEO accession # GPL13226). Target intensities were analyzed to determine differential gene expression in granulosa cells from aged vs. young cows. A total 169 genes were differentially expressed (≥ 2 fold-change; P≤0.05) between age groups. In conclusion, granulosa cells collected at the time of selection of the dominant follicle exhibited age-related changes in the transcriptome that may explain follicle-associated loss of oocyte competence in aged cows.

overall_design: Granulosa cells of the dominant follicle at the time of selection (aged vs.young cows). Three biological replicates (each composed of one aged and one young cow). 3 Three technical replicate (dye swap). One biological or technical replicate per array.

middle: I


title: PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-mediated Survival of Proneural Glioma Cells.

status: Public on Mar 22 2016

city: Boston

first: Gilbert

middle: Joseph

last: Rahme

state: MA

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Identification of critical survival determinants of PDGF-driven proneural glioma. Results provided information about the genes and pathways that are regulated by PDGF signaling in PDGF-driven proneural glioma and led to the assessment of the importance of the USP1-ID2 axis in proneural glioma.

overall_design: Total RNA was obtained from untreated and Dox treated PDGF-driven glioma spheroid cells (PDGF-GSC) which had been isolated from the Gfap-tTa/Tre-PDGFB mouse model used in our study. The data were analyzed to determine the genes that are regulated by PDGF signaling in PDGF-driven glioma.

middle: J

first: Mark

middle: A

last: Israel


title: Influence of ATM-mediated DNA damage response on genomic variation in human induced pluripotent stem cells (NimbleGen CNV)

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

type: Genome variation profiling by genome tiling array

summary: Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. We show that following reprogramming the early and late replicating genome is differentially affected by CNVs in ATM deficient iPSCs relative to wild type iPSCs. Specifically, the early replicating regions had increased CNV losses during retroviral reprogramming. This differential CNV distribution was not present after later passage or after episomal reprogramming. Comparison of different reprogramming methods in the setting of defective DNA damage response reveals unique vulnerability of early replicating open chromatin to retroviral vectors.

overall_design: 4 cell lines, all in duplicates

first: Junjie

last: Lu

first: Takayo

last: Sasaki


overall_design: Total RNA obtained from PDGF-driven glioma spheroid cells (PDGF-GSC) and primary tumors arising in the Gfap-tTa/Tre-PDGFB mouse model used in our study was analyzed to determine to which subtype of GBM these specimens belonged.


title: Regulation of gene expression in chronic lymphocytic leukemia cells in response to arsenic trioxide.

first: M Ángeles

last: García-Pardo

summary:
Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of malignant CD5+ B lymphocytes (CLL cells) in the peripheral blood, and their progressive infiltration in lymphoid organs. Despite the efforts made, CLL remains an incurable disease. It is therefore crucial to continue searching for new therapeutic agents and targets. Arsenic trioxide (ATO) induces apoptosis in all CLL cases and it could constitute an efficient therapy for this disease.
We used Affimetrix microarray technology to characterize the global gene expression profile underlying CLL cell response to ATO, with the aim of identifying the ATO mechanism of action as well as new therapeutic targets in CLL.

overall_design: MEC-1 cells (CLL-derived) were incubated with or without 5 µM ATO for 24 h and total RNA was extracted and used to hybridize an Affymetrix GeneChip® Human Gene 1.0 ST Array.

first: Angeles

first: Irene

last: Amigo-Jiménez

first: Noemí

last: Aguilera-Montilla

first: Elvira

last: Bailón


title: Chronic Alcohol Consumption Alters micro-RNA Radiation Responses in the Mouse Liver

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

country: France

institute: IRSN

summary: Accumulating evidence suggests that lifestyle-related factors may influence radiation responses and the resulting cancer risks through epigenetic mechanisms, such as miRNA regulations. Chronic alcohol consumption is a major risk factor for various pathologies, including alcoholic liver disease. We have recently shown that consumption of Japanese sake promotes glutathione metabolism and anti-oxidative activities in the liver of irradiated C57BL/6 mice. Here we show that chronic alcohol consumption resulted in elevated ciculating levels of the inflammatory cytokine TNF-α and that it triggered specific miRNA regulations (such as the upregulation of the radio-resistant miR-210) that are susceptible to influence the resulting radiation effects in the mouse liver.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Japanese sake was administrated to C3H mice irradiated with 3 Gy X-rays. miRNA expression was measured in the livers of 3 mice for each experimental group.

first: Tetsuo

last: Nakajima

first: Bing

last: Wang

first: Mitsuru

last: Nenoi


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

overall_design: Refer to individual Series


title: Pretreatment microRNA expression impacting on epithelial to mesenchymal transition predicts intrinsic radiosensitivity in head and neck cancer cell lines and patients [microRNA expression].

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Purpose: Predominant causes of head and neck cancer recurrence after radiotherapy are rapid repopulation, hypoxia, fraction of cancer stem cells and intrinsic radioresistance. Currently, intrinsic radioresistance can only be assessed by ex-vivo colony assays. Besides being time-consuming, colony assays do not identify causes of intrinsic resistance. We aimed to identify a biomarker for intrinsic radioresistance to be used before start of treatment and to reveal biological processes that could be targeted to overcome intrinsic resistance.
Experimental design: We analyzed both micro- and messenger RNA expression in a large panel of HNSCC cell lines. Expression was measured on both irradiated and unirradiated samples. Results were validated using modified cell lines and a series of laryngeal cancer patients.
Results: MiRs, mRNAs and gene sets that correlated with resistance could be identified from expression data of unirradiated cells. The presence of epithelial to mesenchymal transition (EMT) and low expression of miRs involved in the inhibition of EMT were important radioresistance determinants. This finding was validated in two independent cell line pairs, in which the induction of EMT reduced radiosensitivity. Moreover, low expression of the most important miR (miR-203) was shown to correlate with local disease recurrence after radiotherapy in a series of laryngeal cancer patients.
Conclusions: These findings indicate that EMT and low expression of EMT-inhibiting miRs, especially miR-203, measured in pre-treatment material, causes intrinsic radioresistance of HNSCC, which could enable identification and treatment modification of radioresistant tumors.

overall_design:
32 HNSCC cell lines from different subsites, 2 timepoints (mock irradiated and 6 hours after 4 Gy)
All cell lines were obtained from Professor R. Grénman (University of Turku, Finland), who has a panel of well characterized HNSCC cell lines with known radiosensitivity.

middle: C

first: Jelle

last: tenHoeve

first: Reidar

last: Grénman

first: Lodewyk

middle: F

last: Wessels

first: Ron

last: Kerkhoven

first: Hein

last: te Riele

first: Michiel

last: van den Brekel

first: Marcel

last: Verheij

first: Adrian

last: Begg


title: Rice (Oryza sativa L. Koshihikari) mature dry seed transcriptomes under a record hot summer of 2010 in the Kanto region of Japan using DNA microarray and MapMan analyses approach

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. Japan, especially western and central parts, has seen record high temperatures in the last decade, and the rice kernel quality has decreased; specifically a reduction the first-grade of rice has been seen. In this study, we specifically looked at the harvested rice in a town of the central Kanto-plains (Japan) during the year 2010, which saw day-time temperatures go above the critical limits ranging from 34 to 38C at the final stages of seed development and maturity to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial) were obtained Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki prefecture in September 2010, as grade 1 (labeled as Y1), grade 2 (labeled as Y2), and grade 3 (out-of-grade, labeled as Y3). The research objective was to examine in particular alterations in gene expressions genome-wide in grade 2 (Y2) and grade 3 (Y3) seeds over the grade 1 (Y1) following the high-temperature spike using a high-throughput omic-approach DNA microarray (Agilent 4 x 44K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. Rice seed quality analysis revealed, as expected, low quality in Y3 > Y2 over Y1, in taste, amylose, protein and fatty acid degree, but not in water content. Transcriptome profiling data revealed 124 and 373 up-regulated and 106 and 129 down-regulated genes in Y2 and Y3, respectively. Bioinformatics analysis of differentially expressed genes revealed changes in function of genes related to metabolism, including starch metabolism (e.g., alpha amylase), defense/stress response, fatty acid biosynthesis and hormones. This research provides for the first time the seed transcriptome profile for the classified low grades (2 and out-of-grade) of rice under an actual stressed environmental condition of high temperature.

overall_design: Comparison between O. sativa L. japonica cv. Koshihikari grown in a commercial field in Ami town,Kanto plains of Ibaraki prefecture, Japan. Seeds of grade 1, 2 and 3 (out-of-grade) labeled as Y1, 2, and 3, respectively, were pooled (12 each) and ground in liquid nitrogen for total RNA extraction followed by DNA microarray analysis using the dye-swap approach (Agilent) pooled).

