title: Interhemispheric differences in gene expression of the cerebral cortex in humans and macaque monkeys

status: Public on Mar 29 2017

city: Barcelona

first: Gerard

last: Muntane

address: Doctor Aiguader 88

department: Biologia Evolutiva

country: Spain

institute: UPF

summary: Handedness and language are two well-studied examples of asymmetrical brain function in humans. Approximately 90% of humans exhibit a right-hand preference, and the vast majority shows left-hemisphere dominance for language function. Although genetic models of human handedness and language have been proposed, the actual gene expression differences between cerebral hemispheres in humans remain to be fully defined. In the present study, gene expression profiles were examined in both hemispheres of three cortical regions involved in handedness and language in humans and their homologues in rhesus macaques: ventrolateral prefrontal cortex, posterior superior temporal cortex (STC), and primary motor cortex. Although the overall pattern of gene expression was very similar between hemispheres in both humans and macaques, weighted gene correlation network analysis revealed gene co-expression modules associated with hemisphere, which are different among the three cortical regions examined. Notably, a receptor-enriched gene module in STC was particularly associated with hemisphere and showed different expression levels between hemispheres only in humans.

overall_design:
Rhesus macaque (Macaca mulatta) brains were dissected from frozen samples collected post-mortem from 5 different individuals. From each hemisphere, samples were dissected from the inferior ramus of the arcuate sulcus in the ventrolateral prefrontal cortex (which is homologues to area 44 of human Broca's area), the posterior superior temporal cortex (homologue of Wernicke's area), and the primary motor cortex from the forelimb control region. The macaque brains were obtained from Wisconsin National Primate Research Center (Madison, WI). All animals were housed in accordance with NIH, USDA, and AWA regulations, and overseen by the IACUCs of the respective institutions (National Research Council (US) Committee for the Update of the Guide for the Care and Use of Laboratory Animals, 2011). The time between death and tissue freezing was, in those cases for which this information was available, never longer than 6 h.
----------------------------
This represents the Rhesus data only

last: Muntané

first: Gabriel

last: Santpere

first: Andrey

last: Verendeev

first: William

middle: W

last: Seeley

first: Bob

last: Jacobs

middle: D

last: Hopkins

first: Arcadi

last: Navarro

first: Chet

middle: C

last: Sherwood


title: MicroRNA Expression in Bone Marrow-Derived Human MSCs

status: Public on Mar 24 2017

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

country: USA

institute: FDA

summary:
Six commercially available MSC lines were expanded from passage 3 to 7 and their miRNA expression was evaluated using microarray technology.
Statistical analyses of our data revealed that 71 miRNAs out of 939 examined were expressed by this set of MSC lines at all passages and the expression of 11 miRNAs were significantly different between passage 3 and 7.

sample_organism:
Homo sapiens
unidentified

overall_design: Randomized Block Design - Repeated Measures Experiment: MSCs from 8 different donors at 3 passages (passages 3, 5, & 7) with technical replicates at each passage

middle: H

first: Abhinav

last: Kumar

first: Raj

middle: K

last: Puri


title: Identification of binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028 [ChIP]

status: Public on Mar 27 2017

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip analysis of DNA specifically bound to anti-σ54 from mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type and ΔrpoN mutant cultures containing plasmid pPBHP192 expressing protein DctD250

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: DNA specifically bound to anti-σ54 was harvested from mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type (three biological replicates) and ΔrpoN mutant (two replicates) cultures that contain plasmid pPBHP192 (expressing protein DctD250). DNA was labeled and hybridized to an overlapping high density oligo array.

first: Steffen

last: Porwollik

first: Anna

last: Karls


title: Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome [H3K9me2 ChIP]

status: Public on Mar 21 2017

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary:
H3K9me2 profiles and Fft3 occupancy in fission yeast.
Heterochromatin can be epigenetically inherited in cis, leading to stable maintenance of gene expression states. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here we identify Fft3, a homolog of the mammalian SMARCAD1 Snf2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 bound to heterochromatic loci suppresses turnover of parental histones and is critical for the epigenetic transmission of heterochromatin in cycling cells. Surprisingly, Fft3 also localizes to several euchromatic loci where it is required for proper replication progression. Fft3 promotes nucleosome stability at these loci to prevent R-loop formation that can impede replication machinery. Strikingly, overexpression of the Clr4/Suv39h methyltransferase, which is also required for efficient replication through these loci, suppresses phenotypes associated with the loss of Fft3. Thus, we find that Fft3 promotes nucleosome stability to facilitate heterochromatin inheritance and also acts in parallel to Clr4 ensure proper replication of euchromatic regions.

overall_design: Whole cell extract DNA and DNA recovered from WTor fft3∆ - immunoprecipitated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract DNA) or with Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

first: Nitika

last: Taneja

first: Martin

last: Zofall

first: Vanivilasini

last: Balachandran

first: Gobi

last: Thillainadesan

first: Tomoyasu

last: Sugiyama

first: David

last: Wheeler

first: Ming

last: Zhou

middle: I


title: Serum microRNA analysis of primary ovarian cancer patients

status: Public on Mar 19 2017

city: Fukuoka

first: Kohei

last: Miyata

state: FUkuoka

address: 7-45-1 Nanakuma, Jonan-ku

department: Faculty of Medicine

country: Japan

institute: Fukuoka University

summary: To validate prediction marker of ovarian cancer patients, comprehensive analysis of serum microRNA of ovarian cancer patients were performed.

overall_design: Sera of seventeen primary ovarian cancer and five normal ovary or benign ovarian tumor patients were enrolled this study. Among these, sera of eleven patients were obtained at before and after operation.  Total RNA obtained from thirty-four sera were analyzed with SurePrint G3 Human miRNA.

first: Satoshi

last: Fukagawa

first: Fusanori

last: Yotsumoto

first: Shingo

last: Miyamoto


title: Identification of regulatory activities for σ54 (RpoN) in Salmonella Typhimurium ATCC14028 [expression]

type: Expression profiling by genome tiling array

summary: Transcriptional profiles of mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type and ΔrpoN mutant cultures containing plasmid pPBHP192 expressing protein DctD250

overall_design: Total RNA was harvested from three biological replicates of mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type and ΔrpoN mutant cultures that contain plasmid pPBHP192 (expressing protein DctD250).


title: Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome [H3-FLAG ChIP]

summary:
H3-FLAG incorporation in Schizosaccharomyces pombe
Heterochromatin can be epigenetically inherited in cis, leading to stable maintenance of gene expression states. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here we identify Fft3, a homolog of the mammalian SMARCAD1 Snf2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 bound to heterochromatic loci suppresses turnover of parental histones and is critical for the epigenetic transmission of heterochromatin in cycling cells. Surprisingly, Fft3 also localizes to several euchromatic loci where it is required for proper replication progression. Fft3 promotes nucleosome stability at these loci to prevent R-loop formation that can impede replication machinery. Strikingly, overexpression of the Clr4/Suv39h methyltransferase, which is also required for efficient replication through these loci, suppresses phenotypes associated with the loss of Fft3. Thus, we find that Fft3 promotes nucleosome stability to facilitate heterochromatin inheritance and also acts in parallel to Clr4 ensure proper replication of euchromatic regions.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  H3-FLAG in synchronous culture of fission yeast.


title: Analysis of gene expression profile in 5-fluorouracil (5-FU)-resistant human colon cancer cells

city: Seoul

first: Ho-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: We analyzed the differentially regulated genes in 5-fluorouracil-resnstant human colon cancer cells to discover novel biomarkers involved in 5-FU resistance in colorectal cancer.

overall_design:
The 5-FU resistant colorectal cancer cells were generated using HCT 116 human colon cancer cell line by treatment of cells with increasing concentrations of 5-FU more than 6 months.
The basal gene expression profile in parental and 5-FU-resistant cells were analyzed and compared.

first: Ji-Young

last: Ahn


title: TaqMan whole peripheral blood miRNA profiles of HIV-1-infected donors with different clinical characteristics

status: Public on Mar 16 2017

city: Shanghai

first: Lingyan

last: Zhu

address: 2901 Caolang Road, Jin Shan District

country: China

institute: Shanghai Public Health Clinical Center, Fudan University

summary: This study used TaqMan low-density arrays to identify and quantitate whole peripheral blood miRNAs of 23 chronically HIV-infected subjects with different clinical characteristics and sought to identify a diagnostic/prognostic miRNA signature to diagnose/predict the outcome of chronic HIV infection

overall_design: Blood samples were from 23 chronically HIV-infected subjects. Differentially expressed miRNAs were found between extreme groups of CD4+ T cell count (CD4low: CD4 < 250 VS CD4high: CD4 > 450) and of viral load (VLlow: VL<2000 VS VLhigh: VL>10000)

first: Jianqing

last: Xu

first: Chao

last: Qiu


title: Transcriptome of healthy gingival tissue in aggressive periodontitis

city: Piracicaba

first: Tiago

last: Taiete

state: São Paulo

address: Avenida Limeira 901

department: Prosthodontics and Periodontics

country: Brazil

institute: Piracicaba Dental School - University of Campinas

summary: This study evaluated the transcriptome of healthy gingival tissue in patients with a history of generalized aggressive periodontitis (GAgP) and chronic periodontitis (CP) and in subjects with no history of periodontitis (H), using microarray analysis.

