title: Comparative analysis of 1-methyl-4-phenylpyridinium (MPP+) and manganese induced neurotoxic effects on DNA methylation in dopaminergic neurons

status: Public on Oct 04 2017

city: Pune

first: Santosh

middle: Chandrakant

last: Narwade

state: Maharashtra

address: Ganeshkhind Road

department: Department of Zoology

country: India

institute: University of Pune

summary: Idiopathic Parkinson’s disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to L-DOPA differentiate both, the differences at the neuronal level are largely unknown. We investigated the morphological, physiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP+) and manganese (Mn). While Mn was neurotoxic at lower dose, MPP+ toxicity entailed oxidative damage, mitochondria dysfunction and glycolytic shift. Morphological analysis highlighted mitochondrial damage, while morphometric analysis indicated loss of neuronal processes in the MPP+ model and not in the Mn model. Elecrophysiological analysis demonstrated lower number of spikes and firing frequency in MPP+ treated cells, while it was unchanged in the Mn model. High throughput transcriptomic analysis revealed upregulation of 694 and 603 genes and down-regulation of 428 and 255 genes in the MPP+ and Mn models respectively. Many differentially expressed genes were unique to either models and contributed to neuroinflammation, metabolic and mitochondrial function, apoptosis and nuclear function, synaptic plasticity, neurotransmission and cytoskeletal architecture. Analysis of the JAK-STAT pathway with implications for neuritogenesis, neuronal proliferation and nuclear function revealed contrasting profile between Mn and MPP+ models. Genome-wide DNA methylation profile revealed significant differences between both models and substantiated the epigenetic basis of the difference in the JAK-STAT pathway. We conclude that iPD and atypical Parkinsonism represent a divergent neurotoxicological manifestation at the dopaminergic neuronal level with implications for pathobiology and to evolve novel therapeutics

overall_design:
DNA methylation analysis of control N27 cells was carried out as described (Kelkar et al. 2009, Rajpathak et al. 2014).
DNA methylation analysis of Mn treated N27 cells was carried out as described (Kelkar et al. 2009, Rajpathak et al. 2014).
DNA methylation analysis of MPP+ treated N27 cells was carried out as described (Kelkar et al. 2009, Rajpathak et al. 2014).
For each group, three independent biological replicates were subjected to methylation array (Agilent technologies Inc). Genomic DNA was isolated from cells of different experimental groups, subjected to proteinase K digestion in the presence of 1% SDS, followed by phenol: chloroform extraction, RNase A treatment and precipitation using NaCl and ethanol. Genomic DNA (2 µg) was sheared into 1.5-2 kb fragments by sonication and the fragments were denatured by heating at 95OC and hybridized on to a Rat GE 4x44K v3 Microarray slides (Agilent Technologies, CA, USA) each with 4x44K arrays, containing 44,000 probes of 22,583 genes. After hybridization at 42OC for 16 h, the slides were washed, blocked and then incubated in anti-5-methylcytosine antibody (1h at 25OC). Slides were then washed and incubated in cy3 labeled anti-mouse IgG (1h at 25OC), washed and scanned at 5 uM resolution at 543 nm. Scanarray software was used for data acquisition, mean or median intensity calculation of each spot and normalization.

middle: C

first: Deepti

last: Deobagkar

first: RB

last: Mythri

first: M

middle: M

last: Bharath


title: Identification of gene expression changes in RGC neurons treated with synaptogenic proteins

status: Public on Oct 15 2017

city: La Jolla

first: Nicola

last: Allen

state: CA

address: 10010 North Torrey Pines Rd

country: USA

institute: Salk Institute

summary: Astrocyte-secreted proteins induce synapse formation between isolated retinal ganglion cell (RGC) neurons in culture. We asked whether 2 of these proteins, glypican 4 (Gpc4) or thrombospondin 1 (TSP1) induce synapse formation by regulating gene expression in RGCs.

overall_design: 6 samples. 3 conditions, 2 biological replicates per condition. Alone (untreated) RGCs; plus Gpc4 treatment 12 hours; plus TSP1 treatment 12 hours.

middle: J


title: Comparison between mouse hepatocytes derived from wt and YAP transgenic livers

status: Public on Oct 19 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Primary isolated hepatocytes derived from wildtype mice are compared with hepatocytes isolated from YAP(S127A) transgenic mice (Tschaharganeh at al., 2013 Gastroenterology, PMID 23419361). YAP induction was done for 8 weeks and livers showed hyperplasia without signs of malignant transformation.

overall_design: Three independent wildtype mice are compared with three independent YAP transgenics.

first: Stefan

last: Thomann

first: Kai

last: Breuhahn


title: Expression data from human hepatocarcinoma HCC-1.2 cell line treated by erlotinib

status: Public on Oct 26 2017

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

summary:
Tyrosine kinase inhibitors represent a new generation of targeted drugs for cancer treatment and chemoprevention. The EGF receptor inhibitor erlotinib is under discussion for chemoprevention of hepatocellular carcinoma.
A comprehensive analysis of gene expression and respective pathways regulated by erlotinib is needed.

overall_design: Human hepatocarcinoma cell line HCC-1.2 was treated in vitro by erlotinib  and changes in gene expression were analysed by microarray technique.

first: Nataliya

last: Rohr-Udilova

first: Martha

last: Seif

first: Hubert

last: Hayden

first: Markus

last: Jeitler


title: Evidence of stress in beta cells obtained with laser capture microdisssection from pancreases of brain-dead donor

status: Public on Oct 17 2017

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Isolated islets used for transplantation are known to be stressed, which can result from the circumstances of death, in particular brain dead, the preservation of the pancreas with its warm and cold ischemia, from the trauma of the isolation process, and the complex events that occur during culture tissue. Isolated islets used for transplantation are known to be stressed, which can result from the circumstances of death, in particular brain death, the preservation of the pancreas with its warm and cold ischemia, from the trauma of the isolation process, and the complex events that occur during tissue culture. The current study focused upon the events that occur before the islet isolation procedure. Pancreases were obtained from brain dead donors (n=7) with mean age 50 (11) and normal pancreatic tissue obtained at surgery done for pancreatic neoplasms (n=7), age 69 (9). Frozen sections were subjected to laser capture microdissection (LCM) to obtain beta-cell rich islet tissue, from which extracted RNA was analyzed with microarrays. Gene expression of the two groups was evaluated with differential expression analysis for genes and pathways. Marked changes were found in pathways concerned with endoplasmic reticulum stress with its unfolded protein response (UPR), apoptotic pathways and components of inflammation. In addition, there were changes is genes important for islet cell identify. These findings advance our  understanding of why islets are stressed prior to transplantation, which may lead to strategies to reduce this stress and lead to better clinical outcomes.

overall_design: beta-cell Enrichment with LCM and Global Gene Expression Profiling Using Affymetrix Microarray

first: Gordon

last: Weir

first: Aref

last: Ebrahimi


title: Heterogeneity in early lymphoid compartments [qPCR]

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: In order to understand the developmental trajectories of early lymphocyte development it is crucial to prospectively isolate stage and lineage specific cells. It has become clear that early lymphoid progenitor compartments in the bone marrow are molecularly and functionally heterogeneous which warrants further investigation to refine the marker combinations used to isolate these progenitors. An initial antibody screen revealed extensive surface marker heterogeneity amongst early lymphoid progenitors. This heterogeneity was resolved using single cell gene expression assays and single cell in vitro differentiation assays, identifying marker combinations that isolate functionally distinct populations. In addition, using reporter transgenic mice we were able to identify a set of surface markers that can be used alone or in combination with classical targets to identify specific stages of B-cell development. B-cell stages based on transgene expression which were used for screening purposes were verified by RNASeq. The data provides a greater resolution of the complexity of the lymphoid progenitor compartment within the bone marrow than has been understood to date and provides novel tools for the further identification of cell populations in B-lineage development.

overall_design: qPCR gene expression profiling of mouse common lymphoid progenitors (CLPs). Four 96-well plates with pre-amplified single CLP bone marrow cell cDNA (with 10 and 20 cell controls) were loaded on to a 96.96 Dynamic Array Chip for Gene Expression. Samples Ids follow where SS<X> denotes well ID, and P<X>denoted the plate. Controls include well where no RT is performed (noRT) and 10 and 20 cell controls.

first: Christina

middle: T

last: Jensen

last: Lang

first: Mikael

last: Sigvardsson


title: miRNA Expression Profile and Effect of Wenxin Granule in Rats with Ligation-Induced Myocardial Infarction

status: Public on Oct 31 2017

city: Beijing

first: Aiming

last: Wu

address: Haiyuncang No.5

country: China

summary: miRNAs are small (approximately 22 nucleotides) noncoding RNAs which post-transcriptionally regulate gene expression by binding complementary sequences within messenger RNA transcripts. miRNAs are likely to regulate many complex processes in the body, indeed aberrant expression of various miRNAs has been implicated in numerous disease states. They have been shown to participate in cardiovascular disease pathogenesis including atherosclerosis, coronary artery disease, myocardial infarction (MI), heart failure and cardiac arrhythmias. To investigate the expression profiles of miRNA in MI, left ventricular tissues from 3 MI rats and 3 non-MI rats (control) that were collected for miRNA expression microarray analyses to explore the role of miRNA in the pathogenesis of MI. To assess the pathways predicted to be targeted by differentially expressed miRNAs in MI, we performed pathway analysis using the online DIANA miRPATH tool. The miR-1 and miR-133, the most abundant miRNAs in the heart, were chosen for further validation by the quantitative real-time polymerase chain reaction, and their expression trends were consistent with the microarray data. Additionally, the effect of Wenxin Granule on miR-1 and miR-133 expression was observed in present study.