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Ranjith

middle: K

last: Bakku

first: Kyoungwon

last: Cho

first: Akihiro

last: Kubo

first: Shoshi

last: Kikuchi

first: Masami

last: Yonekura

first: Motohide

last: Hori

first: Seiji

last: Shioda

first: Ganesh

last: Agrawal


title: Brdt KO mice: Wild-type vs. Mutant

status: Public on Mar 18 2016

city: Tel Aviv

first: Shimi

last: Barda

address: 6 Weizman Street

department: Lis Maternity Hospital

country: Israel

institute: Tel Aviv Sourasky Medical Center

summary: Transcriptional profiling of mouse pituitary tissue comparing WT with Brdt KO mice. Goal was to determine the effects of Brdt absence on pituitary gene expression.

overall_design: Four pools each of total RNA (three mice per pool) extracted from Brdt-/- and wild-type mice. Biological replicates: 2 WT replicates, 2 Brdt KO replicates.


title: Differential Expression of Skeletal Muscle Genes Following Admnistration of Clenbuterol to Exercised Horses

city: Davis

first: Heather

last: Knych

state: California

address: 620 W.  Health Sciencse Drive

department: CAHFS

institute: University of California Davis

summary:
Background: Clenbuterol, a beta2-adrenergic receptor agonist, is used therapeutically to treat respiratory conditions in the horse.  However, by virtue of its mechanism of action it has been suggested that clenbuterol may also have repartitioning affects in horses and as such the potential to affect performance.  Clenbuterol decreases the percent fat and increases fat-free mass following high dose administration in combination with intense exercise in horses.  In the current study, microarray analysis and real-time PCR were used to study the temporal effects of low and high dose chronic clenbuterol administration on differential gene expression of several skeletal muscle myosin heavy chains, genes involved in lipid metabolism and the β2-adrenergic receptor. The effect of clenbuterol administration on differential gene expression has not been previously reported in the horse, therefore the primary objective of the current study was to describe clenbuterol-induced temporal changes in gene expression following chronic oral administration of clenbuterol at both high and low doses.  Steady state clenbuterol concentrations were achieved at approximately 50 hours post administration of the first dose for the low dose regimen and at approximately 18-19 days (10 days post administration of 3.2 μg/kg) for the escalating dosing regimen.  Following chronic administration of the low dose (0.8 µg/kg BID) of clenbuterol, a total of 114 genes were differentially expressed, however, none of these changes were found to be significant following FDR adjustment of the p-values.  A total of 7,093 genes were differentially expressed with 3,623 genes up regulated and 3,470 genes down regulated following chronic high dose administration.  Of the genes selected for further study by real-time PCR, down-regulation of genes encoding myosin heavy chains 2 and 7, steroyl CoA desaturase and the β2-adrenergic receptor were noted.  For most genes, expression levels returned towards baseline levels following cessation of drug administration.
Conclusion: This study showed no evidence of modified gene expression following chronic low dose administration of clenbuterol to horses.  However, following chronic administration of high doses of clenbuterol alterations were noted in transcripts encoding various myosin heavy chains, lipid metabolizing enzymes and the β2-adrenergic receptor.

overall_design: Five healthy horses were studied.  Twenty-two of the horses received 0.8 µg/kg clenbuterol PO BID for 30 days and an additional 4 horses received 0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days.  Muscle biopsy samples were collected one day prior to administration of the first dose of clenbuterol and at a number of times post drug administration.  A final sample was collected one-week post administration of the final dose (35 days post administration of the first dose).  The tissue was transferred to a cryovial containing RNAlater (Qiagen Inc, Valencia, CA) and stored at -20° C until processed. Total RNA was purified using a miRNeasy Mini kit (RNeasy Mini, Qiagen Inc, Valencia, CA) and following the manufacturer’s instructions. Total RNA integrity was assessed using the Experion Automated Electrophoresis System (Bio-rad, Hercules, CA).  Only RNA samples with RIN ≥ 8 and 260/280 ratios between 1.7 and 2.1 were used.  Equine specific microarrays (EquGene-1.0-st; Affymetrix, Santa Clara, CA), containing expression profiling of 30,559 well-characterized genes using 504,603 probes were utilized. To reduce biological noise as a result of genetic variability, each horse was analyzed separately and served as their own control for comparison of baseline samples to day 14 (low dose administration) or day 28 (escalating dose regimen).  Five biological replicates per time point were tested.  Purified total RNA (5 µg) was used for cDNA synthesis in accordance with the Ambion® WT Expression assay kit (Affymetrix, Santa Clara, CA) manufacturer’s protocol. In vitro transcription was used to incorporate biotin labels using the GeneChip® WT Terminal Labeling system (Affymetrix, Santa Clara, CA) and samples hybridized to the Equine microarray. Arrays were washed and stained on a Fluidics Station 450 (Affymetrix, Santa Clara, CA) and scanned on a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA) in accordance with manufacturer’s protocols.   The microarrays were evaluated for differential gene expression using Transcriptome Analysis Console (TAC) and for hybridization quality control using Expression Console Software (Affymetrix, Santa Clara, CA).  In brief, a total of five Cell Intensity Files were generated per time point, uploaded and normalized under the following conditions: PM (perfect match)-only as a PM intensity adjustment and the Robust Multichip Analysis (RMA) quantification method. For evaluation of the assays performance the number of differentially expressed genes detected between baseline and day 14 (low dose administration) or day 28 (escalating dose regimen) were assessed. Based on the TAC software user’s manual, genes with mean transformed ratios significantly less than -2 and larger than +2 were considered significantly regulated.  A number of the significant genes were selected by filtering the genes using an ANOVA (p value < 0.05). A Pearson's correlation coefficient was used to calculate linear dependence between time point and baseline samples to evaluate the correlation coefficient, where 1 was a positive correlation and 0 was no correlation.  For each probeset, expression at day 14 (low dose administration) or day 28 (escalating dose regimen) was compared to expression at baseline in the same horse using a paired t-test.  Fold changes and their confidence intervals were calculated by exponentiating (base 2) the mean within-horse difference in expression for each gene and the associated t confidence intervals.  P-values were adjusted for multiple testing using the False Discovery Rate (FDR) method. Analyses were conducted using the statistical software environment R, version 3.0.2 (R Core Team, 2013).

first: H

first: L

middle: H

last: Harrison

first: S

last: Steinmetz

first: N

last: Chouicha

first: P

last: Kass


title: Gene expression signatures of ischemia on porcine kidney

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers, 2 rue de la miletrie

institute: Inserm U1313 IRMETIST, Université de Poitiers, CHU de Poitiers-Service Biochimie

summary: Using an oligonucleotide microarray we performed differential transcriptomic analysis of porcine kidneys subjected to intense ischemic stress which could be observed in donors deceased after circulatory death situation (60 min warm ischemia then 24h of cold storage in University of Wisconsin solution) compared to healthy kidneys (n=3). 43 genes were differentially expressed in ischemic versus healthy kidneys (adjusted p value <0.05 + log2 fold change >0.5 or <-0.5). Functional enrichment analysis via Gene ontology revealed relevant biological processes and signaling pathways such as: cellular responses to stress and cell cycle adaptation, metabolism modification, RNA reprograming, cellular phenotype changes and inflammation. Our data showed that ischemia is a dynamic process, with important transcriptional modifications on major pathways. We uncovered a number of targets which we will further validate as biomarkers and therapeutic targets to optimize organ quality.

overall_design: ISCHEMIA samples: Three independent porcine kidney (from different Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then flushed with cold (4°C) University of Wisconsin preservation solution (UW) and stored at 4°C for 24h, then kidneys were immediatly sampled and frozen. CONTROL samples: Three independent porcine kidney (from different Large White pig) were removed and then immediatly sampled and frozen.

first: Sophie

last: Lamarre

first: Lidwine

last: Trouilh

first: Thierry

last: Hauet


title: Enterohemorrhagic Escherichia coli: impact of short chain fatty acid treatment on virulence gene expression

status: Public on Mar 23 2016

city: Toronto

first: Debora

middle: Eleanor

last: Barnett Foster

state: Ontario

address: 350 Victoria Street

department: Chemistry and Biology

institute: Ryerson University

summary: transcriptome analysis of enterohemorrhagic E. coli treated with either one of two different concentrations of short chain fatty acid mixes or the corresponding sodium chloride osmolarity control

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

overall_design: four conditions: 30mM SCFA mix; 30mM NaCl control; 172mM SCFA mix: 172 mM NaCl control. Biological replicates: 4 per group

first: Tracy

last: Lackraj

first: Jee

last: Kim

first: Seav-Ly

middle: L

last: Tran

middle: E


title: Divisional History Identifies Differential Precursor Contributions in Native and Perturbed Hematopoiesis and Reveals Functionally Distinct Stem Cell Subsets