overall_design: Healthy gingival tissue was taken from GAgP (n = 4), CP (n = 4) and H subjects (n = 4). Total RNA from 12 tissues samples (4 per group) was employed in microarray analysis. Data from H subjects were used as control.

first: Marcio

middle: Z

last: Casati

first: Renato

last: Casarin


title: Changes in miRNA expression during wound healing in mouse aged skin

status: Public on Mar 25 2017

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

summary: To identify the candidate miRNAs that might compromise wound healing and contribute to the age-associated delay in wound repair, global miRNA profiling was performed in mouse back telogen skin of young (8-week-old) and aged (2-year-old) animals.

overall_design: A full-thickness 3 mm wound was introduced by punch biopsy onto mouse back skin at the telogen stage of the hair cycle. Skin samples were collected on days 0, 3, 5, and 7 after wounding and were snap-frozen in liquid nitrogen.

first: Eerik

last: Aunin

first: Natalia

last: Botchkareva


title: Gene expression signatures for lumber 5 dorsal horn of spinal cord in spinal nerve ligation (SNL) mice with WTD intervention

status: Public on Mar 28 2017

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: For development of gene expression of L5 spinal tissue in SNL mice, L5 spinal nerve was first tightly ligated to construct the neuropathic pain model, and sham-operated group as a control. After chronic administrations of vehicle (distilled water, 10 mg/kg) or WTD (12.60 g/kg, p.o.), L5 spinal cord of dorsal horn were collected, and then, Agilent Whole Mouse Genome Microarray 4×44K expression profiling were employed as a discovery platform to identify genes with the potential to provide basis for the clinical application of WTD for neuropathic pain. A 579-gene consensus signature was identified that distinguished between sham and SNL samples, and a 456-gene consensus signature was identified that distinguished between WTD and SNL samples. Expression of 12 genes (Crk1, Fgf13, Fgfr1, Crk1, Adrbk1, Erbb3, Gnas, Vegfa, Crk1, Erbb3, Drd2, Gnas) were identified as the efficacy of differentially expressed genes.

overall_design: Gene expression in lumber 5 dorsal horn of spinal cord of ICR mice was measured 21 days after chronic administration of vehicle (saline, 10 ml/kg, p.o.), vehicle (saline, 10 ml/kg, p.o.) and WTD (12.60 g/kg, p.o.) in sham group, SNL group and WTD group, respectively.

first: Y

first: C

last: Wang


title: Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome

first: Shiv

last: Grewal

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

overall_design: Refer to individual Series


title: microRNA profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis.

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

summary: microRNA profiling of a cellular model of colorectal cancer progression, which is based on four defined derivates of a CRC cell line that resulted from EMT/MET transitions and phenotypically recapitulate the metastatic cascade: epithelial-like primary tumor, mesenchymal-like tumor cells growing in soft agar or as colonospheres, and mouse xenografts of the latter resulting in lung-metastasis comprised of epithelial-state cells.

overall_design: Colorectal cancer cell line DLD1 and its derivatives were maintained in McCoy`s 5A Medium (Invitrogen) containing 10% fetal bovine serum (FBS, Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin.

first: Heiko

last: Hermeking


title: Gut microbiota transplantation in conventional mice

city: Toulouse

first: Matteo

last: Serino

address: Baylac place

country: France

institute: INSERM UMR1220-IRSD

summary:
Gut microbiota dysbiosis characterizes systemic metabolic alteration, yet its causality is debated. To address this issue, we transplanted antibiotic-free conventional wild-type mice with either dysbiotic (“obese”) or eubiotic (“lean”) gut microbiota and fed them either a NC or a 72%HFD. We report that, on NC, obese gut microbiota transplantation reduces hepatic gluconeogenesis with decreased hepatic PEPCK activity, compared to non-transplanted mice. Of note, this phenotype is blunted in conventional NOD2KO mice. By contrast, lean microbiota transplantation did not affect hepatic gluconeogenesis. In addition, obese microbiota transplantation changed both gut microbiota and microbiome of recipient mice. Interestingly, hepatic gluconeogenesis, PEPCK and G6Pase activity were reduced even once mice transplanted with the obese gut microbiota were fed a 72%HFD, together with reduced fed glycaemia and adiposity compared to non-transplanted mice. Notably, changes in gut microbiota and microbiome induced by the transplantation were still detectable on 72%HFD. Finally, we report that obese gut microbiota transplantation may impact on hepatic metabolism and even prevent HFD-increased hepatic gluconeogenesis. Our findings may provide a new vision of gut microbiota dysbiosis, useful for a better understanding of the aetiology of metabolic diseases.
all livers are from NC-fed mice only.

overall_design: 6-wk-old C57Bl/6 male mice were fed a normal chow (NC) for 4 weeks. Mice have been transplanted with the vehicle (reduced PBS), or lean or obese gut microbiota. At the sacrifice by cervical dislocation, livers were dissected and snap-frozen in liquid nitrogen per each mouse.

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Aluminum stress study in wheat and wheat-rye addition lines 3R and 6R.

status: Public on Mar 17 2017

city: Winston-Salem

first: Naike

last: Salvador

state: NC

address: 1 Medical Center Blvd

institute: Wake Forest Baptist Medical Center

summary: Transcriptional profiling of three different genotypes (wheat cv Chinese Spring, and  the wheat-rye addition lines 3R and 6R) comparing control and 24h exposure to 200 μM de AlCl3. The goal was to determine the effects of AlCl3 on global gene expression in each genotype and study the differences between them.

overall_design:
Two-condition experiment (control vs aluminum exposure), for three genotypes (wheat cv Chinese Spring, wheat-rye addition line 3R, wheat-rye addition line 6R). Biological replicates: 3 control replicates, 3 aluminum exposed replicates.

Please note that the experiments have been performed technically as dual channel (eg, Cy3 and Hy5-labeled samples hybridized to the same array) but processed as though they are single channel. Therefore there are total 9 raw data files for 18 samples and the corresponding raw data file (for each samples) is indicated in the sample description field.

***Please note that the 3R and 6R  lines are called 'addition lines'. They are composed of the complete genome of Triticum aestivum + a pair of chromosomes from secale cereale (3R or 6R).****

last: Salvador Moreno


title: Comparative gene expression profiles of dental follicleand and papilla tissues at E17 and PN2

status: Public on Mar 30 2017

first: Ping

last: Dang

address: Anxiang bei li

institute: 306 hospital

summary:
The aim of this study was to determine the differences in dental follicle and papilla tissues of mouse first lower molar between E17 and PN2 at the molecular level by combinational use of laser microdissection and microarray.
Two-condition experiment

overall_design: Differentially expressed genes that either up-regulated or down-regulated by over 2-fold between E17 and PN2 group  in dental follicle and papilla tissues were compared.

first: Qinghuang

last: Tang

first: Han-Sung

last: Jung


title: Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis

city: Nantong

first: cheng

last: xiang

address: Qixiu Road NO.19

institute: Nantong University

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

summary: RNA samples were extracted from the paired rat untreated hippocampus 7 days after the FF transection. The general RNA quality was evaluated by RIN. RNA quantity and purity were assessed using K5500 micro-spectrophotometer. A260/A280 ≥1.5 and A260/A230 ≥1 indicated acceptable RNA purity, and RIN value ≥7 using the Agilent 2200 RNA assay indicated acceptable RNA integrity (Table. S1). Genomic DNA contamination was evaluated by gel electrophoresis .Three independent samples were assayed to evaluate the reproducibility of the experimental procedure. Using the microarray expression profiles, 103 (74 activated and 29 repressed) lncRNAs differentially expressed in the hippocampus after the FF transection were identified.