overall_design: The male Sprague-Dawley (SD) rats weighted 200±20 g, were acquired from Beijing Vital River Laboratory Animal Technology Co., Ltd, (license number SCXK (Beijing) 2012-0001). All rats received humane care in compliance with the Guide for the Care and Use of Laboratory Animals. The study was performed with approval of the Animal Care Committee of Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine. And efforts were made to minimize the number of animals used. The MI Rat Model was established by a direct coronary artery ligation surgery method. Before surgery, the rats were anaesthetized with1% pentobarbital sodium (50mg / kg) intraperitoneally, and a twelve-lead electrocardiogram (ECG) was performed preoperatively. After left thoracotomy, the left anterior descending coronary artery was ligated directly at the location between the pulmonary cone and the left atrial appendage under its origin 2-3mm in model group except the control (sham-operated) group. In the control group, the left anterior descending artery was not occluded. Additional a twelve-lead ECG was performed postoperatively the day after the surgery. Whether the surgery was successful can be judged by Q wave in postoperative ECG, compared with preoperative ECG. Three rats with successful coronary artery ligation surgery were assigned into the model group. Meanwhile, three rats without coronary artery ligation were assigned to the control group. Distilled water was administered to the rats intragastrically for 4 weeks, after which the rats were euthanized and dissected to isolate the heart for the subsequent experiments. Left ventricular samples were obtained for RNA extraction and hybridization on Agilent miRNA Microarrays.

first: Lixia

last: Lou

first: Jianying

last: Zhai

first: Dongmei

last: Zhang

first: Limin

last: Chai

first: Bo

last: Nie

first: Haiyan

last: Zhu

first: Yonghong

last: Gao

first: Hongcai

last: Shang

first: Mingjing

last: Zhao


title: Differential gene expression and transport functionality in the bundle sheath versus mesophyll - a potential role in leaf mineral homeostasis

status: Public on Oct 22 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
The bundle sheath cells (BSCs) layer – a presumed control point for radial transport of water and solutes between the vasculature and the leaf mesophyll cells (MCs) – is still largely understudied. Using isolated protoplasts, we found that 45% of the 90 genes differentially expressed in BSCs vs. MCs are membrane related and 20% are transport related, suggesting unique functionality of membrane transport in the BSCs, supported also by functional assays (electrophysiology and fluorescence imaging).
A tight control of long distance transport is required for the optimization of the hydro-mineral homeostasis of organs in plants under fluctuating ambient conditions. The mechanism of ion selectivity and absorption from the xylem to the leaf is still poorly understood. The bundle sheath (BS), tightly enwrapping the leaf vasculature, has been suggested as a part of this mechanism, acting as a selective barrier which regulates the radial transport of water and solutes from the xylem to leaf cells. This suggestion relies on the anatomy, as well as on the recent physiological transport assays of the BS and its cells (BSCs).   We hypothesized that the unique transport functionality of the BSCs is manifested in its transcriptome. To test this, we compared the transcriptomes of individually hand-picked protoplasts of GFP-labeled BSCs and non-labeled mesophyll cells (MCs) of Arabidopsis thaliana leaves. Indeed, in conformation of our hypothesis, 45% of the 90 genes differentially expressed in BSCs vs. MCs are membrane related and 20% are transport related, with the proton-pump AHA2 as a prominent example. Moreover, fluorescence imaging using the potentiometric dye (di-8 ANEPPS) revealed a more negative membrane potential of the BSCs protoplasts compared to those of MCs, and electrophysiological assays (patch-clamp) showed that the major, AKT2-like, membrane K+ conductances of BSCs and MCs had different voltage dependency ranges. Combined, these differences are compatible with an expected possibility of simultaneous but oppositely directed transmembrane K+ fluxes in BSCs and MCs in otherwise similar conditions.

overall_design: 6 Samples (arrays) were performed. We generated pairwise comparison between the 2 different cell types (triplicates) using Partek Genomics Suite.

first: Noa

last: Wigoda

first: Tianyuan

last: Yang

first: Ling

last: Yu

first: Menachem

last: Moshelion

first: Nava

last: Moran


title: Global miRNA expression profiles of fibroblast-like synoviocytes in patients with rheumatoid arthritis and osteoarthritis

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

summary: Fibroblast-like synoviocyte (FLS) constitutes a major cell subset of rheumatoid arthritis (RA) joint. Dysregulation of microRNAs (miRNAs) contributes to FLS activation in the context of chronic inflammation. However, functional association of the miRNAs-targets relationships characterizing FLS phenotypes in RA has not been fully elucidated yet. Thus, we uncovered the novel miRNA-target interactions characterizing pathologic phenotypes of RA-FLS. We performed microarray analyses of miRNA in RA- and osteoarthritis (OA) FLS with or without interleukin-1β (IL-1β) stimulation. The miRNA-target prediction and network model-ing were performed using TargetScan and Cytoscape. Identified miRNA-target relationships and their cellular functions were validated in vitro.

overall_design: To identify miRNA expression signatures of FLS from rheumatoid arthritis patients, we isolated FLS from synovial tissues of RA and osteoarthritis (OA) patients and stimulated FLS with IL1β. Finally, we analyzed gene expression profiles of both IL1β-stimulated RA-FLS and OA-FLS

first: Sungyong

last: You

first: Daehee

last: Hwang

first: Wan-Uk

last: Kim


title: PKR1 overexpression in heart

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

summary: Effect of overexpression of PKR1 in mice hearts on the cardiac transcriptome

overall_design: RNA was isolated from hearts of mice overexpressing PKR1 (n=3) and of WT mice (n=3) and hybridized to microarrays.


title: Cytotoxic effects of radiocontrast dyes on human umbilical cord mesenchymal stem cells

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Discography is an imaging procedure typically performed on patients who report extended periods of pain.Usually radiocontrast agents are used to diagnose the discogenic low back pain.
This study was focused on investigating the effects of two clinically used, non-ionic radiocontrast dyes, isovue-370 and omnipaque-240, on the human umbilical cord mesenchymal stem cells (UC-MSCs). Human UC-MSCs were cultured and treated with various concentrations of Omnipaque and Isovue for 24 hr. The cell growth was inhibited by both the dyes.
The results showed that both the dyes significantly affected the cell morphology and viability as well as caused apoptosis in UC-MSCs.  The global gene expression analysis showed that the most effected genes were those involved in the apoptosis, DNA damage and toxicity.

overall_design: Human umbilical cord derived MSCs were cultured in vitro and treated with 1:4 (dye:medium) of either Omnipaqe or Isovue for 24 hrs. Gene expression of treated cells was compared to untreated cultured cells.

first: Naimisha

last: Beeravolu

first: Christina

last: McKee

first: Mick

last: Perez-Cruet

first: George

middle: D

last: Wilson

first: Rasul

last: Chaudhry


title: Alterations in the hepatic gene expression in mice exposed to a maternal high fat diet in utero [Microarray]

status: Public on Oct 02 2017

city: Bronx

first: Maureen

last: Charron

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

summary:
Exposure to a high fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. We used gene expression microarray to examine mRNA expression patterns in liver of offspring exposed to a Control or HF maternal diet. WT mice were fed a Control (9.5% fat, 3.59 kcal/g) or HF (35.5% fat, 5.29 kcal/g) diet for 2 wk before mating, throughout pregnancy and lactation. Offspring were weaned to a low fat (5.6% fat, 3.4 kcal/g) diet and were sacrificed at 5wks of age. Exposure to a maternal HF milieu activated genes of immune response, inflammation, and hepatic dysfunction. Conversely genes of lipid metabolism and biogenesis were down regulated especially in the cholesterol biosynthesis pathway.
In summary, exposure to a maternal HF diet significantly alters the gene expression patterns in the liver of exposed offspring and contributes to development of metabolic disease later in life.

overall_design: Total RNA was extracted from 6 control and 7 HF, then pooled.  First and double strand cDNA was generated using SuperScript Double-Stranded cDNA synthesis Kit (Invitrogen). Two chip study was performed.

first: Yoshinori

last: Seki


title: Alterations in the hepatic epigenome in mice exposed to a maternal high fat diet in utero

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of polychaete-enhanced testicular maturation in male broodstock of the black tiger shrimp (Penaeus monodon)

status: Public on Oct 30 2017

city: Pathum Thani

first: umaporn

last: uawisetwathana

address: 113 Thailand Science Park

department: Biosensing Technology Research Unit

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

summary: The study aimed to determine effect of polychaetes as a shrimp feed on male reproductive maturation at transcriptional level through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Thus, the experiment was to compare transcriptomic profiles of two different parts of reproductive organs, namely testes (TT) and vas deferens (VD), of domesticated 17-month-old between two different feeds, namely commercial pellet and polychaetes after feeding for one month. Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR.  Selected genes were further characterized.

overall_design: A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,973 features. RNA samples were extracted from TT and VD of before feeding (week 0; w0) and after feeding with commercial pellet (C) and polychaetes (P) for one month (week 4; w4) from Shrimp Genetic Improvement Center , Thailand. The RNA from week 0 were labeled with Cy3 dye as a reference and those from week 4were labeled with Cy5 dye.

first: Rungnapa

last: Leelatanawit

first: Umaporn

last: Uawisetwathana

first: Amornpan

last: Klanchui

first: Juthatip

last: Kudej

first: Suwanchai

last: Phomklad

first: Somjai

last: Wongtripop

first: Pikul

last: Jiravanichpaisal

first: Nitsara

last: Karoonuthaisiri


title: Expression profiling by array in the splenic marginal zone lymphoma (SMZL)

city: Nankoku

first: Tomonori

last: Higuchi

state: Kochi

address: Kohasu, Okpcho

country: Japan

institute: Kochi University

summary:
The transformation mechanism into a high-grade malignancy of SMZL has not been well studied.
To define and compare the differentially expressed genes between primary SMZL cells at the different clinical periods, we analyzed the gene expression profiles using the CodeLink Human Whole Genome Bioarray.

overall_design: The gene expression profiles of primary SMZL cells derived from indolent and aggressive phases (SL-15PB and SL-22PB, respectively) were surveyed.