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: To uphold appropriate homeostasis of short-lived blood cells, immature blood cells need to proliferate vigorously. Here, using a conditional H2B-mCherry labeling mouse-model, we characterize hematopoietic stem cell (HSC) and progenitor proliferation dynamics in steady state, upon physiological aging and following several types of induced stress. Following transplantation, HSCs shifted towards higher degrees of proliferation that was sustained long-term. HSCs were, by contrast, poorly recruited into proliferation following cytokine-induced mobilization and after acute depletions of selected blood cell lineages. Using indexed single cell sorting coupled to multiplex gene expression analyses, proliferation history separated candidate HSCs into units with distinct molecular and functional attributes. Our data thereby highlight that HSC proliferation following transplantation is fundamentally different not only from native hematopoiesis but also from other stress contexts, and demonstrate the power of divisional history as a functional criterion to resolve HSC heterogeneity.

overall_design: qPCR gene expression profiling of mouse hematopoietic stem cells (HSCs). Four 96-well plates with pre-amplified single HSC bone marrow cell cDNA (with no template controls) were loaded on to a 96.96 Dynamic Array Chip for Gene Expression. Samples Ids follow where 2w or 5w denotes weeks chase before HSC isolation, and P<X>denoted the plate. No cell was sorted into 2 wells on each plate were = No template controls.

first: Petter

last: Säwen

first: David

last: Bryder

first: Stefan

last: Lang


title: Gene expression profiling in male rat germ cells after chronic cyclophosphamide treatment

city: Montreal

first: Anne Marie

middle: Lucie

last: Downey

state: Quebec

address: 3655 Promenade Sir William Osler, Room 115

department: Pharmacology and Therapeutics

institute: McGill University

summary: To further understand the effects of chronic cyclophosphamide treatment on spermatogenesis, we used whole genome microarrays to identify differentially expressed genes in pachytene spermatocytes and round spermatids from treated and control male rats.

overall_design: Pachytene spermatocytes and round spermatids from rats treated chronically with cyclophosphamide were isolated and profiled for changes in gene expression.

first: Anne

first: Barbara

last: Hales

first: Bernard

last: Robaire


title: Dual Function of Tropodithietic Acid as Antibiotic and Signaling Molecule in Quorum Sensing

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: The marine bacterium Phaeobacter inhibens produces tropodithietic acid (TDA), a broad-spectrum antibiotic and anticancer agent. TDA allows P. inhibens to antagonize other bacteria, including several pathogens, and eukaryotes. Since recently antibiotics are also discussed to function as intermicrobial signals. Here we show that ~10% of the genes of P. inhibens are strongly influenced by N-acyl-homoserine lactone (AHL) mediated quorum sensing (QS), switching the bacterium’s life style from attached to free-living. In an AHL negative mutant of P. inhibens subinhibitory concentrations of TDA caused the same regulatory effect as the AHL. This demonstrates that bacteria can produce antibiotic compounds not only as weapons, but also to substitute their endogenous AHL molecule in QS. The dual function of TDA probably supports the QS system to accelerate regulatory processes and points to a so far neglected role of antibiotics at subinhibitory concentrations in the environment and in microbial interactions.

overall_design: Comparison of whole transcriptomes of wildytype, quorum sensing mutants (pgaI and pgaR) and pgaI grown supplemented with subinhibitory concentration of the antibiotic TDA. RNA isolated in the late exponential growth phase. 4 biological replicates investigated for each strain.

first: Paul

middle: G

last: Beyersmann

first: Kwangmin

last: Son

first: Roman

last: Stocker

first: Markus

last: Göker

first: Irene

last: Wagner-Döbler

first: Meinhard

last: Simon

first: Thorsten

last: Brinkhoff


title: Expression data of genes from the gustatory cortex follwing novel taste learning

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

country: United Kingdom

institute: University of Edinburgh

summary:
Novel taste memories, critical for animal survival, are consolidated to form long term memories which are dependent on translation regulation in the gustatory cortex
We used microarray for identification of genes involved in novel taste learning at two time points- 1 and 3 hours following memory formation for novel taste

overall_design: Adult rats were separated into two groups- novel tatse (0.1% sacchain) and water, two time points were used 1, 3 hours following learnin. Rna was extracted and hybridized on Affymetrix microarray

first: Sharon

last: Inberg

first: Eyal

last: Jacob

first: Alina

last: Elkobi

first: Efrat

last: Edry

first: Akiva

last: Rappaport

first: T

first: J

middle: D

last: Armstrong

first: Noam

last: Shomron

first: Metsada

last: Pasmanik-Chor

first: Kobi

last: Rosenblum


title: Mechanisms of Pancreatic Acinar Cell Neoplasia Associated with Gene Expression Changes caused by Dietary Exposure of Rats to Ammonium perfluorooctanoate, Wyeth 14,643 or Diethylhexyl phthalate

city: Newort on tay

first: Simon

last: Plummer

address: 23 Wellgate Street

institute: Micromatrices Associates ltd

summary:
To identify putative procarcinogenic gene changes associated with  pancreatic acinar cell neoplasia in rats exposed to peroxisome proliferator activated receptor alpha agonists, we performed transcription profiling in the pancreas of  rats fed diets containing the pancreatic carcinogen Wyeth 14,643 (Wy) at  procarcinogenic (50ppm) and non-carcinogenic (20ppm) doses for 1, 7, 28 and 90 days. The effects of these treatments were compared to those of ammonium perfluorooctanoate (APFO) 300 ppm, an agent shown to induce pancreatic acinar cell adenomas in rats, and diethylhexylphthalate (DEHP) 12,000 ppm, an agent not shown to produce pancreatic acinar cell tumors.
To assess whether this putative mechanism(s) of carcinogenesis occurs in ‘target’ cells we have also performed transcriptional profiling in isolated pancreatic acinar cells obtained from animals exposed to these compounds in vivo.

overall_design: Treatment-induced changes in gene expression were assessed in the pancreas by two-colour hybridisation of fluorescently labelled (Cy5/Cy3) cRNAs from three separate animals for each treatment against cRNA generated from a common ‘reference’ (control) made by pooling pancreatic RNA samples extracted from control (vehicle-treated) animals. Two hybridisations were performed in duplicate in order to incorporate a ‘dye swap’. Hence, there were 5 arrays per treatment group.

middle: M

first: Clifford

middle: R

last: Elcombe


title: Expression data from β-globin let7 HeLa tet off cells treated with doxycycline

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: We used microarray to determine the genes whose expression was changed at six hours after doxycycline treatment

overall_design: Cells were transfected with β-globin let7 wt constructs. Two-condition experiment; HeLa tet off cells overexpressed control vs HeLa tet off cells treated with doxycycline for six hours

first: Takeshi

last: Yoshikawa

first: Motoyuki

last: Otsuka


title: Transcript Profiling of Periaqueductal Gray in Response to Electroacupuncture on Rats

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

summary: The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and low responders (NR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in spinal dorsal horn induced by 2Hz/100Hz electroacupuncture in HR and NR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in dorsal horn. Transcriptome profiling analysis found that some co-regulated genes related with electroacupuncture or 2Hz or 100Hz fruqencies. These co-regulated genes were plasticity-related by GO analysis.

overall_design:
Periaqueductal Gray in Response to Different Frequencies Electroacupuncture on Rats.
Rats were exposed to different frequencies (2Hz or 100Hz) electroacupuncture stimlation for 30 min and nociceptive testing and returned to home cages for 1 hours before sacrificed. According to the sensitivity of the analgesic response to 2Hz or 100Hz EA stimulation, the rats divided into four groups: 2Hz-HR group, 2Hz-NR group, 100Hz-HR group and 100Hz-NR group. Subsequently analyzed their dorsal horn transcript profile using cDNA microarrays, the rats were without receiving electroacupuncture as control. The tissue of periaqueductal gray of four or five rats were selected for transcript analysis in each group. The five control rats were mixed and labeled with cy5, each rat of experiment groups was labeled with cy3.

first: Ke

last: Wang

first: Fei

last: He

first: Libo

last: Lin

first: Qinghua

last: Zhang


title: Derivation and differentiation of haploid human embryonic stem cells [SNP array]

status: Public on Mar 16 2016

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

institute: The Hebrew University of Jerusalem

summary: Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution.

overall_design: Single nucleotide polymorphism (SNP) array analysis with Illumina Infinium Omni2.5Exome-8 BeadChips was performed on a total of 4 samples, including undifferentiated haploid and diploid human parthenogenetic embryonic stem cells in G1.