overall_design: The hippocampal tissue (denervated and untreated) from three paired Sprague–Dawley rats was quickly harvested on ice. For distant shipping, all the tissues were immediately frozen in liquid nitrogen. Total RNA was then extracted with TRIzol reagent following the manufacturer’s instruction. The RNA integrity number (RIN) was evaluated to judge the integrity of RNA samples using Agilent 2200 Bioanalyzer (Agilent Technologies, USA) following the manufacturer’s protocol. The purity of RNA samples was evaluated by agarose gel electrophoresis and ultraviolet spectrophotometer K5500 (Beijing Kaiao Technology Development Co., Ltd, China). Fluorescent complementary DNA (cDNA) was synthesized from about 2 µg of total RNA using an Amino Allyl MessageAmp II Kit (Life Technologies, USA). Hybridization with RiboArrayTM lncDETECTTM RAT Array 1*12K was performed following the manufacturer’s instruction (Ribo, China). After washing, the slides were scanned and analyzed with GenePix 4000B Microarray Scanner (Molecular Devices, USA). The microarray data was corrected by 50% scaling method to eliminate the system error of the experiment. Fold change was calculated by 2-Fold change=log2 (normalized intensity of treat/normalized intensity of control).

first: Cheng

last: Xiang

first: Bingying

last: Deng


title: HIV positive (n=4) and HIV negative (n=4) serum miRNA screen

city: Kensington

first: Daniel

last: Murray

state: NSW

address: The Kirby Institute, Wallace Wurth Building, UNSW Australia

department: Immunovirology and pathogenesis program

country: Australia

institute: Kirby Institute

summary: Evaluation of all human miRNAs in HIV positive and negative individuals. Used to validate RNA extraction from serum. Also used to determine which miRNAs were present in the serum of HIV+ individuals.

first: Kazuo

last: Suzuki

first: Sean

last: Emery

first: Anthony

last: Kelleher


title: A Long Noncoding RNA TTN-AS1 Controls Esophageal Squamous Cell Carcinomas by Functioning as a Competing Endogenous RNA and Scaffolding mRNA Stabilizing Protein HuR [Agilent]

city: Nanjing

first: chenyu

last: lin

address: Longmian Road No.639

department: Life science

institute: China Pharmaceutical University

summary:
BACKGROUND & AIMS: Emerging long non-coding RNAs (lncRNAs) have been demonstrated to be associated with progression of various cancers. In the current study, we identified a novel lncRNA-TTN-AS1 and dissected the underlying mechanisms by which lncRNA-TTN-AS1 induced carcinogenesis of esophageal squamous cell carcinoma (ESCC).
METHODS: ESCC and adjacent non-malignant specimens from 7 ESCC patients were chosen to analyze the expression profiles of lncRNA-miRNA-mRNA using multiple microarrays. The novel lncRNA-TTN-AS1 was identified using multiple bioinformatics platforms. Levels of lncRNA-TTN-AS1 in tissues from 148 ESCC patients were verified by qRT-PCR and in situ hybridization. The biological function and mechanism of action of lncRNA-TTN-AS1 were performed both in vivo and in vitro using gain-of and loss-of function assays on TE-13 cells and KYSE-410 cells, luciferase reporter assays, RNA immunoprecipitation (RIP) assays and RNA pull-down assays.
RESULTS: lncRNA-TTN-AS1 levels were upregulated in ESCC tissues compared with adjacent non-malignant tissues, and correlated with poor prognosis. LncRNA-TTN-AS1, as an oncogene, promoted ESCC cell proliferation and prevented apoptosis. Additionally, lncRNA-TTN-AS1 increased snail1 levels by competitively binding to miR-133b, thereby facilitating epithelial-mesenchymal transition (EMT) cascades. Sharing miR-133b binding sites, lncRNA-TTN-AS1 as a ceRNA also derepressed FSCN1 mediated by miR-133b. Notably, lncRNA-TTN-AS1 stabilized FSCN1 mRNA by interacting directly with the mRNA stabilizing protein HuR, resulting in ESCC invasion-cascades and activation of FSCN1/β-catenin.
CONCLUSION: lncRNA-TTN-AS1 sponges miR-133b to govern the expression of snial1 and FSCN1, which promotes ESCC cell proliferation and metastasis. It also combines with HuR to modulate FSCN1 in ESCC cell lines. Our findings may provide a novel target for ESCC anti-metastatic therapies.

overall_design: Using microarrays to compare expression profiles of miRNAs in ESCC tissues and adjacent normal tissues.

first: Chenyu

last: Lin

first: Shengnan

last: Zhang


title: Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome [BrdU IP]

first: Shiv

last: Grewal

summary:
BrdU profiling of replication activity in hydroxyurea treated synchronous  culture of fission yeast.
Heterochromatin can be epigenetically inherited in cis, leading to stable maintenance of gene expression states. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here we identify Fft3, a homolog of the mammalian SMARCAD1 Snf2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 bound to heterochromatic loci suppresses turnover of parental histones and is critical for the epigenetic transmission of heterochromatin in cycling cells. Surprisingly, Fft3 also localizes to several euchromatic loci where it is required for proper replication progression. Fft3 promotes nucleosome stability at these loci to prevent R-loop formation that can impede replication machinery. Strikingly, overexpression of the Clr4/Suv39h methyltransferase, which is also required for efficient replication through these loci, suppresses phenotypes associated with the loss of Fft3. Thus, we find that Fft3 promotes nucleosome stability to facilitate heterochromatin inheritance and also acts in parallel to Clr4 ensure proper replication of euchromatic regions.

overall_design: cdc25-22 cells carrying thymidine kinase and human nucleoside transporter expression modules were arrested at the G2/M boundary. After release into the cell cycle in minimal medium supplemented with hydroxyurea and 5’-bromo-2’-deoxyuridine (BrdU) cells were collected at time corresponding to maximal septation index and fixed by treatment with sodium azide. BrdU labeled DNA was recovered by immunoprecipitation, amplified by random-primed PCR and after conjugation with Cy5 (IP) or Cy3 (input DNA) analyzed on Agilent 60mer array.

first: Nitika

last: Taneja

first: Martin

last: Zofall

first: Vanivilasini

last: Balachandran

first: Gobi

last: Thillainadesan

first: Tomoyasu

last: Sugiyama

first: David

last: Wheeler

first: Ming

last: Zhou


title: Identification of regulatory activities and binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028

first: Michael

last: McClelland


title: Acutely Injured Kidneys Release Proteins into the Serum that Cause Oxidative Stress

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary:
NRK cells were exposed to serum-free, 10% FBS (control), 10% serum sampled from rats 24 hours after sham surgery (no kidney injury control), or 10% serum sampled from rats 24 hours after I/R AKI surgery (kidney injury serum). After 48 hours of exposure to serum, the NRK cells were harvested and processed for Agilent microarray
We previously conducted a Phase I Clinical Trial in which Mesenchymal Stem/Stromal Cells (MSCs) were administered to patients at risk for developing acute kidney injury (AKI), and which suggested that MSC therapy is safe and effective in preventing both postoperative AKI and progression to CKD.  It is well understood that AKI creates an internal environment that adversely affects not only the kidneys but also the function of distant organs and tissues.  To study the consequences of the AKI environment on MSCs and renal cells, we developed an in vitro assay of exposing MSCs or cultured tubular cells (NRK Cells) to serum from animals that had AKI, or SHAM surgeries.  Compared to SHAM sera, exposure of cells to AKI serum caused increased intra-cellular resazurin reduction, and activation of anti-oxidant genes,

overall_design: 12 samples, 3 biological replicates each, from four different growth conditions: serum free, fetal bovine serum, sham serum, and AKI serum.

first: Jon

last: Ahlstrom

first: Christof

last: Westenfelder


title: Salmonella enterica serovar Typhimurium gene expression in exponential and stationary phase cultures

city: Dublin

first: Shane

last: Dillon

address: Kevin Street

department: School of Biological Sciences

country: Ireland

institute: Dublin Institute of Technology

summary: Transcriptional profiling of Salmonella Typhimurium strains SL1344 in exponential and stationary phase cultures

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: The transcriptome of wild-type Salmonella Typhimurium SL1344 was determined in cultures grown in LB (Lennox broth) to exponential phase (OD 0.2) and stationary phase (OD 2.0)

first: Andrew

middle: S

last: Cameron

first: Carsten

last: Krӧger

first: Laurens

last: Beran

first: Charles

middle: J

last: Dorman


title: MiR-9-3p augments apoptosis induced by H2O2 through down regulation of Herpud1 in glioma

city: Hohhot

first: yong

middle: ping

last: mu

address: No1,Tongdao North Street

institute: Inner Mongolia Medical University

summary: MicroRNAs are short, single-stranded non-coding RNA molecules that function as regulators of tumor progression in various cancers, including glioma. The present study sought to investigate the biological functions of miR-9-3p in glioma progression. The results of a microRNA microarray indicated that microRNA-9-3p (miR-9-3p, miR-9*) is down-regulated in high-grade (grades III and IV) gliomas compared with non-tumor tissues. These results were confirmed with real-time PCR. The miR-9-3p expression level was associated with age and tumor grade. Herpud1 was regulated by miR-9-3p in glioma cells and tissues and was identified as a miR-9-3p target with luciferase reporter assays. Glioma cells transfected with miR-9-3p mimics or HERPUD1-RNAi had more apoptotic cells than them in control after induced by H2O2. Our results indicated that low expression of miR-9-3p results in a high level of Herpud1, which may protect against apoptosis in glioma.