first: Yumiko

last: Hashida

first: Masanori

last: Daibata


title: The transcriptomic signature of diteray zinc supplementation in sheep

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

summary: In the present study, we studied the effect of dietray zinc (Zn) supplementation on the transcriptome profile of lactating ewes. The main objective was to evaluate the effect of Zn-supplementation on the overall transcriptome and the altered pathways and biological processes in lactating ewes. A previously custom-designed oligo microarray platform (GPL20576) was used to profile the transcriptome of 15 ewes at two time points [T0 (before supplementation) and T40 (after 40-days supplementation period; n = 30). The Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of control and treated animal transcriptomes revealed a large set of differentially expressed genes. Functional analysis showed several pathways and biological processes that have been altered following Zn-supplementation to the diet.

overall_design: Lactating crossbred ewes (N = 15; 3 to 4 y of age and 55 to 65 kg BW) have been acclimatized (4-wk) on a basal diet containing a maintenance level of Zn (79 mg Zn/animal/day), before being randomly assigned to 2 treatment groups based on their Zn-supplementation status [supplemented (ZINC; n=10) and unsupplemented control (CTR; n =5)]. During the experimental period (40 d), the CTR group kept receiving the basal diet where the ZINC group received a diet supplemented with Zn (212 mg Zn/animal/day). Following completion of the treatment, blood samples were collected from each individual animal directly into Paxgene blood collection tubes, processed and stored at -20˚C till further analyses. All samples yielded high quality RNA that was tested prior the microarray setup.

first: Mery

last: Giantin

first: Mauro

last: Dacasto

first: Federica

last: Castellani

first: Lisa

last: Grotta

first: Fiorentina

last: Palazzo

first: Giuseppe

last: Martino


title: Global profiling of microRNAs in peripheral blood and synovial fluid mononuclear cells of patients with Enthesitis Related Arthritis

city: Lucknow

first: Sushma

last: Singh

state: Uttar Pradesh

address: Raebareli Road

department: Clinical Immunology

institute: Sanjay Gandhi Post Graduate Institute of Medical Sciences

summary: Enthesitis related arthritis (ERA) is the most common category of juvenile idiopathic arthritis in Asia. MicroRNA dysregulation has been shown in chronic arthritides however there is no data in ERA. MicroRNA dysregulation in ERA may help understand the pathogenesis of disease. Thus we determined the difference  in global miRNA expression in peripheral blood mononuclear cells (PBMCs) of patients with ERA (n=8) as compared to healthy controls (HC) (n=8) and further to understand the changes at the site of inflammation, the PBMCs profile was compared with the synovial fluid mononuclear cells (SFMCs) (n=8) of patients with ERA.

overall_design: Agilent one-color experiment,Organism: Homo sapiens, Agilent Human miRNA 8x15k Arrays AMADID: 021827

first: Amita

last: Aggarwal


title: A mutation in the viral sensor 2’-5’-oligoadenylate synthetase 2 causes failure of lactation. [human]

status: Public on Oct 18 2017

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

summary: We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 100-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

overall_design: Gene expression analysis of T47D cells with wild-type or mutant mouse Oas2 with (+DOX) or without (-DOX) dox induction of the mOas2 gene.

first: Samantha

middle: R

last: Oakes

first: David

last: GallegoOrtega

first: Prudence

last: Stanford

first: Simon

last: Junankar

first: Wendy

middle: W

last: Au

first: Zoya

last: Kikhtyak

first: Anita

last: von Korff

first: Marcelo

last: Sergio

first: Andrew

last: Law

first: Stephanie

middle: L

last: Allerdice

first: Adelaide

middle: I

last: Young

first: Catherine

last: Piggin

first: Belinda

last: Whittle

first: Edward

last: Bertram

first: Matthew

last: Naylor

first: Jesse

last: Donovan

first: Alexei

last: Korennykh

first: Christopher

last: Goodnow

first: Moira

middle: K

last: O'Bryan

last: Ormandy


title: Circulating serum miRNAs as potential diagnostic biomarkers for oesophageal adenocarcinoma

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

institute: Flinders University

summary:
Exosomes were purified from 250 ul serum using ExoQuickTm. The presence of particles consistent in size with exosomes (60-150nm) was confirmed using a Nanosight LM10.   miRNA was extracted from exosomes  using an miRNeasy Serum/Plasma kit (Qiagen, #217184). miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel  (Life technologies, #4461104). The panel consisted of probes for 754 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v14. MegaplexTM Primer Human Pool A v2.1 and Human Pool B v2.0 or v3.0
The poor prognosis and rising incidence of oesophageal adenocarcinoma highlight the need for improved methods for detection of this cancer. Molecular biomarkers offer potential for this. The potential for circulating miRNAs as biomarkers in some other cancers has been shown, but circulating miRNAs have not been well characterized in oesophageal adenocarcinoma. This study investigated whether circulating miRNAs could be used to detect oesophageal adenocarcinoma.

overall_design: OpenArray high throughput real time PCR of microRNAs -- 19 patients without oesophageal disease, 10 patients with non-dysplastic Barrett's Oesophagus, 18 patients with  locally advanced Oesophageal Adenocarcinoma

first: Karen

last: Chiam

first: Tingting

last: Wang

first: David

last: Watson

first: George

last: Mayne

first: Tanya

last: Irvine

first: Tim

last: Bright

first: Lorelle

last: Smith

first: Imogen

last: White

first: Joanne

last: Bowen

first: Dorothy

last: Keefe

first: Sarah

last: Thompson

first: Michael

last: Jones


title: Smooth-muscle-cell differentiation in airways

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary:
This experiment was performed in order to investigate the difference in the gene expression pattern between differentiated airway/vascular smooth muscle cells and progenitors for alveolar myofibroblasts in embryonic lung. To answer this question, we  genetically labeled Smooth muscle actin-expressing cells using Sma-Cre-ERT2 crossed with Tomato Cre-reporter line. This line allows to label both airway/vascular smooth muscle cells (high SMA expression) and progenitors for alveolar myofibroblasts (low SMA expression). Mice were treated with tamoxifen at embryonic day E15.5 and cells from embryonic lungs were collected at E18.5.
Mice used in this study were offspring from RjOrl:SWISS (CD1) [mother] x STOCK Tg (Acta2-cre/ERT2)12Pcn Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/sbel (Acta2-CreERT2; tdTomatoflox) [father]

overall_design: RNA from primary isolated mesenchymal cells from mouse lung was SPIA amplified and hybridized on Agilent 80k arrays (three groups, isolated from 3 mice each = 9 samples in total)

first: Alena

last: Moiseenko


title: Liver transcriptomic response to fasting, high glucose or a high fructose challenges in wild-type C57Bl/6J male mice

status: Public on Oct 13 2017

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: Microarrays experiment was performed to detail the global programme of gene expression in liver of WT male mice in response to fasting (for 24h) or challenged with high glucose or high fructose compared to mice fed ad libitum.

overall_design: Eight week-old male mice from C57B/l6 genetic background (Charles River) were fed a chow diet ad libitum with or without 20% Glucose or Fructose for 24 hours in drinking tap water or fasted for 24 hours and sacrified at ZT16. There are 24 samples, each from an individual mouse (n=6 animals/group).

first: Alexandra

last: Montagner

first: Edwin

last: Fouché

first: Géraldine

last: Michel

first: Claire

last: Naylies

first: Arnaud

last: Polizzi

first: Alison

last: Iroz

first: Fadila

last: Benhamed

first: Catherine

last: Postic

first: Yannick

last: Lippi


title: ChIP from Candida albicans cells (3153A-parental and Sor125(55)-mutant) with H3pan-ac and H4pan-ac

city: Rochester

first: Hironao

last: Wakabayashi

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester

type: Genome binding/occupancy profiling by genome tiling array

summary:
Sorbose resistant Candida albicans mutant strain [Sor125(55)] derived from parental strain [3153A] has characteristic Ch5 monosomy plus Ch4/7b trisomy.
ChIP-chip data showed marked elevation of H4 histone acetylation on monosomic Ch5 in Sor125(55) mutant compared with parental strain (3153A). There was no remarkable diffrence in H4 acetylation level on other chromosomes between those strains and no difference in H3 acetylation on all chromosomes.

overall_design: Comparison of histone acetylation between mutant strain [Sor125(55), Ch5 monosomy plus Ch4/7b trisomy] and parental strain [3153A]

first: Elena

last: Rustchenko


title: Identification of genes and pathways that regulated by PHF20 via gene expression profile analysis in U87 cell with PHF20 silencing

city: Xi’an

first: Tianlong

last: Liu

address: No. 127 West Changle Road

department: Pharmacy

institute: Xijing Hospital

summary:
Glioblastoma (GBM) is the most common tumor of the central nervous system with poor prognosis. PHF20 was highly expressed in primary human glioma specimens. However, the molecular mechanism of by which PHF20 regulated glioblastoma remains poorly understood.
In the study, we investigate the gene expression profile of that regulated by PHF20 in U87 cells.

overall_design: The U87 cell lines were infected with shPHF20 while shCON was used as control. And the assays were performed in triplicate. Total RNA in the samples was isolated for double-strand cDNA synthesis, IVT and aRNA fragmentation. Then, it was processed for hybridization with The PrimeView™ Human Gene Expression Array (Affymetrix). The raw data were normalized, and then differentially expressed genes were screened. Finally, gene ontology analysis, KEGG pathway analysis and network analysis were performed to find the hub genes and pathways that regulated by PHF20.

first: Yuwen

last: Li


title: CDK7 Inhibition Suppresses Melanoma Growth By Depleting A Super-enhancer Associated Achilles Lineage Cluster [Array]

status: Public on Oct 23 2017

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Cutaneous malignant melanoma (CMM) lacks targeted therapies beyond the oft-circumvented BRAF inhibitors.  Part of the difficulty in treating melanomas has been attributed to a strong survival program controlled by melanocyte transcription factors such as MITF - a phenomenon first described in melanoma as “lineage dependency.”  Recently, a highly selective covalent CDK7 inhibitor (THZ1) has been shown to potently suppress the growth of various cancers through the depletion of master transcription-regulating oncogenes and the disruption of their attendant super-enhancers.  We now show that melanoma cells are highly sensitive to CDK7 inhibition and that a melanocyte “lineage cluster,” whose members are transcriptionally driven by super-enhancers, is also strongly suppressed by THZ1.  These results point to CDK7 inhibition as a viable strategy to deprive oncogenic transcription and suppress tumor growth in melanoma.