first: Dieter

last: Egli

first: Nissim

last: Benvenisty


title: Effects of muscle regeneration after injury on overloading-induced hypertrophy

status: Public on Mar 12 2016

city: Matsumoto City

first: Fuminori

last: Kawano

state: Nagano

address: Niimura 2095-1

department: Graduate School of Health Sciences

institute: Matsumoto University

summary:
Cardiotoxin was injected into left soleus muscle of adult rats. Right muscle was kept intact. Ambulation recovery was allowed for 8 weeks.
After 8 weeks of regeneration period, both left and right soleus muscles were overloaded by the transection of synergists' tendons for 2 weeks.

overall_design: We tested 6 muscles for each group. RNA samples were mixed with same amount from each muscle toward analysis by microarray.

first: Kawano

last: Fuminori


title: Real-time Quantitative PCR analysis of the expression of TGFB-pathway target genes on 3D-cultured chemoresistant colon carcinoma cells

status: Public on Mar 10 2016

city: Pisa

first: Roberto

last: Giovannoni

address: Via Derna, 1

department: Biology

country: Italy

institute: University of Pisa

summary: The aim of the study was to elucidate which TGFB signaling pathway molecules are involved in the colon cancer chemoresistance. The PCR array used for this experiments was 84 Human TGF-β Signaling Targets (Cat. N. PAHS-235ZA, Qiagen)

overall_design: The expression of 84 Human TGF-β Signaling Targets genes was analyzed by RT2 profiler PCR array (PAHS-235ZA, Qiagen) using the StepOne Plus instrument (Applied Biosystems) following the manufacturer’s protocol. Two independent experiments were performed for each group of treatment. Untreated cells were used as reference control sample. The mRNA expression levels of each gene in each cell treatment were normalized using the expression of the housekeeping genes B2M, GAPDH, RPLP0, HPRT1 and ACTB.

first: Gabriele

last: Romano


title: Comparative analysis of gene expression in response to LL-37 treatment

status: Public on Mar 11 2016

city: Hsinchu

first: Pei-Wen

last: Tsai

address: Kuang-Fu Rd.

country: Taiwan

institute: National Tsing Hua University

summary: To identify the potential LL-37-responsed genes, we treated cells with or without LL-37 and their correspondent transcriptional profiles were compared. Total 104 significant genes were identified. Among them, 70 genes are upregulated in repsonse to LL-37 while 34 genes are downregulated in comparison with the control cells.

overall_design: LL-37 responsed gene was measured after 3 h growth in YPD followed by 30 min of incubation in the presence of 5 ug/ml LL-37 in RPMI.  Two batches of five independent experiments were performed.

first: Chung-Yu

last: Lan


title: Expression quantitative trait loci (eQTL) analysis of mouse lung tumors

status: Public on Mar 14 2016

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: To detect genetic variations affecting gene expression in mouse lung tumor tissue, we carried out a genetic linkage study on the transcriptome of lung tumors induced by urethane in an (A/J x C57BL/6)F4 intercross population, whose individual lung tumor multiplicity (Nlung) is linked to the genotype at the pulmonary adenoma susceptibility 1 (Pas1) locus (containing the Kras-37-bp marker) . In particular, susceptible animals carry the A/J-derived version of Pas1 in homozygousity or in heterozygousity, while tumor-resistant animals carry the C57BL/6-derived version. We found that expression levels of 1,179 and 1,579 genes are modulated by an expression quantitative trait locus (eQTL) in cis and in trans, respectively (LOD score > 5). Of note, the genomic area surrounding and including the Pas1 locus regulated 14 genes in cis and 857 genes in trans. In lung tumors of the same (A/J x C57BL/6)F4 mice, we found 1,124 genes whose transcript levels associated with Nlung (FDR < 0.001). The expression levels of about a third of these genes (n = 401) were regulated by the genotype at the Pas1 locus. Pathway analysis of the sets of genes associated with Nlung and regulated by Pas1 revealed a set of 14 recurrently represented genes that are components or targets of the Ras–Erk and Pi3k–Akt signaling pathways. In conclusion, our results illustrate the architecture of germline control of gene expression in mouse lung cancer: they highlight the importance of Pas1 as a tumor-modifier locus, attribute to it a novel role as a major regulator of transcription in lung tumor nodules and strengthen the candidacy of the Kras gene as the effector of this locus.

overall_design: Female animals of the lung tumor-susceptible A/J strain (A) were mated with males of the lung tumor-resistant C57BL/6 strain (B), and offspring were bred to the fourth generation (ABF4). At 4 weeks of age, 143 male ABF4 mice were treated with a single intraperitoneal injection of the chemical carcinogen urethane to induce the development of lung tumors. When the animals were 40 weeks of age, they were killed, the lungs were removed for tumor counting (values of lung tumor multiplicity [Nlung] varied substantially among individuals, ranging from 1 to 33 in the animals that developed tumors), and a single lung tumor, 1–1.5 mm in diameter, was excised from each for RNA extraction.

first: Francesca

last: Colombo

first: Chiara

last: Cotroneo

first: Alice

last: Dassano

first: Loris

last: De Cecco

first: Tommaso

last: Dragani

first: Giacomo

last: Manenti

first: Angela

last: Pettinicchio


title: The transcriptional profile of deoxycholate-induced sporulation in Clostridium perfringens food poisoning isolate

status: Public on Mar 13 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Clostridium perfringens type A is a common source of food poisoning in humans. Vegetative cells sporulate in the small intestinal tract and produce a major pathogenic factor, C. perfringens enterotoxin (CPE) during sporulation. Although sporulation plays a critical role in the pathogenesis of food poisoning, the mechanisms to induce in vivo sporulation remain unclear. Bile salts had been identified to mediate sporulation, and we have confirmed deoxycholate (DCA)-induced sporulation in C. perfringens strain NCTC8239 co-cultured with human intestinal epithelial Caco-2 cells. In this study, we performed global transcriptome analysis of strain NCTC8239 to elucidate the mechanism to induce sporulation by DCA.

overall_design: From the 55 contigs of C. perfringens strain NCTC8239, 2778 coding sequences were extracted. We designed a DNA probe by utilizing eArray provided by Agilent Technologies. The custom 8×15K oligonucleotide array, containing 60 mer oligonucleotide probes for 2,778 genes in strain NCTC8239, 2 bacterial control genes: 16S rRNA and 23S rRNA, and 3 human control genes: beta-2-microglobulin, glucuronidase beta and 18S rRNA, were ordered to Agilent Technologies. Each probe was spotted in five-fold on each microarray. Each strain was run in triplicate or quadruplicate.

first: Mayo

last: Yasugi

first: Mahfuzur

last: Sarker

first: Masami

last: Miyake


title: Plasma-specific microRNA responses in rats treated with acute toxicity doses of aristolochic acid I

first: Ze'an

last: Zhang

address: Room 1403, No. 1 Building, Cai Lun Road

institute: Shanghai University of Traditional Chinese Medicine

summary: In the present study, goal was to scan the potential biomarker for acute kidney injury induced by aristolochic acid I (AAI).We utilized the microarry analysis to investigate the microRNA (miRNA) expression profile in kidneys from rat treated by 40mg/kg AA I for 2-6 days. miRNAs with significantly different expression of global miRNA expression profile were validated by qRT-PCR. For miRNAs still significantly disregulation, we further examined the expression in plasma of rats treated with AAI dosed at 10, 20 and 40mg/kg AAI for 2-6 days by qRT-PCR. miRNAs with significantly dysregulation in plasma, their expression in brain, liver and heart was examined for kicking out the non-specific disregulation in AAI induced acute kidney injury, so that the significant dysregulation miRNAs with specificity in kidney and plasma was found as potential biomarkers for AAI induced acute kidney injury.

overall_design: Five control and 15 kidneys treated with 40mg/kg AAI on day 2, 4 and 6 was examined by microarray.

first: Jiaying

last: Shen

first: Zhongping

last: Deng

first: Zean


title: Study of microRNA associated with cisplatin's anti-tumor effect in hepatocellular carcinoma

first: Satoshi

last: Kondo

summary: The miRNAs expression was markedly altered with the treatment of cisplatin in vitro and various miRNAs induced by cisplatin also may contribute to tumor growth in vitro.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 1719 human miRNA probes in the cell lines in vitro that were treated with and without cisplatin.