overall_design: Total 4 samples were analyzed. Two were glioma tissues and two were controls.

first: Xiulan

last: Su


title: Gene expression analysis to identify target genes of miR-150 in Burkitt lymphma cell lines

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

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

summary: The oncogenic transcription factor MYC regulates expression of protein-coding genes, microRNAs and long non-coding RNAs. Here we show that overexpression of the MYC-repressed miR-150 severely impaired growth of Burkitt lymphoma (BL) cells. AGO2-RIP-Chip revealed two novel miR-150 targets, ZDHHC11 and ZDHHC11B, as the two most enriched genes, followed by MYB, a known miR-150 target. ZDHHC11 and ZDHHC11B encode both protein-coding and non-coding transcripts and contain a strikingly high number of miR-150 binding sites, i.e. 18 and 62, respectively. Effective targeting of ZDHHC11 and ZDHHC11B by miR-150 was confirmed by luciferase assay and for the ZDHHC11 protein by Western blot. Furthermore, we identified a circular ZDHHC11 transcript which contains the miR-150 binding site region and interacts strongly with miR-150. Knockdown of both MYB and ZDHHC11/ZDHHC11B significantly impaired growth of BL cells. Moreover, downregulation of ZDHHC11/ZDHHC11B also resulted in reduced MYB levels in BL cells. Together, our results demonstrate that elevated levels of MYB required for the high proliferative state of BL cells are ensured in two ways. First, MYC represses the tumor suppressor miR-150, which prevents its inhibitory effects on MYB expression. Second, the novel miR-150 targets ZDHHC11 and ZDHHC11B are required for maintaining high MYB levels in BL cells.

overall_design:
ST486 and DG75 BL cell lines with low endogenous miR-150 levels were transduced with either miR-150 overexpression vector or control empty vector. AGO2 RNA immunoprecipitation was performed followed by expression analysis of all known mRNAs and >15 000 lncRNAs (based on LNCipedia) to identify target genes of miR-150 in BL
Please note that Cy5 signals in raw data files represent unrelated samples; Each Cy3 sample was mixed with the same amount of a Cy5-labeled sample, which was non-relevant for this study, and hybridized at 65C overnight on Agilent-050524 SurePrint G3 Custom Human 8x60K Microarrays.

first: Klaas

last: Kok

first: Izabella

last: Slezak-Prochazka

first: Jan-Lukas

last: Robertus

first: Jesper

last: Bruining

first: Mina

middle: M

last: Tayari

first: Bea

last: Rutgers

first: Debora

last: de Jong

first: Jasper

last: Koerts

first: Berend

last: Tillema

first: Jun

last: Li

first: Jeroen

middle: E

last: Guikema

first: Ilja

last: Nolte

first: Arjan

last: Diepstra

first: Lydia

last: Visser

first: Joost

last: Kluiver

first: Anke

last: van den Berg


title: Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome [HU + BrdU IP]

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

institute: NCI

type: Genome variation profiling by genome tiling array

summary:
BrdU profiling of replication activity in synchronous  culture of fission yeast.
Heterochromatin can be epigenetically inherited in cis, leading to stable maintenance of gene expression states. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here we identify Fft3, a homolog of the mammalian SMARCAD1 Snf2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 bound to heterochromatic loci suppresses turnover of parental histones and is critical for the epigenetic transmission of heterochromatin in cycling cells. Surprisingly, Fft3 also localizes to several euchromatic loci where it is required for proper replication progression. Fft3 promotes nucleosome stability at these loci to prevent R-loop formation that can impede replication machinery. Strikingly, overexpression of the Clr4/Suv39h methyltransferase, which is also required for efficient replication through these loci, suppresses phenotypes associated with the loss of Fft3. Thus, we find that Fft3 promotes nucleosome stability to facilitate heterochromatin inheritance and also acts in parallel to Clr4 ensure proper replication of euchromatic regions.

first: Nitika

last: Taneja

first: Martin

last: Zofall

first: Vanivilasini

last: Balachandran

first: Gobi

last: Thillainadesan

first: Tomoyasu

last: Sugiyama

first: David

last: Wheeler

first: Ming

last: Zhou


title: Mesenchymal Transition in Human Mesothelial Cells In Vitro and Ex Vivo  [TGF-β1 and IL-1β treatment]

status: Public on Mar 22 2017

city: Madrid

first: Vicente

last: Ruiz-Carpio

address: Nicolás Cabrera, 1

department: Biología Celular e Inmunologia

institute: Centro de Biología Molecular "Severo Ochoa"

summary: Peritoneal dialysis (PD) is an effective form of renal replacement therapy. A significant proportion of patients who initiate PD suffer from PD-related clinical complications, including peritoneal membrane damage, which may limit the duration of treatment. Mesothelial-to-mesenchymal transition (MMT) significantly contributes to the peritoneal dysfunction related to PD. Hence, we analyzed the genetic reprograming of the MMT-process with the aim to identify new biomarkers that may be tested in PD-patients. Microarray analysis revealed a partial overlapping of MMT induced in vitro and MMT of effluent-derived mesothelial cells (ex vivo), and that MMT, both in vitro and ex vivo, is mainly a repression process being higher the number of genes that are down-regulated than those that are induced. According to cellular morphology and the number of altered genes and pathways, the MMT ex vivo could be subdivided into two stages: early/epitheliod and advanced/non-epitheliod. We could demonstrate by RT-PCR array analysis that a number of genes differentially expressed in effluent-derived non-epitheliod cells also showed significant differential expression when comparing standard versus low-GDP PD fluids. Among the secreted proteins that are up-regulated along the MMT process thrombospondin-1 (TSP1), collagen-13 (COL13), vascular endothelial growth factor A (VEGFA), and gremlin-1 (GREM1) were selected to be measured in PD effluents. TSP1, COL13 and VEGFA, but not GREM1, showed significant differences between early and advanced stages of MMT, and their expression were associated with high peritoneal transport status. The results establish a proof of concept about the feasibility of MMT-associated secreted proteins as biomarkers in PD.

overall_design: Two approach: in vitro model, with two-condition experiment, HPMC vs. HPMC treated with TGF-β1 and IL-1β; ex vivo model, with three-condition experiment, HPMC vs. Epithelioid HPMC and HPMC vs. Non-Epithelioid HPMC. Biological samples: in vitro model, two control samples and two treated cells samples; ex vivo model, 1 control sample, 8 Non-Epithelioid samples and 9 Epithelioid samples. This series contains the  HPMC vs. HPMC treated with TGF-β1 and IL-1β.

first: Manuel

last: López-Cabrera

first: Pilar

last: Sandoval

first: Pedro

last: Botías

first: Jesús

last: García-Cantalejo


title: Gene expression profiles in the liver of spontaneously hypertensive rats at different stages of hypertension

status: Public on Mar 15 2017

city: Estado de México

first: Ronquillo Sánchez

middle: Sánchez

last: María Dolores

state: Tlalnepantla

address: Av. De los Barrios No. 1, Los Reyes, Iztacala

department: Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: The objective of this study was to characterize differences in the global gene expression profiles of spontaneously hypertensive rats (SHR) and Wistar Kyoto rats (WKY) at different stages of hypertension. Using RNA isolated from liver of SHR and WKY rats, we compared the gene expression profiles by microarrays. Differential gene expression was detected in the liver of SHR rats compared to WKY control rats, possibly contributing to hypertension

overall_design: Three-condition experiment, WKY vs. SHR1 liver tissue, WKY vs. SHR3 liver tissue, SHR1 vs. SHR3 liver tissue.

first: María

last: Ronquillo

first: Jorge

last: Ramírez

first: Rafael

last: Villalobos


title: Affymetrix SNP array data for the Pacific oyster

city: Qingdao

first: Haigang

last: Qi

state: Shandong

address: 7 Nanhai Rd.

department: Key Laboratory of Experimental Marine Biology

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: The Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community.

overall_design: A total of 96 Pacific oysters were genotyped according to the manufacturer's directions to assess the performance of the oyster SNP array. All DNA were extracted from mantle tissues using a standard phenol-chloroform method.