overall_design: Cell number-normalized expression microarray in SK-MEL-5 upon treatment with THZ1 or siMITF and corresponding controls

first: Philip

last: Eliades

first: Brian

last: Abraham

first: Camilla

last: Christensen

first: Nicholas

last: Kwiatkowski

first: Zhenyu

last: Ji

first: David

last: Miller

first: Benchun

last: Miao

first: Raj

last: Kumar

first: Michael

last: Taylor

first: Ching

middle: N

last: Njauw

first: Kwok-Kin

last: Wong

first: Nathanael

last: Gray

first: Hensin

last: Tsao

first: Lars

last: Anders


title: Transcriptome analysis of annotated coding genes and sORF at 74 accessions of A. thaliana

status: Public on Oct 03 2017

city: Iizuka

first: Kazumasa

last: Shirai

state: Fukuoka

address: 680-4 Kawazu

department: Frontier Research Academy for Young Researchers

institute: Kyushu Institute of Technology

summary: We applied previously designed array  in order to widely cover all types of genes of 74 A. thaliana accessions.

overall_design: The 18-days-old seedlings of 74 accessions were growing on 1% agar plates containing Murashige and Skoog (MS). Aerial parts of seedling were processed in two biological duplicates in each accession.

first: Fumio

last: Matsuda

first: Ryo

last: Nakabayashi

first: Masanori

last: Okamoto

first: Maho

last: Tanaka

first: Akihiro

last: Fujimoto

first: Minami

last: Shimizu

first: Kazuo

last: Shinozaki

first: Motoaki

last: Seki

first: Kazuki

last: Saito

first: Kousuke

last: Hanada


title: Multigenerational effect of antibiotic tetracycline on transcriptional responses of D. magna and its relationship to higher levels of biological organizations

status: Public on Oct 16 2017

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

summary: Given the risk of environmental pollution by pharmaceutical compounds and the effects of these compounds on exposed ecosystems, ecologically relevant and realistic assessments are required. However, many studies have been mostly focused on individual responses in a single generation exposed to one-effect concentration. Here, transcriptional responses of the crustacean Daphnia magna to the antibiotic tetracycline across multiple generations and effect concentrations were investigated. The results demonstrated that tetracycline induced different transcriptional responses of daphnids that were dependent on dose and generation. For example, reproduction-related expressed sequence tags (ESTs), including vitellogenin, were distinctly related to the dose-dependent tetracycline exposure, whereas multigenerational exposure induced significant change of molting-related ESTs such as cuticle protein. Sixty-five ESTs were shared in all contrasts, suggesting a conserved mechanism of tetracycline toxicity regardless of exposure concentration or time. Most of them were associated with general stress responses including translation, protein and carbohydrate metabolism, and oxidative phosphorylation. In addition, effects across the dose-response curve showed higher correlative connections among transcriptional, physiological, and individual responses than multigenerational effects. In the multigenerational exposure, the connectivity between adjacent generations decreased with increasing generation number. The results clearly highlight that exposure concentration and time trigger different mechanisms and functions, providing further evidence that multigenerational and dose-response effects cannot be neglected in environmental risk assessment.

overall_design: The experimental design consisted of four tetracycline concentration (control, 0.1, 1.0, and 10.0 mg L-1) and for four exposure generations (F1, F2, F3, and F4). Only the control treatment and the treatment of 1.0 mg per liter were xposed for four generations. All exposures were run in duplicate

first: Hyun

middle: Y

last: Kim

first: Tae

last: Jeong

first: Seungho

last: Yu

first: Karel

last: De Schamphelaere

first: Sang


title: Analysis of gene expression in human primary hepatocytes (HPPs) in response to the treatment of hPXR antagonist (SPA70) and agonists (rifampicin, SR12813, and TO90137)

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: A common set of hPXR targeting genes has been identified by comparing the gene expression profiles of HPPs treated with SPA70 and different agonists in single or combinations.

overall_design: Gene expression of HPPs treated with PA70 and different agonists in single or combinations have been compared in triplicate

first: Taosheng

last: Chen

first: Jing

last: Wu

first: Yueming


title: Microarray analysis of deepwater response in recombinant inbred line  (T65 x Bhadua)

city: Nagoya

first: Takeshi

last: Kuroha

address: Chikusa-ku Furo-cho

institute: Bioscience and Biotechnology Center,  Nagoya University

summary: To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and 3 significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.

overall_design: 87 samples from each recombinant inbred lines including their parental lines were analyzed. Eight-leaf-stage plants were put into the tank of 160 cm height and completely submerged in water. After 6h submergence treatment, the leaves were removed and total RNA was isolated from the region between 1 cm upper part from the uppermost and the basal node in the main culm.

first: Atushi

last: Fukushima

first: Motoyuki

last: Ashikari


title: Expression data from muscle of vitamin A restricted steer.

city: Tsukuba

first: Masayuki

last: Hayashi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Metabolism and Nutrition

institute: National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science

summary:
Vitamin A (VA) restriction for beef cattle improves meat marbling. However, its molecular mechanisms are not completely elucidated.
We performed microarray analysis to clarify effect of VA restriction on longissimus thoracis muscle gene expressions in Japanese Black steers.

overall_design: 13 to 14 month of age Japanese Black steers (n = 6) were divided to two groups. Vitamin A suppemented group (n = 3) was supplemented VA during experimental period. Vitamin A restricted group (n = 3) was restricted dietary VA intake. Steers were fattened during 7 months, then longissimus thoracis muscle tissue samples were obtained.

first: Kyouko

last: Kido

last: Hodate


title: Expression data from periparturient bos taurus

status: Public on Oct 05 2017

city: Helsinki

first: Nanbing

last: Qin

address: Koetilantie 5

department: Department of Agricultural Sciences

country: Finland

institute: University of Helsinki

summary:
The liver of dairy cows naturally displays a series of metabolic adaptation during the periparturient period in response to the increasing nutrient requirement of lactation. The hepatic adaptation is partly regulated by insulin resistance and it is affected by the prepartal energy intake level of cows.
We aimed to investigate the metabolic changes in the liver of dairy cows during the periparturient at gene expression level and to study the effect of prepartal energy level on the  metabolic adaptation at gene expression level.B13:N13

overall_design: Sixteen Ayrshire dairy cows were allocated to a controlled-energy diet (CON) or a high-energy diet (HIGH) for 6 weeks before the predicted parturition. Microarrary was conducted for liver samples at 8 d prior to the predicted parturition (-8 d) and 1 d and 9 d after the actual parturition (1 d and 9 d).

first: Kari

last: Elo


title: Alterations in the hepatic epigenome in mice exposed to a maternal high fat diet in utero [HELP]

city: Bronx

first: Maureen

last: Charron

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
Exposure to a high fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. We performed genome-wide DNA methylation analysis to examine DNA methylation patterns in liver of offspring exposed to a Control or HF maternal diet. WT mice were fed a C (9.5% fat, 3.59 kcal/g) or HF (35.5% fat, 5.29 kcal/g) diet for 2 wk before mating, throughout pregnancy and lactation. Offspring were weaned to a low fat (5.6% fat, 3.4 kcal/g) diet and were sacrificed at 5wks of age. DNA methylation analysis revealed the majority of differentially methylated regions were hypermethylated in HF liver. Chromosomal distribution analysis showed hypermethylation hot spots on chromosomes 4 (atherosclerosis susceptibility QTL1) and 18 (insulin dependent susceptibility 21). Most of the hypermethylated genes in these hot spots are associated with cardiovascular system development and function.
In summary, exposure to a maternal HF diet significantly alters the DNA methylation patterns in the liver of exposed offspring and contributes to programmed development of metabolic disease later in life.

overall_design: High molecular weight genomic DNA was extracted from liver in mouse exposure to a control or high fat (HF) diet in utero (n=3 each group). Genome wide methylation analysis was performed using HELP assay.

first: Yoshinori

last: Seki

first: Masako

last: Suzuki


title: Gene expression profiling: Quiescence vs. Senescence

status: Public on Oct 01 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Using cDNA arrays, we compared the reversible (quiescence) and irreversible (senescence) growth arrest conditions in osteosarcoma cell line, U2OS, which resulted in certain overlapping and unique gene expression signatures.

overall_design: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray

first: Anwar

last: Tarique

first: Ramakrishna

last: Gayatri


title: Expression profile of BCR-ABL+ colonies, isolated from methylcellulose

first: Florian

last: Bellutti

address: Veterinärplatz 1

institute: University of Veterinary Medicine

summary: BCR-ABL was used to transform Cdk6+/+, Cdk6-K43M or Cdk6-/- bone marrow cells. RNA was isolated from individual colonies formed in methylcellulose at day 10 post-transduction

overall_design: Cdk6+/+ versus Cdk6-K43M or Cdk6-/- cells; 4 biological replicates

first: Bellutti

last: Florian

first: Sexl

last: Veronika


title: Transcriptome profile of BLR E.coli

summary: RecA independent pathway has not been explored as RecA dependent pathway, i.e., the enzymes involved and the circumstances that trigger the pathway are not well understood.

overall_design: Organism : Escherichia coli , Agilent custom E.coli Gene Expression  8x15k Array (AMADID: 019439) designed by Genotypic Technology Private Limited

first: Muniasamy

last: Neerathilingam


title: Transcriptome profiling of Lactococcus garvieae 21881 in response to different stress conditions

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

country: Spain

institute: Complutense University of Madrid

summary: Transcriptome analysis of Lactococcus garvieae 21881 in response to different stress conditions: 42 ºC, high salt concentration and presence of linoleic acid.