first: Miwa

last: Tatsuta

first: Tsutomu

last: Masaki


title: Digital expression profiling identifies CDC5L, RECQL4, and CDK4 as potential oncogenes in a cohort of pediatric osteosarcoma tumours

first: Jeff

middle: W

last: Martin

state: ON

address: 555 University Avenue

institute: Hospital for Sick Children

summary: Osteosarcoma is the most common malignancy of bone, and occurs most frequently in children and adolescents. Currently, the most reliable technique for prognostication is measuring histopathologic tumor necrosis following preoperative chemotherapy, and favourable prognosis is signified by 90% or greater estimated necrosis of the tumour. Neither genetic testing nor molecular biomarkers have been described for this tumour. We used the novel nanoString mRNA expression analysis system to analyzed total RNA from 35 flash-frozen sporadic paediatric osteosarcoma biopsy and resection specimens to quantify mRNA expression for 17 oncogenes and tumour suppressor genes. Three oncogenes, cell cycle regulator gene CDC5L, the RecQ DNA helicase gene RECQL4, and the cyclin-dependent kinase gene CDK4, were more highly expressed (p<0.05) in tumours which responded poorly to neoadjuvant chemotherapy. A similar trend (p<0.10) was identified for the osteoblast-specific transcription factor gene RUNX2. No statistically significant difference existed in comparing expression of CDC5L, RECQL4, CDK4, and RUNX2 between biopsy and resection samples. Additionally, analysis of expression data in the context of histological subtype yielded preliminary results for deducing molecular subtypes of osteosarcomas. Osteoblastic osteosarcomas possessed higher expression of CDKN1A, PTEN, and RUNX2 relative to their fibroblastic counterparts (p<0.05). This research study shows that CDC5L, RECQL4, and CDK4 tumour expression levels may be useful for identifying patients who may not benefit from the current standardized chemotherapy regimen.

overall_design: Total RNA was isolated from 52 pediatric osteosarcoma samples (prechemotherapy biopsies and resections), 3 osteosarcoma cell lines, and normal human osteoblasts. nanoString mRNA expression analysis was applied to samples split between 3 batches to compare samples based on clinical and pathologic data reports, and to compare samples with normal human osteoblasts. For 43 samples, there were complete data and the RNA was successfully assayed. Analysis was performed using R.

first: J

first: S

last: Chilton-MacNeill

last: Squire

first: M

last: Zielenska


title: LOC283731 promoter hypermethylation prognosticates survival after radiochemotherapy in IDH1 wild-type glioblastoma patients

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

country: Germany

institute: Heidelberg University Hospital

type: Methylation profiling by genome tiling array

summary: MGMT promoter methylation status is currently the only established molecular prognosticator in IDH wild-type glioblastoma multiforme (GBM). Therefore, we aimed to discover novel therapy-associated epigenetic biomarkers. After enrichment for hypermethylated fractions using methyl-CpG-immunoprecipitation (MCIp), we performed global DNA methylation profiling for 14 long-term (LTS; >36 months) and 15 short-term (STS; 6–10 months) surviving GBM patients. Even after exclusion of the G-CIMP phenotype, we observed marked differences between the LTS and STS methylome. A total of 1,247 probes in 706 genes were hypermethylated in LTS and 463 probes in 305 genes were found to be hypermethylated in STS patients (p values < 0.05, log2 fold change ± 0.5). We identified 13 differentially methylated regions (DMRs) with a minimum of four differentially methylated probes per gene. Indeed, we were able to validate a subset of these DMRs through a second, independent method (MassARRAY) in our LTS/STS training set (ADCY1, GPC3, LOC283731/ISLR2). These DMRs were further assessed for their prognostic capability in an independent validation cohort (n = 62) of non-G-CIMP GBMs from the TCGA. Hypermethylation of multiple CpGs mapping to the promoter region of LOC283731 correlated with improved patient outcome (p < 0.03). The prognostic performance of LOC283731 promoter hypermethylation was confirmed in a third independent study cohort (n = 89), and was independent of gender, performance (KPS) and MGMT status (p < 0.0485, HR = 0.63). Intriguingly, the prediction was most pronounced in younger GBM patients (<60 years). In conclusion, we provide compelling evidence that promoter methylation status of this novel gene is a prognostic biomarker in IDH1 wild-type/non-G-CIMP GBMs.

overall_design: Global DNA methylation profiling in 14 long-term and 15 short-term surviving glioblastoma patients. DNA of 7 normal brain samples were pooled to create a control DNA for two-color analysis.

first: Andreas

last: Mock


title: miR-222 is necessary for exercise-induced cardiac growth and protects against pathological cardiac remodeling.

status: Public on Mar 03 2016

city: Boston

first: XIAOJUN

last: LIU

state: Massachusetts

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary:
miR-222 overexpression leads to promotion of proliferation and hypertrophy and inhibition of apoptosis in in primary neonatal rat ventricular cardiomyocytes (NRVMs).
Isolated primary neonatal rat ventricular cardiomyocytes were plated in 6 cm BD Primaria tissue culture dishes. Transfection of microRNA precursors or scramble control (0.4 μM) was carried out using Lipofectamine RNAiMAX (Invitrogen) as recommended by the manufacturer. Forty-eight hours after transfection, RNAs from cultured cells and tissues were isolated with Tryzol (Invitrogen) following the manufactures’ manuals. Total RNA was harvested and submitted to the Dana-Farber Cancer Institute Molecular Diagnostics Laboratory for assay. These results revealed miR-222 regulated gene expression in primary neonatal rat ventricular cardiomyocytes.

overall_design: Gene expression in NRVM cells tranfected with control scramble precursor (4 samples) or miR-222 precursor (4 smaples ) was evaluated using Affymetrix Rat Genome 230 v2.0.

first: Xiaojun

last: Liu

first: Junjie

last: Xiao

first: Han

last: Zhu

first: Xin

last: Wei

first: Colin

last: Platt

first: Federico

last: Damilano

first: Chunyang

first: Vassilios

last: Bezzerides

first: Pontus

last: Boström

first: Lin

last: Che

first: Chunxiang

first: Bruce

last: Spiegelman

first: Anthony

last: Rosenzweig


title: Effects of LXR activation in zebrafish larvae

status: Public on Mar 07 2016

city: Houston

first: Maria

last: Bondesson

state: Texas

address: 3605 Cullen Blvd

department: Biology & Biochemistry

institute: University of Houston

summary: The Liver X Receptors (LXRs) play important roles in multiple metabolic pathways, including fatty acid, cholesterol, carbohydrate and energy metabolism. To expand the knowledge of the functions of LXR signaling during embryonic development, we performed a whole-genome microarray analysis of Lxr target genes in zebrafish larvae treated with either one of the synthetic LXR ligands T0901317 or GW3965. Assessment of the biological processes enriched by differentially expressed genes revealed a prime role for Lxr in regulating lipid metabolic processes, similarly to the function of LXR in mammals. In addition, exposure to the Lxr ligands induced changes in expression of genes in the neural retina and lens of the zebrafish eye, including the photoreceptor guanylate cyclase activators and lens gamma crystallins, suggesting a potential novel role for Lxr in modulating the transcription of genes associated with visual function in zebrafish. The regulation of expression of metabolic genes was phenotypically reflected in an increased absorption of yolk in the zebrafish larvae, and changes in the expression of genes involved in visual perception were associated with morphological alterations in the retina and lens of the developing zebrafish eye. The regulation of expression of both lipid metabolic and eye specific genes was sustained in 1 month old fish. The transcriptional networks demonstrated several conserved effects of LXR activation between zebrafish and mammals, and also identified potential novel functions of Lxr, supporting zebrafish as a promising model for investigating the role of Lxr during development.

overall_design: Wild type zebrafish WIK embryos were collected after spawning. At 4 days post fertilization (dpf), zebrafish larvae were transferred to 6-well plates (pools of 30 embryos/well) in 3 mL of embryo media (E3: 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.3 mM MgSO4). Larvae at 4 dpf were treated with DMSO as vehicle control, 2 mM T0901317 (T0) or 1 mM GW3965 (GW). Final DMSO concentration in all treatments and control was 0.1%. Treatments were renewed after 24 h and larvae were collected for RNA extraction at 6 dpf. Treatments with vehicle (0.1% DMSO), T0 and GW were performed in biological quadruplicates of pools of RNA. Array corresponding to sample 33576 (T0 treatment replicate 2) was excluded from microarray data analysis.

first: Caroline

last: Pinto

first: Philip

last: Jonsson

first: JanAke

last: Gustafsson


title: Gene expression profile of primary cortical neurons from necdin-null mouse embryo

first: Koichi

last: Hasegawa

address: 3-2 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

summary: Necdin, a pleiotropic protein expressed predominantly in postmitotic neurons of mammals, regulates neuronal development and survival by interacting with various regulatory proteins. To understand a novel function of necdin, we analyzed gene expression profile of primary cortical neurons prepared from necdin-null mice at embryonic day 14.5.