first: Kai

last: Song

first: Chunyan

last: Li

first: Wei

last: Wang

first: Busu

first: Li

first: Guofan

last: Zhang


title: microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri

status: Public on Mar 10 2017

city: Beihai

first: Xin

last: Liao

state: Guangxi

address: 2# JinHaian Road

department: School of Life Sciences

institute: Nanjing University

summary: Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to Lipopolysaccharide (LPS). First, we determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of TLR4 and NF-κb(v-rel) which were commonly used immune response indicators. Then we performed miRNA microarray analysis on gill samples collected at the time point to select the differentially expressed miRNAs. Finally, we used real-time quantitative PCR to detect the expression patterns of amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the most upregulated and most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.

overall_design:
Fifteen microliters of LPS in PBS suspension (1 mg/ml) were injected into the cavum of amphioxus, and the same dosage of PBS was injected as the negative control. After that, the injected amphioxuses were cultured at 25 °C and were separately collected at different time points after injection (i.e. 2, 6, 12, 24, 48, and 72h). The gills were rapidly removed and frozen by liquid nitrogen for RNA extraction.
The 12h timepoint is represented in this Series.

first: Junyuan

last: Chen


title: Long Noncoding RNA and mRNA Expression Profile in clear cell renal cell carcinoma

city: Guangzhou

first: Zheng

last: Zaosong

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Five matched clear cell renal cell carcinoma and normal tissues were used for microarray.

overall_design: lnRNA and mRNA expression profile in 5 pairs of clear cell renal cell carcinoma tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays

first: Zaosong

last: Zheng

first: Fengjin

last: Zhao

first: Wenlian

last: Xie


title: Transcriptional Response of Mycobacterium tuberculosis to Arabinomannan-specific Immune Sera

status: Public on Mar 09 2017

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv exposed to immune sera from C57/BL6 mice immunized with a conjugate of Bacillus anthracis protective antigen and arabinomannan vs. protective antigen alone

overall_design: Two condition experiment, arabinomannan-PA conjugate immune sera exposed vs. PA alone sera exposed. Biological replicates: 3 of each condition, independently exposed and harvested. One replicate per array, third array is a dye-flip.

last: Prados-Rosales


title: Microarray profiling and co-expression network analysis of lncRNAs and mRNAs associated with acute leukemia in adult

status: Public on Mar 14 2017

city: Shanghai

first: Hui

last: Cheng

address: 168 Changhai Road

institute: Changhai Hospital, Second Military Medical University

type: Expression profiling by high throughput sequencing

summary: To understand the distinct mechanisms in leukemogenesis between ALL and AML and to identify markers for diagnosis and treatment, lncRNA and mRNA expression profiles of AML and ALL patients and healthy controls were generated by using microarray analysis

overall_design: Differentially expressed mRNAs and lncRNAs in 12 leukemic (6 AML patient samples and 6 ALL patient samples) and 6 normal bone marrow-derived mononuclear cells (BM-MNCs) controls were measured


title: Expression analysis of chicken chorioretinal tissues in control and myopic eyes with or without violet light

status: Public on Mar 08 2017

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: To find the possible molecular mechanism of myopia protection by violet light, we performed expression microarray analysis of chick chorioretinal tissue. The mRNA were obtained at day 13 from the following four groups: control eyes with or without violet light exposure and covered eyes with or without violet light exposure, and then the gene expression pattern was compared among them. Principle component analysis, which is to find major patterns of variability in gene expression, was performed and we found that the largest gene population (PC1, positive: n = 138, negative: n = 292) was affected by violet light treatment. On the other hand, the second largest gene population (PC2, positive: n = 120, negative: n = 23) was affected in the eyes covered with a plastic lens. The previously reported myopia-related genes such as Bmp2, Ednrb, Fgf2, Igf1, Il18, Irbp, Lumican, Sfrp1, Tgfb1, Vegfa, Vip, and Wnt2b were not found in the PC1 group in vivo, which indicates that they responded less to violet light. In the PC1 group, only one myopia protective gene, EGR1 (ZENK, zif268), was found among the previously reported myopia related genes.

overall_design: Sixteen eyeballs of eight chicks from the two experiment groups were divided into four subgroups: violet-/control, violet+/control, violet-/covered, violet+/covered. Total RNA of the four eyeballs in each subgroup were extracted and mixed. Total RNA was analyzed using Chicken (V2 026441) Gene Expression Microarray 4 x 44K (Agilent 153 Technologies, California, USA).

first: Hidemasa

last: Torii

first: Toshihide

last: Kurihara

first: Yuko

last: Seko

first: Kazuno

last: Negishi

first: Kazuhiko

last: Ohnuma

first: Takaaki

last: Inaba

first: Motoko

last: Kawashima

first: Xiaoyan

last: Jiang

first: Shinichiro

last: Kondo

first: Maki

last: Miyauchi

first: Yukihiro

last: Miwa

first: Yusaku

last: Katada

first: Keiichi

last: Kato

first: Kinya

last: Tsubota

first: Hiroshi

last: Goto

first: Megumi

last: Hatori

first: Kazuo


title: Real-time quantitative PCR analysis of human plasma miRNA from rheumatoid arthritis patients with or without interstitial lung disease

city: Tsukuba

last: Furukawa

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: RNA was isolated from 200μl plasma samples and cDNA was synthesized. Real-time RT-PCR analysis was performed to evaluate miRNA expression in the plasma pool from 17 RA patients with RA-ILD or the plasma pool from 17 RA patients without ILD using Human miRNome microRNA PCR Panel I+II (Exiqon).

overall_design: qPCR miRNA expression profiling. Plasma samples from 17 donors were used in control and test.

first: Shomi

last: Oka


title: Transcriptomic analysis of H. perforatum L. pistils for the identification of genes related to aposporous apomixis.

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

country: Italy

institute: University of Verona

summary: Apomixis defines a number of reproductive strategies, which, unlike sexual reproduction, permit the inheritance of the maternal genome over generations without genetic recombination events. The key biological features of apomixis are the failure of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and eggs, and their autonomous development in functional embryos through parthenogenesis and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell (Koltunow and Grossniklaus 2003). Recently gained biological information has shown that H. perforatum is an attractive model system for the study of a naturally occurring form of asexual reproduction called aposporous apomixis, This research describes a global gene expression analysis of H. perforatum ovaries collected from sexual and aposporous plant accessions for the purpose of identifying genes and processes potentially associated with aposporous apomixis in this model species.

overall_design: Pistils were collected from three sexual and three apomictic plants at developmental points corresponding to the Arabidopsis flower stages 10 and 14. Pistils were collected and immediately frozen in liquid nitrogen. To minimize biological variation 15 pistils were collected from each plant.

first: Giulio

last: Galla

first: Alice

last: Patella

first: Sara

last: Zenoni

first: Linda

last: Avesani

first: Lothar

last: Altschmied

first: Tim

last: Sharbel

first: Gianni

last: Barcaccia


title: Hyaluronic acid synthesis is required for zebrafish tail fin regeneration

city: Stanford

first: James

last: Chen

address: 269 W. Campus Drive, CCSR 3150

department: Chemical and Systems Biology

institute: Stanford University

summary: Using genome-wide transcriptional profiling and whole-mount expression analyses of zebrafish larvae, we have identified hyaluronan synthase 3 (has3) as an upregulated gene during caudal fin regeneration. has3 expression is induced in the wound epithelium within hours after tail amputation, and its onset and maintenance requires fibroblast growth factor, phosphoinositide 3-kinase, and transforming growth factor-β signaling. Inhibition of hyaluronic acid (HA) synthesis by the small molecule 4-methylumbelliferone (4-MU) impaired tail regeneration in zebrafish larvae by preventing injury-induced cell proliferation. In addition, 4-MU reduced the expression of genes associated with wound epithelium and blastema function. Treatment with the glycogen synthase 3-kinase inhibitors rescued 4-MU-induced defects in cell proliferation and tail regeneration, even though only a subset of wound epithelium and blastema markers was restored. Our findings uncover a role for HA biosynthesis in zebrafish tail regeneration and its epistatic relationships with other regenerative processes.

overall_design: Zebrafish embryos were raised until 2 days post-fertilization (dpf) and their caudal tail fins were amputated just posterior to the notochord.  Uncut larvae and larvae amputated at 2 dpf were then raised for an additional day (1 day post-amputation, dpa) and posterior tissues were again amputated but then collected on ice.  Total RNA was extracted from the posterior tissues and genomic DNA was removed. Approximately 1 ug of total RNA was isolated from 150 tails per each condition and two rounds of amplification was performed using the MessageAmp II aRNA Kit.  cDNA synthesis and labeling, hybridization to the NimbleGen Zebrafish Gene Expression 385K array, microarray scanning, and data compilation were performed at the Stanford Functional Genomics Center, according to guidelines established by Roche NimbleGen.  Subsequent analysis was performed using DNASTAR ArrayStar software.