sample_organism:
Lactococcus garvieae 8831
Lactococcus garvieae 21881

overall_design: Reference design experiment comparing samples of Lactoccocus garvieae 21881 exposed to different stress conditions. Three biological replicates for each condition (presence on the medium of high concentration of salt, linolieic acid and growth at 42 degrees Celsius). The results were referenced to a equimolar mixture of L. garvieae strains 21881 and 8831 grown at 29 degrees Celsius

first: Monica

first: Alicia

last: Gibello

first: Maria

last: Blanco

last: Cutuli

first: Victoria

last: Lopez-Alonso

first: Jose

middle: F

last: Fernández-Garayzabal

first: Guillermo

middle: H

last: Lopez-Campos


title: miRNA expression in rat medial entorhinal cortex layers during postnatal development

status: Public on Aug 01 2017

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

summary: To examine how miRNAs differ between medial entorhinal cortex layers during postnatal development, we analyzed the miRNA expression in layer II and the deep layers (III-VI) at postnatal ages P2, P9, P23 and P45 in wildtype Long Evans rats. The expression of the two most significantly differentially expressed miRNAs were validated by in situ hybridization.

overall_design: miRNA expression was measured in medial entorhinal cortex layer II and the deep layers (III-VI) at postnatal ages P2, P9, P23 and P45

middle: C


title: Gene expression profile altered by orthodontic tooth movement during healing of surgical alveolar defect

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

summary: An OTM-related healing model was established where a maxillary second premolar was protracted into the critical-sized defect for 6 weeks (Group DT6). As controls, natural healing models without OTM were set at 2 weeks (Group D2) and at 6 weeks (Group D6) after surgery. Total RNAs were extracted from dissected regenerated tissues and additionally from sound alveolar bone as a baseline (Group C). mRNA profiling was performed using microarray analysis.

overall_design: Total RNA was extracted either from the regenerated tissue in the defect and adjacent alveolar bone surrounding the root of the maxillary second premolar (Groups D2, D6, and DT6) or from the sound alveolar bone tissue around the maxillary premolar roots (Group C) to perform DNA microarray analysis.

first: Su-Jung

last: Kim

first: Eun-Kyung

last: Choi

first: Seung-Hak

last: Baek


title: protein levels in BRAF/MEK inhibitor resistance melanoma cells treated with PF3758309 [CR]

status: Public on Jul 31 2017

city: Toronto

first: Hezhe

last: Lu

state: Ontario

address: 600 University Ave

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

summary: 3 BRAF/MEK inhibitor resistance melanoma cells were treated with PAK inhibitor PF3758309 for 48 hr, the cell lysis were analyzed by RPPA  profiling by protein array (RPPA)

overall_design: 3 pair of samples were analyzed (control and PF3758309 treatment group) by RPPA, more than 200 of proteins were tested

first: Shujing

last: Liu

first: Gao

last: Zhang

first: Meenhard

last: Herlyn

first: Xiaowei

last: Xu


title: Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

city: Lanzhou

first: quanwei

last: zhang

state: Gansu

address: Anning District of Lanzhou

institute: Gansu Agriculture University

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

summary: The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75 Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.

overall_design: China’s northwest provinces, particularly Gansu province, have breeding populations that include Dorper, Poll Dorset, Texel, Suffolk, South African Mutton Merino, Borderdale, Gansu Alpine Merino, and Gansu Morden varieties of sheep. These are widely farmed in the foothills of the Hindu Kush and Himalaya as well as on the Qinghai/Tibetan Plateau, all regions ranging from 1000m to 5500m above sea level. In order to better adapt to these climates and environments, the Gansu Morden sheep breed was hybridized with Dorper, Poll Dorset and Small-Tail Han sheep. The resulting hybrids, which contain 75.0% foreign high-quality sheep genetics, were selected for planned crossbreeding. This new breed and other sheep breeds were selected and used for the present analysis of copy number variations by SNP50 BeadChip array, with the aim of generating a fuller understanding of sheep genetic resources.

first: Youji

last: Ma

first: Quanwei

first: Zengkui

first: Xingxu

last: Zhao

first: Yong


title: In vitro procedures exacerbate chromosome instability in early cleavage stage embryos

status: Public on Sep 24 2017

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

summary: Chromosomal instability (CIN) occurs at high frequency during early in vitro embryogenesis and is known to be associated with early embryonic loss in humans. The chromosomal stability of in vivo-conceived cleavage stage embryos largely remains unknown. Here, we applied haplotyping and copy number profiling to investigate genomic architecture of 171 single bovine blastomeres and to compare the nature and frequency of CIN between in vivo embryos, in vitro embryos produced from ovum pick up with ovarian stimulation (OPU-IVF), and in vitro produced embryos from in vitro matured oocytes without ovarian stimulation (IVM-IVF). Our data shows that CIN is significantly lower in in vivo conceived cleavage stage embryos when compared to in vitro cultured embryos, as genomic stability of single blastomeres in both IVF embryos was severely compromised (P<0.0001)

overall_design: Five young healthy, cycling Holstein Friesian heifers (Bos Taurus) were used as donors for oocytes and embryos. The semen from the same bull was used for embryo production in all five cows. Blood samples from the donor cows (mothers) and semen from the bull (father) were used to extract bulk DNA (DNeasy Blood and Tissue kit, Qiagen, Germany). Bulk DNA was also obtained from the parents of the bull (paternal grandparents) and from the available parents of cows (maternal grandparents; only for crosses 4757, 8301 and 9617).  All cows were submitted to hormonal stimulation with subsequent ovum pick up or in vivo embryo collection. After hormonal treatments, cows were left untreated for a month before they were slaughtered. Ovaries were collected separately and retrieval of the oocytes was followed by routine in vitro embryo production.  The embryos were treated with pronase to dissolve zona pellucida and single blastomeres were retrieved from zona free embryos and whole-genome amplified (WGA) using commercial multiple displacement amplification kit (Repli-G Single Cell kit, Qiagen). WGA products and bulk parental and grandparental DNA were then SNP genotyped on BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA). Subsequently, the SNP logR and SNP B-allele frequency (BAF) values, as well as the discrete SNP genotype calls were obtained for each single cell and applied in further single-cell analysis to obtain genome-wide haplarithm profiles using a modified version of the siCHILD algorithm (Zamani Esteki et al. 2015).

first: Olga

last: Tšuiko

first: Maaike

last: Catteeuw

first: Aspasia

last: Destouni

first: Osvaldo

last: Bogado Pascottini

first: Urban

last: Besenfelder

first: Vitezslav

last: Havlicek

first: Katrien

last: Smits

first: Ants

last: Kurg

first: Andres

last: Salumets

first: Thomas

last: D’Hooghe

first: Thierry

last: Voet

first: Ann

last: Van Soom

first: Joris

last: Vermeesch


title: Real-time quantitative PCR analysis of retrogradely labeled stellate neurons in LII of the rat medial entorhinal cortex

first: Lene

last: Olsen

summary: We compared miRNA expression in FACS-sorted, retrogradely labeled stellate neurons with other medial entorhinal cells, and found 7 miRNAs to be upregulated in stellate cells.

overall_design: qPCR array expression profiling of FACS sorted labeled and unlabeled cells from five biological replicates. qPCR array expression profiling of total RNA from dissected medial entorhinal cortex of two biological replicates


title: Identification of systemic injury response genes in Drosophila melanogaster

status: Public on Sep 30 2017

city: Glendale

first: Jennifer

last: Hackney Price

state: Arizona

address: 4701 Thunderbird Rd  M/C 2352, New College

department: Mathematical and Natural Sciences

country: USA

institute: Arizona State University

summary: The systemic response to injury in Drosophila melanogaster is characterized by the activation of specific signaling pathways that facilitate the regeneration of wounded tissue and help coordinate wound healing with organism growth. The mechanisms by which damaged tissues influence the development and function of peripheral non-injured tissues is not fully understood. Injury was induced in early third instar larvae via temperature-dependent cell death in wing imaginal discs. Microarray analysis using RNA isolated from injured and control was used to identify genes underlying the systemic injury response. We identified 150 genes which were differentially expressed in response to localized cell death in wing imaginal discs. Upregulated genes were associated biological processes including carnitine biosynthesis, signal transduction and regulation of oxidoreductase activity while terms associated with downregulated genes included wound healing, imaginal disc-derived wing hair outgrowth, and regulation of glutamatergic synaptic transmission. Pathway analysis revealed that wing disc damage led to changes in fatty acid, cysteine, and carnitine metabolism. One gene, 14-3-3ζ, which encodes a known regulator of Ras/MAPK signaling was identified as a potential regulator of transdetermination during tissue regeneration. Our results raise the possibility that immune function and cell proliferation during wing disc repair and regeneration in Drosophila may require the sulfur amino acid cysteine and its’ metabolites, taurine and glutathione, similar to what has been reported during tissue repair in mammals. Further, it seems likely that imaginal disc damage stimulates the mobilization of fatty acids to support the energetically demanding process of tissue regeneration. The roles of additional genes that are differentially regulated following imaginal disc injury remain to be elucidated.

overall_design: Transcriptional profile of female 3rd instar larvae with (ablating: rnGAL4,UASegr,tubGAL80ts/+) and without (control: TM6, Tb1, tubeGAL80/+) temperature-sensitive cell death induced in wing discs. In total 4 samples:  2 replicates of Ablating and 2 replicates of Control larvae following 24 hours at 30°C degrees which induces cell death in Ablating animals but not Controls.

first: Jesus

last: Contreras Rodriguez

first: Teresa

last: Lupone

first: Ty

last: Leek

first: Tyler

last: Marsh

first: Ashley

last: Almajan

first: Chaz

last: Beckett

first: Sabahat

last: Hussain

last: Broatch


title: protein levels in BRAF inhibitor resistance melanoma cells treated with PF3758309

first: Hezhe

last: Lu

summary: 11 BRAF inhibitor resistance melanoma cells were treated with PAK inhibitor PF3758309 for 48 hr, the cell lysis were analyzed by RPPA  profiling by protein array (RPPA)

overall_design: 11 pair of samples were analyzed (control and PF3758309 treatment group) by RPPA, more than 200 of proteins were tested

first: Shujing

last: Liu

first: Gao

last: Zhang

first: Meenhard

last: Herlyn

first: Xiaowei

last: Xu

first: Wei

last: Guo


title: Expression data of liver tissues from rats with and without methapyrilene treatment