overall_design: Wild-type and necdin-null cortical cells were prepared from mice at embryonic day 14.5.  These cells were incubated in Neurobasal medium supplemented with B27 and differentiated into neurons for 4 days (>97% MAP2-positive postmitotic neurons). Three mice per genotype were used for analysis.

first: Kazuaki

last: Yoshikawa


title: Immune-mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I

status: Public on Mar 05 2016

city: Orange

first: Omar

last: Khalid

state: CA

address: 1201 W La Veta Ave

department: Research

institute: Children's Hospital of Orange County

summary: Comparisons of canine arterial gene expression between control and untreated MPS animals were conducted with a canine-specific microarray covering 43,803 probes (Agilent G2519F 4x44k, Santa Clara, CA), for a total of four comparison groups: MPS ascending aorta vs. control ascending aorta, MPS descending aorta vs. control descending aorta, MPS carotid artery vs. control carotid artery, and finally pooled MPS artery (ascending aorta, descending aorta, carotid artery) vs. pooled control artery. Each comparison used four pairs of MPS vs corresponding age- and gender- matched animals to produce four biologic replicates.

overall_design: Four total comparison groups were made: MPS ascending aorta vs. control ascending aorta, MPS descending aorta vs. control descending aorta, MPS carotid artery vs. control carotid artery, and finally pooled MPS artery (ascending aorta, descending aorta, carotid artery) vs. pooled control artery. Each comparison used four pairs of MPS vs corresponding age- and gender- matched animals to produce four biologic replicate.  These experiments were conducted with dual-channel arrays but the data are presented separately for each channel. Raw data are available in a tar archive on the series record.

first: Raymond

last: Wang


title: Expression profiling of grass-clump dwarf in synthetic hexaploids from triploid hybrids crossed between tetraploid wheat and Aegilops tauschii

status: Public on Mar 02 2016

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines.
Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.

overall_design: Expression patterns were compared between the three synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 8 weeks. Two independent experiments were conducted in each exprement.

first: Ryusuke

last: Matsuda


title: Change in gene expression of a canine melanoma cell line caused by exposure to nonsteroidal anti-inflammatory drugs (NSAIDs) .

status: Public on Mar 09 2016

city: Tokyo

first: Kohei

last: Saeki

state: Tokyo

address: 1-1-1 Yayoi, Bunkyo

institute: The University of Tokyo

summary: Nonsteroidal anti-inflammatory drugs (NSAIDs) has been suggested as adjunctive anti-tumor agents in human and veterinary medicine. However, its anti-tumor molecular machinery is still controversial. Therefore, we performed whole transcriptome analysis to discover gene expression influenced by NSAIDs treatment.

overall_design: A canine melanoma cell line (Mi/CMM1) was treated by three NSAIDs, piroxicam, carprofen, and robenacoxib, at their half maximal (50%) inhibitory concentrations (116 µM, 779 µM, and 156 µM) for 6 hours. Subsequently, total RNA were extracted and microarray analysis was performed to evaluate change in gene expression caused by NSAIDs treatment. Each condition had three biological replicates.

first: Manabu

last: Watanabe

first: Nanako

last: Nakaoka

first: Masaya

last: Tsuboi

first: Ryohei

last: Yoshitake

last: Nishimura

first: Takayuki

last: Nakagawa


title: Analysis of Genomic Copy Number Variation in Equine Recurrent Airway Obstruction

city: College Station

first: Sharmila

last: Ghosh

state: TX

address: VMS Building, Rm 107, 4458 TAMUS

department: VIBS

institute: Texas A&M University

summary: Sixteen severly RAO (Recurrent Airway Obstruction) affected horses were studied. All RAO affected male horses were hybridized with GSM1332974 (Thoroughbred male 1, male reference), and the female horses were with GSM1332975 (Thoroughbred female 2, female reference). Finally results are compared with GSE55266 and two other control horses (SPA-H1-3 and SPA-H1-5) and relatively novel RAO CNVs were reported.

overall_design: 16 RAO affected male and female horses were studied. they are of various breeds. Male and female RAO samples were hybridized with Thoroughbred1, and female samples were hybridized with Thoroughbred2

first: Pranab

last: Das

first: Jean-Pierre

last: Lavoie

first: Cyprianna

last: Swiderski

first: Vincent

last: Gerber

first: Bhanu

middle: P

last: Chowdhary

first: Terje

last: Raudsepp


title: Persistent Effect of mTOR Inhibition on Preneoplastic Foci Progression and Gene Expression in a Rat Model of Hepatocellular Carcinoma

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: We previously identified the mTOR pathway as critical to progenitor cell proliferation in a model of liver injury, we investigated the temporal activation of mTOR signaling in a rat model of hepatic carcinogenesis. The model employed chemical carcinogens and partial hepatectomy to induce progenitor marker-positive HCC.  Rats were administered the mTOR inhibitor rapamycin for a three week period and liver harvested one month following cessation of rapamycin treatment.  Short-term rapamycin treatment resulted in a significant reduction of focal lesion burden.   Microarray analysis was performed to characterize the gene expression signature of persistent focal lesions in the rapamcyin and placebo treated animals.   This analysis revealed a persistent effect of short-term mTORC1 inhibition on gene expression that resulted in a genetic signature reminiscent of normal liver.

overall_design: Laser capture microdissection was performed to specifically isolate persistent focal lesions from formalin fixed paraffin embedded (FFPE) liver sections derived from triplicate placebo and rapamycin treated rats.  In addition, we captured liver tissue from FFPE sections derived from rats that had been administered 2-acetylaminofluorene in combination with 2/3 partial hepatectomy to induce oval cell proliferation and from normal adult rats.  RNA was extracted using Qiagen’s FFPE RNeasy Kit  and analyzed using Affymetrix Rat Gene ST 1.0 arrays.   Unsupervised hierarchical clustering using the 5% of the genes with the highest coefficient of variation across all samples revealed an outlier in the rapamycin treated group.  Additional microarray analyses performed on lesions from that animal demonstrated similar results.  This animal was not an outlier based on any of the other biochemical or physiologic parameters that were measured, leading us to conclude that the array results reflected the heterogeneity of the genetic signature of the focal lesions and response to rapamycin.  The raw expression values from the three arrays on this one animal were averaged for subsequent analyses.

first: Heather

last: Francois-Vaughan

first: Adeola

middle: O

last: Adebayo

first: Philip

last: Gruppuso


title: microRNA expression profiling of response to first-line aromatase inhibitor therapy

city: ROTTERDAM

first: Maurice

last: Jansen

address: Wytemaweg 80

department: MEDICAL ONCOLOGY

institute: ERASMUS MC - CANCER INSTITUTE

summary: The main goal of the study is to define miR expression levels related to clinical and biological parameters. Now in particular, miR expression levels of fresh frozen (estrogen receptor-positive) primary tumors were related to PIK3CA genotype and with progression-free survival in breast cancer patients with metastatic breast cancer that received first-line aromatase inhibitor therapy.

overall_design: Primary breast cancer specimens (N=106) were analyzed for the expression of 768 miRs. The miRs were normalized against the median level of 314 reference assays.

first: Els

last: Berns

first: Kirsten

last: Ruigrok-Ritstier

first: Diana

last: Ramirez-Ardila


title: Transcriptome profile for leaves of rice plants subjected to severe reproductive stage drought stress

status: Public on Mar 01 2016

city: Los Banos

first: Manish

last: Raorane

state: Laguna

address: UP college campus

department: Plant Breeding, Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

summary: To understand how the qDTY12.1 interacts with other genes within the genome to give better physiological adaptations and better yield; the leaves transcriptome of DTY12.1 parents (Vandana , Way Rarem) and DTY12.1 NIL (481-B) were compared under control and drought conditions.

overall_design: Drought induced gene expression was studied in the leaves of the rice plants subjected to severe reproductive stage drought. Seeds of Vandana, Way Rarem, and 481-B were sown into rotovated soil at a rate of 2.0 g m-1  into plots of 3 rows X 3 m. The three genotypes were sown in three replications in a randomized complete block design.

first: Mandy

last: Pueffeld

first: Nese

last: Sreenivasulu

first: Ajay

last: Kohli


title: TNF dependent induction of inhibitory pathways in CD4+ T cells in HIV and LCMV [CD4+ T activation]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: Chronic viral infections caused by HIV in humans or LCMV in mice are characterized by immunodeficiency and chronic inflammation. During chronification, T cells progressively lose effector functions, a process associated with immunoregulatory pathways and known as T-cell exhaustion. A link between ‘exhaustive’ T-cell reprogramming and chronic inflammation has not been established. Using a systems biology approach we demonstrate in HIV and LCMV infection that TNF, a prototypical mediator of chronic inflammation, functions upstream of major immunoregulatory pathways in T cells during chronic viral infection. In vivo blockade of TNFR-signaling interferes with the exhaustive T-cell program during chronic infection and reduces viral loads by several log. Continuous TNFR-signaling during disease progression towards chronic infection seems to be causative for T-cell exhaustion and an important link between immunodeficiency and chronic inflammation. TNF blockade might represent a novel therapeutic option during late stage infections caused by HIV and other virus causing chronic infections.