first: Xiaohu

last: Ouyang

first: Nicholas

last: Panetta


title: Dissecting the biochemical and transcriptomic effects of locally applied heat stress on developing Cabernet Sauvignon grape berries

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary:
Studying the effect of varying durations (1, 7 and 14 days) of locally applied heat stress on grape berries at three developmental stages (middle green, veraison and middle ripening).
Among various environmental factors, temperature is a major regulator affecting plant growth, development and fruit composition. Reproductive development of grapevine and berry composition, are both highly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries tolerance to high temperatures (HS) are poorly understood. Although recent data addressed the consequences on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat stress. In the context of climate change, this work focused on microclimate effect is of particular interest to better understand the consequences of leaf removal (a common viticultural practice) on berry development. HS (+ 8°C) was locally applied to clusters from Cabernet Sauvignon fruiting cuttings at three different developmental stages (middle green, véraison and middle ripening). Samples were collected 1, 7 and 14 days after treatment and used for metabolic and transcriptomic analyses. The results showed dramatic and specific biochemical and transcriptomic changes in heat exposed berries, depending on the developmental stage and the stress duration. When applied at the herbaceous stage, HS delayed the onset of véraison. Heating also strongly altered the berry concentration of amino acids and organic acids (e.g. PHE, GABA, and malate) and decreased the anthocyanin content at maturity. These physiological alterations could be partly explained by the deep remodelling of transcriptome in heated berries. More than 7000 genes were deregulated in at least one of the nine experimental conditions. The most affected processes belong to the categories “stress responses”, “protein metabolism” and “secondary metabolisms”, highlighting the intrinsic capacity of grape berries to perceive heat stress and to build adaptive responses. Additionally, important changes in processes related to “transport”, “hormone” and “transcription” might contribute to the postponing of véraison. Finally, opposite effects depending on heating duration were observed for genes encoding enzymes of the general phenylpropanoid pathway, suggesting that the HS-induced decrease in anthocyanin content may result from a combination of transcript abundance and product degradation.

overall_design: 54 samples; three developmental stages; heat stress and control for 3 timepoints at each stage; 3 replicates per sample.

first: Fatma

last: Lecourieux

first: Philippe

last: Pieri

first: Justine

last: Charon

first: Jérémy

last: Pillet

first: Ghislaine

last: Hilbert

first: Christelle

last: Renaud

first: Erice

last: Gomès

first: Serge

last: Delrot

first: David


title: Estrogen-like activity in cell signaling of lignans

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

summary: Comparing the expression profiles of the genes in response to 17b-estradiol (E2) and lignans (sesamin (SE), enterodiol (ED), enterolactone (EL), matairesinol (MR), pinoresinol (PR)).

overall_design: Two-condition experiment, E2- or each lignan-treated vs. control cells. Three biological replicates, independently grown and harvested. Three replicates per array.

first: Yun

last: Zhu

first: Ryoiti

last: Kiyama


title: miRNA profiling in relapsed or metastatic HNSCC patients treated with cetuximab and platinum therapy

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: By gene expression profiling (GEP) of head and neck squamous cell carcinomas (HNSCC) we were able to identify candidate biomarkers of progression free survival (PFS) in patients treated with cetuximab-based approaches (Bossi et al, Clinical Cancer Research 2016) . Here, the same samples were used for miRNA expression profiling.  Integration of miRNA and gene expression data highlighted 16 miRNAs and 84 genes interconnected in a total of 245 interactions.   After feature selection by smoothed t-statistic support vector machine, we identified a network 3 miRNAs and 5 genes that resulted the most relevant in predicting PFS (AUC=0.992). Overall, using a well defined clinical setting we gave the proof of principle that an integrative miRNA-mRNA expression could greatly contribute to refinement of the biology behind and to the potential identification of a predictive model.

overall_design: Forty tumor specimens from recurrent/metastatic (RM) HNSCC patients were divided according to PFS following cetuximab-CT treatment in long- (14 patients) and short-PFS (26 patients) as detailed in (Bossi, 2016). Briefly, the study design includes two groups balanced for known prognostic factors (Argiris, 2004) (primary tumor site, performance status, weight loss, prior radiotherapy, tumor grade, residual disease at primary tumor site, age, and gender). Long-PFS had a median PFS of 19 months (range 12–36), while short-PFS had a median PFS of 3 months (range 1–5.5).


title: Functional characterization of a WRKY transcription factor involved in the regulation of vacuolar transport and flavonoid biosynthesis in grapevine

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

summary: The WRKY family represents a plant-specific class of zinc-finger transcription factors (TF) well known for regulating abiotic and biotic stress tolerance and also for their emergent role in the control of various developmental and physiological processes (Rushton et al. 2010, Schluttenhofer et al. 2015).   The well-characterized AtTTG2, PhPH3 and BnTTG2 are ortholog WRKY proteins with interchangeable functions ascribed to an emergent clade whose regulatory functions are mainly associated with vacuolar metabolism (Li et al. 2015, Verweij et al. 2016, Gonzalez et al. 2016). In particular, PH3 of Petunia hybrida and TTG2 of Arabidopsis thaliana both act in the control of vacuolar pH and trafficking influencing the deposition of secondary metabolites in the petal epidermal cells and in the seed coat, respectively (Verweij et al. 2016, Gonzalez et al. 2016).    In this study we functional characterized VvWRKY26 identified as the closest grapevine homolog of PhPH3 and AtTTG2 (Wang et al. 2014; Verweij et al. 2016). VvWRKY26 can fulfil the PH3 function in the regulation of vacuolar pH and impact many aspects of transport when constitutively expressed in petunia ph3 mutant. By a global correlation analysis of gene expression and by transient over-expression in Vitis vinifera cv. Sultana, we showed transcriptomic relationships of VvWRKY26 with many genes related to acidification and trafficking in grapevine. Moreover, our results indicate an involvement in flavonoid pathway mainly in the control in PA biosynthesis in grapevine that is supported by its expression profile. Overall, with the identification of VvWRKY26 our studies might pave the way towards the comprehension of regulatory mechanism underlying the acidification that contributes to the final berry quality traits.

overall_design: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvWRKY26 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with a pK7WG2.0 vector containing a non-coding sequence. Six in vitro five weeks old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa). After agroinfiltration, plantlets were rinsed with sterile water and allowed to recover in vitro for six days before collecting material for RNA extraction and transcriptomic analysis

first: Erika

last: Cavallini

first: Laura

last: Finezzo

first: Maura

last: Begheldo

first: Benedetto

last: Ruperti

first: Sara

last: Zenoni

first: Giovanni

middle: B

last: Tornielli


title: Effect of copper (II) chloride treatment on rice leaves

city: Utsunomiya

first: Koji

last: Miyamoto

state: Tochigi

address: 1-1 Toyosatodai

department: Department of Biosciences

institute: Teikyo University

summary: Analysis of leaves of wild-type and jasmonate (JA)-deficeint mutant cpm2 treated with CuCl2. Results provide the role of JA on defence responses after copper chloride treatment.

overall_design: Expression profiling in wild-type and cpm2 leaves treated with or without 1 mM copper (II) chloride was analyzed using one-color method with three biological replicates.

first: Satoshi

last: Ogawa

first: Kazunori

last: Okada

first: Hisakazu

last: Yamane


title: Expression data from starved first larval stage of wildtype and hyl-1(ok976); lagr-1(gk327) C. elegans

status: Public on Mar 07 2017

city: Boulder

first: Mingxue

last: Cui

address: Colorado Ave.

department: MDCB

institute: HHMI, University of Colorado at Boulder

summary: Our understanding of cellular mechanisms by which animals regulate their response to starvation is limited despite the close relevance of the problem to major human health issues.  L1 diapause of Caenorhabditis elegans, where newly hatched first stage larval arrested in response to food-less environment, is an excellent system to study the problem.  We found through genetic manipulation and lipid analysis that ceramide biosynthesis, particularly those with longer fatty acid side chains, critically impacts animal survival during L1 diapause. Genetic and expression analyses indicate that ceramide likely regulate this response by affecting gene expression and activity in multiple regulatory pathways known to regulate starvation-induced stress, including the insulin-IGF-1 signaling (IIS) pathway, Rb and other pathways that mediate pathogen/toxin/oxidative stress responses. These findings provide an important insight into the roles of sphingolipid metabolism in not only starvation response but also aging and food-response related human health problems.