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

summary: We investigated a drug-induced liver injury (DILI) model in rats induced by methapyrilene (MPy) administration. MPy, a former antihistamine and anticholinergic drug, was withdrawn in the 1970ties due to its ability to initiate hepatocarcinogenesis and is now used to induce hepatobiliary injury and biliary epithelial cell hyperplasia. Male Wistar rats (8–10 weeks old, weighing 170–200 g) were randomly assigned to three dosing groups (n=6 per group and time-point) and dosed with MPy at 0, 30 and 80 mg/kg/day by oral gavage. After 4, 8 or 15 days, or after 14 days followed by a recovery period of 10 days (day 24) rats were sacrificed. Increased levels of ALAT, ASAT, AP and ɣ-GT as well as bili-t and total bile acids indicated liver damage (AP and ɣGT indicating biliary effects). They were detectable on day 7 at the high dose of 80 mg/kg MPy and persisted until day 15 at end of treatment. Histopathologically, vacuolation and necrosis of the hepatocytes (predominantly in the periportal region) were seen starting on day 3 - especially in animals treated with 80 mg/kg MPy. These findings were accompanied by periportal mononuclear inflammatory cell filtration. Bile duct proliferation, bile duct hyperplasia and increased numbers of mitoses of hepatocytes were evident at all treatment time points. The frequency and severity of these findings increased with dose and duration of the treatment. Gene expression analysis in liver tissues revealed highly significant transcriptional changes in the high dose group, detectable on day 4 and intensifying over time. Besides genes associated with apoptosis (CASP4, CASP12), detoxification (CYB4B) and proliferation (p21, CCNG1) several were related to bile acid metabolism or transport. For example, bile acid exporters OATP1, NTCP, OATP4 and MOAT1/ OATPB as well as the putative bile acid metabolizing enzymes AMACR, BAAT and ACOX2 were found down regulated in response to MPy treatment. In contrast, mRNAs encoding putative bile acid importers MRP2 and ABCC4 / MRP4 were found up regulated. Most of the deregulated levels returned to control values during the recovery phase except OATP1, MOAT1/ OATPB, which remained slightly elevated. Interestingly, OATP4 followed an inverse trend of deregulation after 10 days of recovery, presumably due to overcompensation. Overall, the expression changes found associated with bile acid metabolism or transport could be linked to detected bile acid level alterations in liver and plasma.

overall_design: Male Wistar rats were (8–10 weeks old, weighing 170–200 g) were randomly assigned to three dosing groups (n=6 per group and time-point) and dosed with methapyrilene (Sigma-Aldrich; in carboxymethylcellulose) at 0, 30 and 80 mg/kg/day by oral gavage. Rats were sacrificed after 4, 8 or 15 days, or after 14 days of treatment followed by a recovery period of 10 days (assigned as day 24).

first: Mira

last: Pavkovic

first: Bjoern

last: Riefke

first: Markus

last: Slopianka


title: Changes in gene expression in the striatum of Drd2Cre; ERK1/ERK2 knockout mice

status: Public on Jul 25 2017

city: Chapel Hill

first: Scott

last: Hutton

state: NC

address: 115 Mason Farm Rd. Rm 8131

department: Neuroscience Center

institute: University of North Carolina

summary:
We knocked out ERK1 and ERK2 in the striatopallidal population of striatal medium spiny neurons and analyzed differences in gene expression at P17, a time of increased synapse formation.
We used whole gene microarray to assess transcriptional changes that occur in the mouse striatum at P17 in response to ERK1/2 deletion in striatopallidal medium spiny neurons.

overall_design: Striatal punches were extracted from Mapk3(Erk1)-/-; Mapk1(Erk2)Floxed/Floxed (control mice) or Drd2Cre;Mapk3(Erk1)-/-; Mapk1(Erk2)Floxed/Floxed (mutant mice) at postnatal day 17. RNA was extracted and analyzed using Affymetrix microarray.

first: William

last: Snider


title: Down modulation of miR-99a/let-7c/miR-125b miRNA cluster predicts clinical outcome in patients with unresected malignant pleural mesothelioma

status: Public on Jul 28 2017

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

type: Non-coding RNA profiling by high throughput sequencing

summary: Malignant pleural mesothelioma (MPM) is an aggressive tumor with a dismal overall survival (OS) and to date few molecular markers are available to guide patient management. This study aimed to identify a prognostic miRNA signature in MPM patients who did not undergo tumor resection. Whole miRNA profiling using a microarray platform was performed on 26 unresected MPM with distinct clinical outcome: 15 patients had aggressive disease (OS<12 months) and 11 patients indolent disease (OS>36 months). Three prognostic miRNAs (mir-99a, let-7c and miR-125b) encoded at the same cluster (21q21) were selected for further validation and tested on publicly available miRNA sequencing data (TCGA) from 72 MPM patients with survival data. A risk model was built based on these 3 miRNAs that was validated by quantitative PCR in an independent set of 30 MPM patients. High risk patients had shorter median OS (7.6 months) as compared with low-risk patients (median not reached). In the multivariate Cox model, a high risk score was an independently associated with shorter OS (HR=3.14; 95% CI, 1.18–8.34; P=0.022). Our study identified that the downregulation of the miR-99a/let-7/miR-125b miRNA cluster predicts poor outcome in unresected MPM.

overall_design: In the present study the whole miRNA profile was evaluated in a cohort of 26 malignant pleural mesothelioma (MPM) sample derived from patients who did not undergo surgery and in 3 nonmalingnat pleura (NMP) as normal control (NC). The comparison between MPM and NC  samples allowed to identify miRNA linked to tumorigenesis. The second aim was the identification of miRNA correlated with overall survival (OS); for this purpose the MPM patients were divided based on the survival rate in: i) long survivors (LS; patients whose OS was greater than 36 months); and ii) short survivors (SS; patients died within 12 months from the diagnosis).

first: Anna

last: Truini

first: Simona

last: Coco

first: Ernest

last: Nadal


title: Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and lcbk1-2 knock-out mutant

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

institute: Guizhou University

summary:
Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the LCBK1 gene in the freezing tolerance of plant, we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on WT and lcbk1-2 plants to compare their genome-wide expression profiles under 22 °C or 4 °C treatment.
The differently expressed genes revealed by transcriptional profiling indicate that LCBK1 may participate in the maintenance of plant ROS homeostasis and acts as a novel positive regulator of CBF-independent pathway to control the freezing tolerance of Arabidopsis.

overall_design: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany) from 2-week-old seedlings of the wild-type and lcbk1-2 grown on 1/2 MS medium containing 2% sucrose at 22˚C or 4˚C treatment for 3hr and 24hr under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1. 6μg of total RNA was used to synthesize biotin-labeled cDNA, which was then hybridized with the ATH1 oligonucleotide chips as instructed by the manufacturer (Affymetrix).


title: Genome-wide data of RNAs associated to Mmi1 in wild type Schizosaccharomyces pombe cells

status: Public on Jul 27 2017

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

type: Expression profiling by high throughput sequencing

summary: Mmi1 is a YTH domain containing protein. We used Solexa Deep Sequencing to identify the mRNas and lncRNAs specifically associated to Mmi1.

overall_design: Solexa libraries were made with RNA purified from anti-Mmi1immunoprecipitations or irrelevant immunoprecipitations from wild type S. pombe cells. Libraries were made in duplicates and sequenced using Illumina HiSeq2000

first: Leila

last: Touat-Todeschini

first: Michael

last: Reuter

first: Nicloas

last: Thierry-Mieg

first: Benoit

last: Gilquin

first: Ramesh

last: Pillai

first: André

last: Verdel


title: Transcriptome changes in Arabidopsis expressing Vitreoscilla hemoglobin under hypoxic and NO donor treatments.

first: Olga

last: Blokhina

address: Viikinkaari 1

department: Biosciences

summary: Hypoxia, a naturally occurring phenomenon, results in tremendous losses in the growth of plants and in their productivity. On the physiological level oxygen deprivation results in distinct metabolic rearrangements, is accompanied by dehydration, and oxidative and nitrosative stresses.   Six to seven core hypoxia-responsive genes, which are always induced under oxygen deprivation, have been shown to include hemoglobin 1 (Hb1) across a wide range of plant species. However, the function of this induced Hb1 is not completely understood .The importance of elevated Hb expression has been attributed mainly to its nitric oxide (NO) scavenging properties, and hence, to the elimination of this free-radical and signaling species. NO is known to accumulate under hypoxia and its level is in reciprocal relationship with the Hb expression levels.  However, evidence has accumulated on Hbs as essential for normal plant development and they take part in the regulation of e.g. flowering, germination and lateral and adventitious root emergence.  The physiological role of induced hemoglobin (Hb) expression and its role in NO scavenging were assessed by introducing bacterial (Vitreoscilla stercoraria) hemoglobin (VHb) to the cytoplasm and mitochondria of Arabidopsis thaliana. Heterologous expression was chosen to avoid interference with developmental functions of endogenous Hbs.  Sixteen day old transformants were subjected to hypoxia or to NO donor treatment (DETA, 500 µM) for 2h and 24h and global changes in gene expression were assessed using a microarray approach.   Both hypoxic and NO-treatment experiments were aimed also to reveal novel functions for Hb under abiotic stress conditions, exemplified by oxygen deprivation and NO/oxidative stresses and during normal development of Arabidopsis transformants on the background of normally expressed endogenous Hbs  Hypoxia, a naturally occurring phenomenon, results in tremendous losses in the growth of plants and in their productivity. On the physiological level oxygen deprivation results in distinct metabolic rearrangements, is accompanied by dehydration, and oxidative and nitrosative stresses.   Six to seven core hypoxia-responsive genes, which are always induced under oxygen deprivation, have been shown to include hemoglobin 1 (Hb1) across a wide range of plant species. However, the function of this induced Hb1 is not completely understood .The importance of elevated Hb expression has been attributed mainly to its nitric oxide (NO) scavenging properties, and hence, to the elimination of this free-radical and signaling species. NO is known to accumulate under hypoxia and its level is in reciprocal relationship with the Hb expression levels.  However, evidence has accumulated on Hbs as essential for normal plant development and they take part in the regulation of e.g. flowering, germination and lateral and adventitious root emergence.  The physiological role of induced hemoglobin (Hb) expression and its role in NO scavenging were assessed by introducing bacterial (Vitreoscilla stercoraria) hemoglobin (VHb) to the cytoplasm and mitochondria of Arabidopsis thaliana. Heterologous expression was chosen to avoid interference with developmental functions of endogenous Hbs.  Sixteen day old transformants were subjected to hypoxia or to NO donor treatment (DETA, 500 µM) for 2h and 24h and global changes in gene expression were assessed using a microarray approach.   Both hypoxic and NO-treatment experiments were aimed also to reveal novel functions for Hb under abiotic stress conditions, exemplified by oxygen deprivation and NO/oxidative stresses and during normal development of Arabidopsis transformants on the background of normally expressed endogenous Hbs