overall_design: freshly isolated CD4+ T cells activated with various conditions to establish RNA fingerprints

first: J

last: Chemnitz

first: M

last: Beyer

first: D

last: Maisel


title: Role of Fun30 remodelers in retrotransposon regulation [ChIP-chip and expression analysis]

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary: Retrotransposable elements are genomic parasites that are both key drivers of evolution and the ancestors of retroviruses. Although host cells have developed numerous mechanisms to keep these elements in check, there is also evidence from yeast to mammals that stressed cells sometimes activate transposition.   Here we show that the fission yeast tf2 retrotransposons are regulated by alternative transcription start site (TSS) usage. Which TSS is used is determined by nucleosome positioning, which is in turn controlled by the Fun30 chromatin remodelers Fft2 and Fft3. By maintaining a high level of nucleosome occupancy at retrotransposon-flanking Long Terminal Repeat (LTR) elements, Fft2 and Fft3 promote the use of a downstream TSS and the production of RNA incapable of reverse transcription and retrotransposition. More generally, we show that Fft2 and Fft3 are involved in repressing the transcriptional response to stress, of which retrotransposon activation is a part. Finally, we show that in stressed cells retrotransposon TSS usage switches, allowing the production of full-length retrotransposon RNA. We propose that allowing retrotransposon transcription from a nonproductive TSS allows for the rapid activation of these elements in times of stress, while preventing their uncontrolled proliferation in the genome.

overall_design: For ChIP samples, duplicate or triplicate immunoprecipitated samples were compared with mock, input, or WT controls. For expression data duplicate or triplicate mutant cDNA samples were compared with triplicate WT cDNA.

first: Jenna

last: Persson

first: Agata

last: Smialowska

first: Karl

last: Ekwall


title: TNF dependent induction of inhibitory pathways in CD4+ T cells in HIV and LCMV [HIV-infected individuals]

overall_design: Analysis of transcription profiles of 20 HIV infected individuals

first: Jens

first: Daniela

first: Marc


title: Evaluation of the physiology of miniature pig fed Shochu distilled water by using mRNA expression profiling.

city: Gifu

first: Shiori

last: Miura

address: Yanagido 1-1

institute: The United Graduate School of Agricultural Science, Gifu Univercity

summary: Shochu distilled water (SDW) was used as a feedstuff for livestock. We have tried to evaluate the physiology of pig during feeding SDW using genomics.

overall_design: 8-9 month old clawn miniature pigs were fed standard dry feed or SDW feeding. SDW feeding composed of standard dry feed: water: SDW= 1:1:1 by the weight ratio.Whole blood gene expression in control and SDW animal was measured at 12 weeks of feeding periods.

first: Junko

last: Takahashi

first: Hitoshi

last: Iwahashi


title: Clostridium botulinum whole genome expression profile after heat shock in continous culture

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary: Clostridium botulinum ATCC 3502 was grown in continuous culture at 39°C, subjected to heat shock at 45°C, and then continuously grown at 45°C. The goal was to determine the impact of stressful temperature to the whole genome expression profile and identify stress adaptation mechanisms.

overall_design: Time series (control,0min,10min,1h,18h,42h, adapt) with two biological replicates and two technical replicates in dye-swaps. Common reference hybridization design.

first: K

last: Selby

first: P

last: Lindström

first: H

last: Korkeala


title: Transcriptome profile for spikelets of rice plants subjected to severe reproductive stage drought stress

first: Manish

last: Raorane

summary: To understand how the qDTY12.1 interacts with other genes within the genome to give better yield under drought; the spikelets transcriptome of DTY12.1 parents (Vandana , Way Rarem) and DTY12.1 NIL (481-B) were compared under control and drought conditions.

overall_design: Drought induced gene expression was studied in the spikelets of the rice plants subjected to severe reproductive stage drought. Seeds of Vandana, Way Rarem, and 481-B were sown into rotovated soil at a rate of 2.0 g m-1  into plots of 3 rows X 3 m. The three genotypes were sown in three replications in a randomized complete block design.

first: Mandy

last: Pueffeld

first: Nese

last: Sreenivasulu

first: Ajay


title: Gene expression profile of miniature pig as animal model for toxicity evaluation by using mRNA expression profiling.

summary: Miniature pig is a useful animal model to clarify the vital reaction and the molecular mechanisms. However, physiclogical response of pig model to sodium azide (AZIDE) stress is not reveal. To establishment of large animal model for evaluate toxic stress, whole blood of miniature pig were assessed with genomics.

overall_design: 7 month old clawn miniature pigs were fed AZIDE feeding. AZIDE dose of 300µg/kg, one hundredth of LD50 was given orally to the miniature pigs. Whole blood gene expression was measured at 0h, 6h and 24h after feeding.


title: Transcriptional Profiling of Apple (Malus x domestica Borkh) Floral Induction in Shoot Apical Meristems

city: Montpellier

first: Jean-Jacques

last: Kelner

address: TA A-108/03 Avenue Agropolis

department: UMR AGAP

institute: Montpellier SupAgro

summary:
Effect of the presence of fruits on the expression of genes possibly involved in floral induction in the terminal meristem of spur bourse shoot.
Investigation on mecanisms involved in Biennial Bearing in mature apple trees cultivar Royal Gala.

overall_design: Two-condition experiment : 'ON' trees (unthinned control) & 'OFF' trees (deflowered) for comparison. Three comparisons at sampling dates : 28, 48 and 119 days after full bloom (DAFB). Two dye switch biological replicates for each treatment and sampling date.

first: Jean-Marc

last: Celton

first: Baptiste

last: Guitton

first: Evelyne

last: Costes


title: Comparison of the transcription (coding and lncRNAs) of in vitro cultured bovine SAM-treated blastocysts and non-treated blastocysts

status: Public on Feb 29 2016

city: Quebec city

first: Habib

middle: A.

last: Shojaei Saadi

address: 2440 bl hochelaga, pavillon inaf

institute: Laval University

summary: Transcriptome (total RNA) profiling of bovine in vitro cultured expanded blastocysts (EB) comparing control non-treated expanded blastocysts with SAM-treated expanded blastocysts. S-Adenosyl methionine (SAM) is the global methyl donor providing methyl group for variety of biomolecules such as DNA , histone, RNA, lipids and etc.

overall_design: Two-condition experiment, bovine non-treated expanded blastocysts (pools of 10) vs bovine SAM-treated expanded blastocysts. Four biological replicates of each tissue were hybridized to four two-color arrays in a dye-balanced design.

middle: A

first: D

last: Gagné

first: É

last: Fournier

first: I

last: Gilbert

first: L

last: Baldoceda-Baldeon

first: M

last: Sirard M

first: C

last: Robert


title: Expression analysis of Arabidopsis thaliana mutant atpme3-1

city: Mont-Saint-Aignan

first: Alain

last: Mareck

address: 2 rue tenieres

department: departement de biologie glycobiologie et matrice extracellulaire végétale

institute: université de rouen Haute Normandie

summary:
Investigation of the effect of atpme3-1 mutant on whole gene expression level
hypocotyls of 96 hours-old plantlets were analyzed for this study

overall_design: A 12plex high density chip was used. Six or 5 biological replicates for each condition. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.

first: Mareck

last: Alain

first: Stéphanie

last: Guénin

first: Julie

last: Hardouin

first: Florence

last: Paynel

first: Kerstin

last: Müller

first: Gaëlle

last: Mongelard

first: Ogier

last: Surcouf

first: Christelle

last: Leroux

first: Azeddine

last: Driouich

first: Patrice

last: Lerouge

first: Allison

last: Kermode

first: Arnaud

last: Lehner

first: Jean

middle: C

last: Mollet

first: Jérôme

last: Pelloux

first: Lauernt

last: Gutierrez


title: Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

status: Public on Feb 16 2016

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

type:
Genome variation profiling by array
Expression profiling by array

summary: Tumor heterogeneity may reduce the efficacy of molecularly guided systemic therapy for cancers that have metastasized. To determine whether the genomic alterations in a single metastasis provide a reasonable assessment of the major oncogenic drivers of other dispersed metastases in an individual, we analyzed multiple tumors from men with disseminated prostate cancer through whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling, and we compared the genomic diversity within and between individuals.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 171 CRPC tumors from 63 patients. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines. Custom Agilent 415K whole human CGH microarrays were used to profile 149 CRPC tumors from 60 patients.  Genomic DNA from tumors was hybridized against a pool of reference normal male DNA.

first: Akash

last: Kumar

first: Colm

last: Morrissey

first: Xiaotun

last: Zhang

first: Lawrence

last: True

first: Roman

last: Gulati

first: Ruth

last: Etzioni

first: Hamid

last: Bolouri

first: Bruce

last: Montgomery

first: Thomas

last: White

first: Jared

last: Lucas

first: Lisha

middle: F

last: Brown

last: Dumpit

first: Navonil

last: DeSarkar

first: Celestia

last: Higano

first: Evan

middle: Y

last: Yu

first: Roger

first: Nikolaus

last: Schultz

first: Min

last: Fang

first: Paul

last: Lange

first: Jay

last: Shendure

first: Robert

last: Vessella

first: Peter

middle: S

last: Nelson


title: Sexually dimorphic gene expression in bovine conceptuses at the initiation of implantation is not reflected in the changes in the endometrial transcriptome.