overall_design: Gravid C. elegans adult animals were bleached with hypochlorite and sodium hydroxide. The resulting eggs were hatched in 8–10 mL S-basal without cholesterol in 15-mL conical tubes, which were placed on an end-over-end rocker (VWR) at 20 °C. 30 hours later, starved L1s were collected for RNA preparations. Wild type and  hyl-1(ok976); lagr-1(gk327) mutant were profiled in triplicate. All replicates were biological replicates.

first: Min

last: Han

first: Yudong

last: Teng


title: Confirmation of the OVOL2 Promoter Mutation c.-307T>C in Posterior Polymorphous Corneal Dystrophy 1

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary:
Purpose: To identify the genetic basis of posterior polymorphous corneal dystrophy (PPCD) in families mapped to the PPCD1 locus and in affected individuals without ZEB1 coding region mutations.
Methods: The promoter and/or coding regions of OVOL2 were screened in the PPCD family in which linkage analysis established the PPCD1 locus and in 26 PPCD probands who did not harbor a ZEB1 mutation. Copy number variation (CNV) analysis in the PPCD1 and PPCD3 intervals was performed on DNA samples from eight probands using aCGH. Luciferase reporter assays were performed in human corneal endothelial cells to determine the impact of the identified potentially pathogenic variants on OVOL2 promoter activity.
Results: OVOL2 screening in the first PPCD1-linked family demonstrated segregation of the c.-307T>C variant with the affected phenotype. In the other 26 probands screened, one heterozygous coding region variant and five promoter region heterozygous variants were identified, though none are likely pathogenic based on allele frequency. Array CGH in the PPCD1 and PPCD3 loci excluded the presence of CNV involving either OVOL2 or ZEB1, respectively. The c.-307T>C variant demonstrated increased promoter activity when compared to the wild-type sequence.
Conclusions: The previously identified and presumed pathogenic OVOL2 promoter variant c.-307T>C was identified in the PPCD family that established the PPCD1 locus. However, the failure to identify presumed pathogenic coding or non-coding OVOL2 or ZEB1 variants, or CNV involving the PPCD1 and PPCD3 loci in 26 other PPCD probands suggests that other genetic loci may be involved in the pathogenesis of PPCD.

overall_design: Eight PPCD probands without a ZEB1 protein-coding region pathogenic variant were analyzed for copy number variation within the PPCD1 (chromosome 20) and the PPCD3 (chromosome 10) loci.

first: Doug

last: Chung

first: Ricardo

middle: F

last: Frausto


title: Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae (ChIP-chip)

first: Andrew

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

summary: Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified S. cerevisiae Fkh1 and Fkh2 as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homo-dimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.

overall_design: 6 total ChIP-chip experiments were analyzed in triplicate.

first: A

first: Reza

last: Kalhor

first: Yan

last: Gan

first: Sanda

last: Villwock

first: Linke

last: Christian

first: Barberis

last: Matteo

first: Lin

last: Chen

first: Oscar

last: Aparicio


title: Adult Female Rat Hippocampal Tissue: Naïve vs. Contextual Fear Conditioned (Trained)[Experiment 1]

city: Boston

first: Danesh

last: Moazed

state: Massachusetts

address: 240 Longwood Ave

department: Cell Biology

institute: Harvard Medical School

summary: naïve and trained rats 24 hours after exposure to the contextual fear conditioning paradigm. Biological replicates: 3 independent pools of 3 animals each, 6 naïve and 6 trained animals, independently conditioned and tissues were independently isolated. One replicate per array.

overall_design: Two-condition experiment, Naïve vs. Trained tissue. Biological replicates: 6 naïve, 6 trained, in two separate pools, independently trained and isoalted. One replicate per array.

first: Rebecca

last: Mathew

first: Antonis

last: Tatarakis

first: Andrii

last: Rudenko

first: Erin

last: Johnson-Venkatesh

first: Yawei

last: Yang

first: Elisabeth

middle: A

last: Murphy

first: Travis

middle: P

last: Todd

first: Scott

last: Schepers

first: Nertila

last: Siuti

last: Martorell

first: William

last: Falls

first: Sayamwong

last: Hammack

first: Christopher

last: Walsh

first: Li-Huei

last: Tsai

first: Hisashi

last: Umemori

first: Mark

last: Bouton


title: Adult Female Rat Hippocampal Tissue: Naïve vs. Contextual Fear Conditioned (Trained)[Experiment 2]

last: Moazed

summary: naïve and trained rats 24 hours after exposure to the contextual fear conditioning paradigm. Biological replicates: 4 naïve and 4 trained animals, independently conditioned and tissues were independently isolated. One replicate per array.

overall_design: Two-condition experiment, Naïve vs. Trained tissue. Biological replicates: 4 naïve, 4 trained, independently trained and isoalted. One replicate per array.

first: Anthony

first: Li-Heui


title: Thrombin-reduced miR-27b attenuates platelet angiogenic activities via enhancing platelet de novo synthesis of anti-angiogenic thrombospondin-1

city: Stockholm

first: Xinyan

last: Miao

address: Karolinska University Hospital-Solna

department: Medicine

country: Sweden

institute: Karolinska Institutet

summary: To identify if platelet activation would result in altered platelet miRNA profile, not only in total RNA sample, also in AGO2-immunoprecipitation(AGO2-IP) products. To determinate if altered platelet miRNAs could regulate de novo protein synthesis of angiogenic factors in activated platelets, and even more importantly, if miRNA-regulated platelet angiogenic factor synthesis could result in changes of platelet angiogenic activities.

overall_design: Platelets samples stimulated with thrombin or vehicle, and followed by AGO2-immunoprecipitation (AGO2-IP) or total RNA extraction. Then, we performed miRNA expression profiling using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis. To validate the results of SAM, the expression levels of selected miRNAs were evaluated using qRT-PCR.


title: Transcriptional profiling of SIV-specific CXCR5+ and CXCR5- CD8+ lymphocytes in rhesus macaques infected with SIVmac251 and SIVE660

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: CD8+ T-cells inhibit virus replication in SIV-infected rhesus macaques (RM). However, it is not clear how SIV infection is controlled in germinal center during chronic SIV infection and limited information exists on the characteristics of CXCR5+ CD8 T cells during chronic SIV/HIV infection. In this study, we used functional genomics to investigate characteristic features and potential mechanisms of CXCR5+ and CXCR5- SIV specific CD8 T cells for the control of pathogenic SIV infection.  Six chronically SIV infected RMs, three SIVE660 infected and three SIV mac251 infected that are positive for Mamu A01 allele were selected and SIV-specific CXCR5+ and CXCR5- CD8 T cells were sorted  based on CXCR5 expression. RNA from sorted cells were extracted and microarray were performed and analysed. Principal component analysis demonstrated that overall gene expression difference between CXCR5+ and CXCR5- SIV-specific CD8 T cells. Interestingly, the CXCR5+ CD8 T cells revealed a distinct gene signature pattern when compared to CXCR5- CD8 T cells. Unlike the CXCR5- CD8 T cells, the CXCR5+ CD8 T cells expressed higher levels of genes associated with Tfh CD4 T cells such as the master transcription factor Bcl6, CD200, and CTLA4 as well as markers associated with Th2 CD4 T cells such as IL-4R (CD124), CCR4, STAT6, NFATC, and IL-10. Effector molecules typically observed in cytotoxic CD8 T cells such as granzyme A, B, and K were expressed at lower levels on CXCR5+ CD8 T cells compared to their CXCR5- counterparts. CXCR5+ CD8 T cells also expressed higher levels of molecules associated with co-stimulation/antigen presentation such as CD40, CD83, 41BBL and MAMU-DRA. The CXCR5+ CD8 also expressed higher levels of inhibitory receptors such as CD200 and SPRY2 but lower levels of other inhibitory receptors CD160 and CD244. The functional consequence of the expression of these molecules is yet to be determined. Additionally, CXCR5+ CD8 T cells expressed higher levels of the anti-apoptotic gene Bcl-2 and lower levels of the pro-apoptotic gene annexin, suggestive of their better survival potential during chronic SIV infection. Collectively, these results demonstrate that SIV specific CXCR5+ CD8 T cells possess a unique gene expression signature compared to SIV-specific CXCR5- CD8 T cells.

overall_design: A total of 12 RNA samples were hybridized on to Rhesus Affymetrix 3' Expression arrays. The study was composed of 6 replicate rhesus macaques subjected to SIVmac251or SIVE660 infection. Samples were taken at various time points during acute and chronic infection (week 24), after CD8+ cell depletion, after CD8+ cell reconstition, and during ART suppression of virus.