overall_design:
Three lines of Arabidopsis thaliana (Landsberg) were used: wild type WT; line C13, expressing Vitreoscilla hemoglobin (VHb) in the cytoplasm; line Mt62 – expressing VHb in mitochondria. Analysis used total RNA isolated from the shoots of 16 days old control plants  (at 0h = 16 day-old plants, start of experiment, and after 2h and 24h) and  from the experimental plants after hypoxic treatment ( 4% O2 for 2h and 24h) and DETA treatment ( 500 µm,  2h and 24 h incubation after the onset of NO release). Treatments were performed separately. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data. Each experimental variant had four biological replicates randomly labelled with three different dyes: Cy3, HyPer5 and Alexa Fluor 488 (See 'Arrays layout' tab).  Each microarray field was used to hybridize three different samples labelled with three different dyes. For each experimental variant there are four raw data files = 4 replicates. Name of the raw data file includes: First 13 digits - Agilent slide number; AxFy - array x, field y; Hy5, Cy3, Al - dyes Hyper 5, Cy3, Alexa 488; WT - wild type, C13 – line expressing VHb in the cytosol; Mt62 – line expressing VHb in mitochondria; c – control; H- hypoxic treatment; DETA - treatment with NO donor DETA; 0h, 2h, 24h - duration of treatment, hours. Gene expression data normalization was performed by R language and BioConductor Packages. First the data was normalized using quantile normalization and in-house modified   version of COMBAT software. We selected significantly regulated probes from the normalized data using Empirical Bayes T-test. Next, probe-level scores were summarized for each gene by taking average of scores of probes targeting the same gene.  In the matrix table LOG FCs which have a T score p value > 0.01, are disregarded and marked as ‘null’.
GPR files:
Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F, 7 slides
AxFy = array x, field y;
Hy5, Cy3, Al = dyes Hyper 5, Cy3, Alexa 488;
WT, C13, Mt62 = wild type, cytoplasmic VHb line 1:3 , mitochondrial VHb line 6:2;
Ctrl = control;
H = hypoxic treatment;
DETA = NO donor DETA   (500  µM) treatment;
0h, 2h, 24h, = duration of the treatment, hours;

first: Petri

last: Törönen

last: Lackman

first: Suvi

last: Sutela

first: Bing

last: Li

first: Heiko

last: Rischer

last: Auvinen

first: Hannu

last: Maaheimo

first: Pauli

last: Kallio

first: Hely

last: Häggman

first: Kurt

middle: V

last: Fagerstedt


title: Aging-induced decline in mucus thickness in mice is associated with changes in microbiota composition and immunity and is sex dependent

status: Public on Aug 28 2017

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: A mucus layer covers and protects the intestinal epithelial cells from direct contact with microbes. This mucus layer not only prevents inflammation but also plays an essential role in microbiota colonization, indicating the complex interplay between mucus composition-microbiota and intestinal health. However, it is unknown whether the mucus layer is influenced by age or sex and whether this contributes to reported differences in intestinal diseases in males and females or with ageing. Therefore, in this study we investigated the effect of age on mucus thickness, intestinal microbiota composition and immune composition in relation to sex.  The ageing induced shrinkage of the colonic mucus layer was associated with bacterial penetration and direct contact of bacteria with the epithelium in both sexes. Additionally, several genes involved in the biosynthesis of mucus were downregulated in old mice, especially in males, and this was accompanied by a decrease in abundances of various Lactobacillus species and unclassified Clostridiales type IV and XIV and increase in abundance of the potential pathobiont Bacteroides vulgatus. The changes in mucus and microbiota in old mice were associated with enhanced activation of the immune system as illustrated by a higher percentage of effector T cells in old mice. Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups.

overall_design: Young (3 months) and old (19 months) male and female C57B1 mice were sacrificed by cervical dislocation. Approximately 1 cm of proximal colon was removed for microarray analysis.

first: Marlies

last: Elderman

first: Bruno

last: Sovran

first: Floor

last: Hugenholtz

first: Katrine

last: Graversen

first: Myrte

last: Huijskes

first: Eva

last: Houtsma

first: Clara

last: Belzer

first: Mark

last: Boekschoten

first: Paul

last: de Vos

first: Jan

last: Dekker

first: Jerry

last: Wells

first: Marijke

last: Faas


title: Microarray transcriptome analysis of soybean genes induced during rhizobial, arbuscular mycorrhizal and their dual symbioses

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: For identification of plant gene networks which interact to initiate and support both rhizobial nodulation and AM fungal colonization, the transcription profiles of soybean genes induced during rhizobial, AM and their dual symbioses.

overall_design: Four different treatments were used: an uninoculated control, inoculation with rhizobium alone (rhizobial symbiosis), inoculation with AM fungus alone (AM symbiosis), and inoculation with rhizobium and AM fungus together (dual symbiosis). After the soybeans inoculated were grown in a glasshouse for 6 weeks, the transcriptome of host genes were analyzed using a cDNA microarray

first: Kazunori

last: Sakamoto

first: Natsuko

last: Ogiwara

first: Tomomitsu

last: Kaji

first: Yurie

last: Sugimoto

first: Mitsuru

last: Ueno

first: Masatoshi

last: Sonoda

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Role of H4K8ac in P. falciparum life cycle [ChIP]

city: Singapore

first: Archana

middle: P

last: Gupta

address: 60 Nanyang Drive

department: School Of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Study of chromatin changes of P. falciparum in response to changes in the levels of histone H4 acetylations especially H4K8ac using chromatin immunoprecipitation coupled to microarray chip (ChIP-on-chip)

overall_design: ChIP-on-chip of P. falciparum intraerythrocyic life cycle upon hyper or hypo acetylated Histone H4 achieved by treating the cells with HDAC inhibitors or mutating the lysine residues respectively

first: Alok

last: Patra

first: Lei

last: Zhu

first: Zbynek

last: Bozdech


title: Gene expression profiling of HepG2 cells after knockdown of β-catenin

status: Public on Sep 01 2017

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

summary: To elucidate the comprehensive changes regulated by β-catenin/TCF-dependent signaling in liver cancer cells, we explored a global gene expression of HepG2 cells after knockdown of β-catenin.

overall_design: HepG2 cells were transfected with control siRNA or two independent β-catenin siRNAs, followed by gene expression profiling using microarray.

first: Yoichi

last: Furukawa


title: Role of H4K8ac in P. falciparum life cycle [gene expression]

summary: Transcriptional analaysis of P. falciparum in response to changes in the levels of histone H4 acetylations especially H4K8ac

overall_design: Transcriptional profiling of P. falciparum intraerythrocyic life cycle upon hyper or hypo acetylated Histone H4 achieved by treating the cells with HDAC inhibitors or mutating the lysine residues respectively


title: Effect of ∆13RAP2.12 overexpression

status: Public on Jul 24 2017

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

institute: Scuola Superiore Sant'Anna

summary: The effect of the overexpression of a stabilized version of the transcription factor RELATED TO APETALA2.12 (RAP2.12) on the transcriptome of Arabidopsis rosettes was investigated. To this purpose, 4-week old rosette of wild-type and 35S:∆13RAP2.12 plants were compared. Samples were composed of pools of 3 plants.

overall_design: In total, 6 samples were analyzed, subdivided in 2 theses with 3 replicates each. 35S:∆13RAP2.12 plants were compared to wild-type plants (Col-0 ecotype).