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

summary: In cattle, maternal recognition of pregnancy occurs on Day 16 via secretion of interferon tau (IFNT) by the conceptus. The endometrium can distinguish between embryos with different developmental competencies. In eutherian mammals, X-chromosome inactivation (XCI) is required to ensure an equal transcriptional level of most X-linked genes for both male and female embryos in adult tissues, but this process is markedly different in cattle than mice. We examined how sexual dimorphism affected conceptus gene expression and amino acid composition as well as the endometrial transcriptome during the peri-implantation period of pregnancy. Of the 5132 genes were differently expressed on Day 19 in male compared to female conceptuses, 2.7% were located on the X-chromosome. Concentrations of specific amino acids were higher in the uterine luminal fluid with male compared to female conceptuses, while female conceptuses had higher expression of specific amino acid transporters (SLC6A19 and SLC1A35). Of note, the endometrial transcriptome was not different in cattle gestating a male or a female conceptus. These data support the hypothesis that, far from being a blastocyst specific phenomenon, XCI is incomplete before and during implantation in cattle. Despite differences in gene expression and amino acid utilization in male versus female conceptuses, the sex of the conceptus itself does not elicit a different response in the endometrium.

overall_design: Following a synchronized estrous cycle, all heifers observed in standing estrus (=Day 0, n=30) were inseminated with semen from a proven sire. All samples were recovered at slaughter on Day 19 following estrus corresponding to the initiation of implantation in cattle, flushed with 10 ml of PBS and the presence of a conceptus was observed under a stereo-microscope (n=24). Each conceptus was dissected into 4 pieces, 3 containing only trophectoderm cells and one containing the embryonic disc along with associated trophectoderm cells, and immediately snap-frozen in liquid nitrogen along with the corresponding intercaruncular endometrium from the uterine horn ipsilateral to the corpus luteum. DNA was extracted from each conceptus with phenol/chloroform treatment and finally re-suspended in 200 μL of milliQ water. Two microliters of each sample were used to perform embryo sexing by PCR amplification of sex-specific polymorphic fragments in the amelogenin gene. N=5 samples of intercaruncular endometirum and the corresponding trophectoderm only sample were anaylsed for gene expression.

last: Ó Gaora

first: Veronica

last: Maillo

first: Constantine

last: Simnitiras

last: Sturney

first: Alan

last: Ealy

last: Spencer

first: Alfonso

last: Gutierrez-Adan

first: Dimitrios

last: Rizos

first: Patrick

last: Lonergan

first: Niamh

last: Forde


title: Ethanol cellular defense induce unfolded protein response in yeast

status: Public on Feb 03 2016

city: Paterna

first: Elisabet

last: Navarro

address: avda Agustin Escardino 7

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

summary: Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-26, isolated from flor wine and traditional fermentations respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR) and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118.

overall_design: Two condition experiment and two strains. CECT10094 and Temohaya-26 strains were harvested at 1h and after exponential phase in presence of 0% and 10% (v/v)ethanol in media. All samples were labeled with Cy5 dye, while a reference pool prepared by pooling the RNA extracted in all samples was labeled with Cy3. Three biological replicates were combined and indirect comparison between slides belonging to stressed and unstressed samples to identify genes whose variation is due to the effect of ethanol was performed. Biological triplicates are included. One replicate per array.

last: Navarro-Tapia

first: Rebeca

last: Kenda Nana

first: Amparo

last: Querol

first: Roberto

last: Pérez-Torrado


title: Gene expression profile of healthy-donor peripheral monocytes, glioblastoma-patient peripheral monocytes, and glioblastoma-infiltrating myeloid cells

status: Public on Jan 23 2016

city: Houston

first: Amy

middle: B

last: Heimberger

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

summary: We compared gene expression profile between healthy-donor peripheral monocytes and glioblastoma-patient peripheral monocytes as well as glioblastoma-patient peripheral monocytes with matched tumor-infiltrating myeloid cells.

overall_design: In the study presented here, 12 samples, including peripheral monocyte samples from 4 healthy donors, peripheral monocytes from 4 GBM patients and matched tumor-infiltrating macrophages extracted from the glioblastoma microenvironment, were used to acquire the mRNA expression (30,275 human genes) via the Phalanx Human Whole Genome OneArray Microarray v5.1 Platform.

first: Konrad

last: Gabrusiewicz

first: Benjamin

last: Rodriguez


title: Global transcriptome response of Staphylococcus xylosus in meat model

status: Public on Jan 04 2016

city: Saint-Genès Champanelle

first: Sabine

last: Leroy

address: Clermont-Ferrand Theix Research Center

department: MICA

institute: INRA

summary: Staphylococcus xylosus is used as starter culture for sausage fermentation for a long time but the molecular mechanisms for its adaptation in meat remained unknown. A global transcriptomic approach was carried out to determine these molecular mechanisms. S. xylosus modulated the expression of about 30% of the total genes during its growth and survival in the meat model. The expression of many genes encoding enzymes involved in glucose and lactate catabolism was up regulated. In parallel, genes encoding transport of peptides and peptidases that could furnish amino acids were up expressed and thus concomitantly a lot of genes involved in amino acids synthesis were down regulated. Finally S. xylosus responded to salt added in the meat model by over expressing genes involved in transport and synthesis of osmoprotectants, Na+ and H+ extrusion and in production of energy through the F0F1-ATPase.

overall_design: Microarray was used to evaluate modification in the transcriptome of S. xylosus C2a strain in the inoculum (Mx) or in meat (V). Three biological replicates were collected on separate days for samples and labelled following a dye-switch design; for each condition one labeling in Cy3 and one in Cy5.

first: Aurore

last: Vermassen

first: Anne

last: de La Foye

first: Régine

last: Talon


title: Neuronal and glial Gene expression from control and healthy patient iPSC-derived cortical neurons (B)

status: Public on Jan 06 2016

city: Boston

first: Tracy

last: Young-Pearse

state: MA

address: HIM 760, 77 Avenue Louis Pasteur

department: Ann Romney Center For Neurologic Disease

institute: Brigham and Women"s Hospital

summary: Neuronal or glial cell fates related gene expression from single cells with variety of sAPPa or total Aβ secretion profiles were presented here.

sample_organism:
Homo sapiens
unidentified

overall_design: Single living human iPSC-derived forebrain neuronal cells with variety of sAPPa or total Aβ secretion profiles were selected and examined for gene expression.

first: Meichen

last: Liao


title: Mycobacterium avium subsp. paratuberculosis K-10 & phoPR comparison

city: Tainan

first: Jenn-Wei

last: Chen

address: No.1, University Road

institute: National Cheng Kung University

summary: To compare the transcriptional profile of K-10 and phoPR in the log phase, and to find out the effects of phoPR on MAP gene expression.

overall_design: There are three replicates from K-10 as the control samples, and three replicates from phoPR used to examine the differences.

first: Joy

last: Scaria

first: Yung-Fu

last: Chang


title: Gene expression profile after SYT9 re-expression during differentiation of CSB-KD SH-SY5Y cells

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

institute: Cancer Research UK

summary: CSB-depletion induced SH-SY5Y differentiation defects can be partially rescued by re-expression of SYT9 gene. This study characterizes the transcriptome signatures upon SYT9 re-expression in CSB-KD SH-SY5Y cells after RA treatment.

overall_design: The Nimblegen human 12 x 135K gene expression array was used to characterize the transcriptome landscape of CSB-KD SH-SY5Y cells overepressing SYT9 before and after RA treatment.

first: Probir

last: Chakravarty

first: Jesper

last: Svejstrup