first: Beatrice

last: Giuntoli

first: Federico

middle: M

last: Giorgi


title: Gene expression from armored CAR T cell and TAMs

city: New York

first: Oladapo

last: Yeku

state: NY

address: 1275 York Avenue, Box 242

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

type:
Expression profiling by array
Other

summary: Compare the gene expression profile among armored IL-12 secreting CAR T cells and second-generation CAR T cells and TAMs recovered from both groups

overall_design: CAR T cells and TAMs were recovered from tumor bearing mice treated with IL-12 secreting or second generation CAR T cells. RNA extracted and gene expression was analyzed with Nanostring

first: O

first: R

middle: J

last: Brentjens


title: Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo [human]

status: Public on Jul 18 2017

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: Six different carbon nanomaterials (CNM) administered by oropharyngeal aspiration to C57BL/6 mice (on 4 consecutive days with 10ug of CNM per day in PBS, sacrificed on 5th day)  and to differentiated THP-1 cells in culture (6 hour and 24 hour, with 100ug of CNM /ml of medium)

overall_design: THP-1 cells were grown in 30 ml of RPMI 1640 media, supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin (PEST) antibiotics and 2mM Ultraglutamine. THP-1 cells were differentiated with 50nm PMA (phorbol-12-myristate-13-acetate) and exposed in six-well plates to six different carbon nanomaterials (CNM) by replacing the old media and adding 100 µg of the CNM in 1 ml of fresh complete RPMI and incubated for 6 or 24 hours

first: Pia

last: Kinaret

first: Veer

last: Marwah

first: Vittorio

last: Fortino

first: Marit

last: Ilves

first: Henrik

last: Wolff

first: Lasse

last: Ruokolainen

first: Petri

last: Auvinen

first: Kai

last: Savolainen

first: Harri

last: Alenius


title: Role of H4K8ac in P. falciparum life cycle

first: Archana

last: Gupta

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans [Gene expression]

city: S. Michele all'Adige (TN)

first: Tobias

last: Weil

address: Via E. Mach, 1

institute: Fondazione Edmund Mach

summary: The fungal pathogen Candida albicans and other pathogens of the CTG clade reassigned the leucine CUG codon to serine and tolerate highly variable levels of both serine and leucine at CUG positions in response to environmental cues. Previous studies found that increased leucine misincorporation levels enhance resistance to drugs but the underlying mechanisms are not known. To clarify the biological role of this tuneable codon ambiguity, we evolved C. albicans strains engineered to mistranslate CUG at elevated levels, in the presence and absence of the antifungal drug fluconazole

overall_design: Expression profiling was performed on evolved C. albicans strains engineered to mistranslate CUG at elevated levels, in the presence and absence of the antifungal drug fluconazole at three different timepoints.

first: Rodrigo

last: Santamaría


title: Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans

platform_organism:
Candida albicans
Candida albicans SC5314


title: Estrogenic effects of ingredients of glyphosate-based herbicide ingredients in human breast cancer cells

status: Public on Jul 14 2017

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

summary: Glyphosate-based herbicides are the major pesticides used worldwide. There is an intense debate on the estrogenic effects of their ingredients. We have compared the estrogenic effects of glyphosate (the active principle), polyethoxylated tallowamine (a co-formulant), and a commercial formulations containing different co-formulants to those of estradiol and bisphenol A in the MCF-7  human breast cancer cell line.  The gene expression profiles were determined using the Affymetrix Human Transcriptome 2.0 Array.

overall_design: MCF-7 cells treated during a period of 48h glyphosate-based herbicide ingredients and the natural hormone 17β-estradiol were subjected to a full transcriptome profiling using the Affymetrix microarray platform.

first: Matthew

last: Arno


title: Rice cell culture: Control vs. Rapamycin treatment

status: Public on Jul 15 2017

city: Ghent

first: Osvaldo

last: Filipe

address: Coupure Links 653

department: Crop Protection

institute: Ghent University

summary: To shed light on the TOR signaling network in crop plants, we investigated the global transcriptome changes in rice suspension cells (cultivar Kitaake) treated with the TOR-specific inhibitor rapamycin.

overall_design: Rapamycin stock solution was prepared in DMSO. Three independent biological repetitions were included in the analysis.

first: David

last: De Vleesschauwer


title: Transcriptomic profiling of fresh-cut lettuce samples (Lactuca sativa L., var Babybel, Batavia bionda), treated with two different sanitizer procedures.

status: Public on Jul 12 2017

city: Rotondella

first: loretta

last: daddiego

state: MT

institute: ENEA C.R. Trisaia

summary: Comparative profiling of fresh-cut lettuce samples treated with an alternative washing solution  (PAA) with respect to standard treated samples STD (SH-treated).We generated a comprehensive repertory of transcripts useful to study the global change induced by two sanitizer  in different time points of storage (T1, T3, and T6).

overall_design:
To investigate transcriptional changes of fresh-cut lettuce leaves  treated with two different sanitizer solution, 12K DNA microarray chips were produced with CustomArrayTM DNA Synthesizer by selecting 12000 Lactuca sativa unigenes from The Gene Index (TGI) Project database. Transcriptional datasets of fresh-cut lettuce leaves during storage were produced and then used to reveal changes in response to the sterilizing agents under investigation.

T1 day 1  (first day of storage)
T3 day 3  (after 3 storage days )
T6 day 6  (after 6 storage days)

first: Loretta

last: Daddiego

first: Fabrizio

last: Carbone

first: Gaetano

last: Perrotta

first: Loredana

last: Lopez


title: Temporal gene expression of human-fetal and glioblastoma stem cell cultures under directed differentiation conditions

status: Public on Jul 13 2017

city: Toronto

first: Peter

middle: B

last: Dirks

state: ON

address: 686 Bay St

department: Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery

institute: The Hospital for Sick Children

summary: Primary glioblastoma (GBM) cultures vary with respect to differentiation competency. We sought to identify putative transcription factors necessary for the differentiation of GBM cultures. In this dataset, we include expression data obtained from 2 human-fetal neural stem cell  (HF-NS) cultures and 2 GBM stem cell (GSC) cultures. We assessed changes in gene expression from 3 timepoints during an in vitro differentiation protocol.

overall_design: Exon microarray analysis of 12 samples total were performed. 2 HFNS cultures and 2 GNS cultures were analyzed at acute timepoints during directed differentiation (days 0, 2, and 9).

first: Ian

middle: D

last: Clarke

first: Nicole

last: Park


title: The profiling of gene expression in the roots of rice

city: Shanghai

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

country: China

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

summary: In order to research the genetic mechanism of deep rooting in rice, we performed the transcriptomic assay of the roots in rice.

overall_design: The root tips about 2 cm length  were used for expression analysis in deep roots and shallow roots in the same plant. Two type rice varieties were used in this study including deep rooting and shallow rooting rice.12 root samples from six rice varieties were obtained in this experiments. The expression profiles were generated using Agilent rice micoarrays.

first: Qiaojun

last: Lou

first: Liang

last: Chen


title: Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans [CGH]

first: Tobias

last: Weil

overall_design: CGH analysis was performed on evolved C.albicans strains grown in presence of fluconazole and the parental strain not subjected to fluconazole.


status: Public on Jul 01 2017

city: Iowa city

first: Xiangbing

last: Meng

state: IA

address: 375 Newton Road

department: OB&GYN

institute: University of Iowa

summary: During TCGA data analysis, we found that expression of many genes was correlated with the expression of MTDH in estrogen receptor (ESR) positive cancers. The effect of estradiol and MTDH on gene expression in endometrial cancer cells was further analyzed.

overall_design: ECC1 cells and ECC1 MTDH-deficient cells were treated with or without estradiol for 24 hours. Gene expression regulated by MTDH and estradiol were analyzed by microarray.

first: Kimberly K

last: Leslie

first: Yujun

last: Li


title: Time-course of genes expression of the dorsal and lateral lineage in the SVZ-RMS-OB post-natal neurogenic system

status: Public on Jun 28 2017

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

institute: CNRS

summary: SVZ neural stem cells of P1 CD1 mouse pups where dorsally or laterally in vivo electroporated with a GFP vector. At variable time after electroporation, fluorescent cells were FACS sorted. Total RNA was exctracted, amplified and submitted to micro-array analysis.

overall_design: 6 time-points were chosen for analysis: 8 hours, 1 day, 2 days, 4 days, 7 days and 14 days. For each time-point 2 to 4 replicates were performed.

first: Christophe

last: Beclin

first: Stefan

last: Wild

first: Philipp

last: Follert

first: Antoine

last: de Chevigny

first: Nathalie

last: Coré

first: Marie-Catherine

last: Tiveron

first: Stephanie

last: Pierson

first: Yann

last: Mahnoun

first: Andreas

last: Bosio

first: Harold

last: Cremer


title: Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy

status: Public on Jul 03 2017

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary: IgA nephropathy (IgAN) is the most common glomerulonephritis in the world. The disease is characterized by galactose deficient IgA (gd-IgA) in the circulation forming immune complexes. The complexes are deposited in the glomerular mesangium leading to inflammation and loss of renal function, but the pathophysiology of the disease is still not fully understood. Using an integrated global transcriptomic and proteomic profiling approach we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsies from patients with IgAN. The influence of galactose deficient IgA (gd-IgA) on mesangial cells was investigated by proteomic profiling. By utilizing the previous published literature curated glomerular cell type-specific genes, we found that mesangial cells and their positive standard genes play a more dominant role in IgAN comparing to the podocyte standard genes. Additionally, the patient clinical parameters (serum creatinine values and estimated glomerular filtration rate - eGFR) significantly correlate with z-scores derived from expression profile of mesangial cell positive standard genes. 22 common pathways were identified both from in vivo microarray data and in vitro mesangial cell mass spectrometry data and the main part was inflammatory pathways. The correlation between clinical data and mesangial standard genes allows for a better understanding of the onset of IgAN.  The genes, proteins and their corresponding pathways identified in this paper give us novel insights into the pathophysiological mechanisms leading to progression of IgAN.

overall_design: RNA from glomerular compartment was extracted and processed for hybridization on Affymetrix microarrays.

first: P

last: Liu

first: E

last: Lassén

first: V

last: Nair

first: C

first: M

last: Katayama

last: Sihlbom

last: Kretzler

last: Betsholtz

first: B

last: Haraldsson

first: W

last: Ju

first: K

last: Ebefors

first: J

last: Nyström


title: Expression data from testes of zebra finch males artificially selected for long or short sperm

status: Public on Jul 17 2017

city: Sheffield

first: Kang-Wook

last: Kim

address: Western Bank

department: Animal and Plant Sciences

institute: The University of Sheffield

summary:
Male zebra finches of a captive population in the University of Sheffield were artificially selected for long or short sperm based on their breeding values for three generations.
We used Affymetrix microarrays to examine gene expression differences between testes of selection line male birds.

overall_design:
At third generation, males with extreme values of total sperm lengths were selected and their testes on both sides were collected for RNA extraction and hybridization on Affymetrix microarrays.
After quality control and normalization, 69 testes from 42 males were retained for further analyses.

first: Clair

last: Bennison

first: Nicola

last: Hemmings

first: Loal

last: Brookes

first: Terry

last: Burke

first: Tim

middle: R

last: Birkhead

first: Jon

last: Slate