first: Geetha

last: Mylvaganam

first: Steven

last: Bosinger

first: Vijayakumar

last: Velu

first: Rama

middle: R

last: Amara


title: MiR-218 regulates heroin seeking behavior by targeting Mecp2

first: Qiumin

last: Le

address: 130 Dong'an Road

institute: Fudan University

summary: Noncoding RNAs, especially microRNAs (miRNAs) have been implicated in the regulation of neuronal functions, such as learning, cognition and memory formation. However, the particular miRNAs involved in drug-induced behavioral plasticity are largely unknown. Here we report a novel regulator, miR-218, that inhibits heroin-induced behavioral plasticity. Network propagation-based method revealed several miRNAs that play key roles in drug-addiction, among which, miR-218 was decreased in nucleus accumbens (NAc) after chronic exposure to heroin. Lentiviral overexpression of miR-218 in NAc could inhibit heroin-induced reinforcement in both conditioning place preference (CPP) test and heroin self-administration (SA) experiment. Luciferase activity assay indicated miR-218 could regulate neuroplasticity related genes and directly target Mecp2 3’UTR. Consistently, Mecp2-/y mice exhibited reduced heroin seeking behavior in CPP test. These data reveal a functional role of miR-218 and its target, Mecp2, in the regulation of heroin-induced behavioral plasticity.

overall_design: Microarray screening was carried out to identify miRNAs responsive to chronic administration of heroin. Arrays used were miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno.

first: Biao

last: Yan


title: Direct mouse fibroblasts toward Leydig-like cells by defined factors

city: guangdong

first: yan

last: yang

address: guangzhou

institute: JiNan university

summary:
Transcriptional profiling of mouse embryonic fibroblasts (MEFs) induced by Dmrt1, Gata4, Nr5a1 transduction, named induced Leydig-like cells (iLCs), comparing control untreated MEFs and mouse adult Leydig cells. Goal was to understand the global transcriptional changes induced by DGN transduction.
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

overall_design: Two-condition experiment,  iLCs vs. MEFs, iLCs vs. Leydig cells.

first: Yadong

last: Huang

first: Zhijian

last: Su


title: Functional characterization of a WRKY transcription factor involved in the regulation of vacuolar transport and flavonoid biosynthesis in petunia

first: Alessandra

last: Amato

overall_design: For stable transformation of Petunia hybrida, the35S:VvWRKY26 construct was inserted into Agrobacterium tumefaciens strain EHA105 by electroporation. Petunia hybrida plants were transformed using the leaf disc method and regenerated transgenic shoots were transferred to soil and hardened off in a temperature-controlled glasshouse.

first: Erika

last: Cavallini

first: Laura

last: Finezzo

first: Maura

last: Begheldo

first: Benedetto

last: Ruperti

first: Sara

last: Zenoni

first: Giovanni

last: Tornielli


title: Oncoscan™ Affymetrix array for pure LCIS, LCIS associated with ILC (invLCIS) and ILC

city: London

first: Salpie

last: Nowinski

address: 3rd Floor Bermondsey Wing, Guy's Hospital

department: Cancer Studies

country: United Kingdom

institute: King's College London

summary: Oncoscan™ Affymetrix array was performed by Affymetrix using DNA extracted from macrodissected FFPE samples

overall_design: Copy number analysis was performed on 30 pure LCIS, 30 invLCIS and paired ILC

first: Elinor

last: Sawyer


title: LncRNA and mRNA Expression in aortic smooth muscle cells with Srf knockout or Myocd over-expression

city: Augusta

first: Xiaochun

last: Long

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

summary: LncRNA and mRNA expression profiles in aortic smooth muscle cells with Srf knockout or Myocd over-expression were analyzed by Arraystar Mouse LncRNA Microarray V3.0.

overall_design: Total RNA samples were extracted from aortic smooth muscle cells with Srf knockout or Myocd over-expression. The LncRNA and mRNA expression profiling was performed using Arraystar Mouse LncRNA microarrays V3.0.


title: Therapeutic targeting of the bent conformation of integrin αvβ8 for fibroinflammatory airway disease

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: fetal tracheal fibroblasts were treated with anti-B8, anti-TCF-B or IgG control, all pairwise comaprisons were made. N=3 for each group

overall_design: This is a 2 color design; dye swaps and a loop design were incorporated.

first: Stephen

last: Nishumura


title: LHRH Receptor Monoclonal Antibody 4F3B10 Induces Apoptosis of HeLa Cells

status: Public on Mar 06 2017

city: Beijing

first: Pei

middle: pei

last: zhang

address: North Yongtaizhuang Road, Haidian District, Beijing, 100192, China.

institute: Beijing TransGen Biotech Company

summary: In this study, based on microarray hybridization and the detections of RTqPCR and Western Blotting, we have shown that HeLa cells treated with LHRH receptor monoclonal antibody 4F3B10 increased protein expressions in Fas signaling pathway, which provided a novel route for the gene therapy of HeLa cells.

overall_design: The effects of antagonist 4F3B10 on HeLa cell proliferation, cell cycle and apoptosis were detected by CCK-8 assay and flow cytometry. Gene expression profiles were utilized to screen the differentially expressed genes in HeLa cells with the effects of antagonist 4F3B10 vs. the control, and analyze the relation among the differentially expressed genes by bioinformatics analysis.

first: Guoli

last: Zhang

first: Peipei

first: Xin

last: Deng


title: Identification of MKK3-dependent wounding-induced genes

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra16-01_mkk3_wounding - identification of mkk3-dependent wounding-induced genes - Is MKK3 involved in the transcriptional regulation of wounding-induced genes? - Col and mkk3 KO plants were wounded with a forceps. Leaves were harvested 2h after the stress.

overall_design: 12 dye-swap - gene knock out, genotype comparison, normal vs transgenic comparison, treated vs untreated comparison

first: Jean

last: Colcombet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Tamoxifen-associated endometrial tumors expose differential enhancer activity for Estrogen Receptor alpha [Microarray Expression]

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Tamoxifen, a small molecule inhibitor that binds the Estrogen Receptor alpha (ERα), blocks breast cancer progression while increasing the risk for endometrial cancer. In this study, we assessed genome-wide ERα-chromatin interactions in surgical specimens of endometrial tumors from patients who were previously treated for breast cancer with tamoxifen, and endometrial tumors from patients who were treated without tamoxifen. We compared ERα and signal at differential ERα sites in endometrial tumors of nine patients who received tamoxifen with endometrial tumors with six patients who never used tamoxifen. In addition, we performed H3K27ac (a marker for activity) ChIPs on the above mentioned endometrial tumors, and assed this signal at differential ERα sites. Compared to endometrial tumors of non-users, tamoxifen-associated endometrial tumors exposed higher H3K27ac intensities at ERα sites that are enriched in tamoxifen-associated endometrial tumors. Four tamoxifen-associated endometrial tumors that we used in our analysis have been previously published as Tumor A, B, D, and E in GSE81213.

overall_design: Gene expression profiling in 111 endometrial tumors

first: Marjolein

last: Droog

first: Ekaterina

last: Nevedomskaya


title: Genetic Analysis of Local Pig Populations in Ghana

city: Cambridge

first: Carole

middle: Anne

last: Sargent

state: Cambs

address: Tennis Court Road

department: Pathology

institute: University of Cambridge

summary: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R and Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed that the ADP of Ghana has both European and Asian genetic signatures. The ADP also displays considerable variation in the MC1R gene. Black coat colour is the most predominant within the breed, with the dominant black alleles of both Asian and European origin contributing to the majority of alleles in the pool. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. Other colour variants may be due to epistatic interactions with additional coat colour loci, or mutations. The wide variations in coat colour patterns suggest that morphology alone cannot be used to adequately characterise Ghanaian local pigs. PCA analysis of SNP genotyping data revealed a strong location effect on clustering of local Ghanaian pigs. Based on this work, we recommend that further studies be carried out on more local pigs to find out the effect of admixture on important adaptive and economic traits of the ADP and other local Sus breeds in Africa to help develop a sustainable conservation programmes to prevent the decline of this genetic resource.

overall_design: 71 independent samples, with one sample replicated. The samples included DNA from 5 animals imported from Europe (European commercial breed background), 20 local animals with known mixed ancestry, and 46 animals classified as local Ashanti Dwarf Pigs. The animals were sampled from six different agro-ecological zones. Animals were selected from different local farms in each area sampled.

first: Richard

last: Osei-Amponsah

first: O

middle: D

last: Adjei

first: Benjamin

last: Skinner

first: Julien

last: Bauer

first: Greger

last: Larson

first: Nabeel

last: Affara


title: Analysis of Gene Expression in Medulloblastoma

status: Public on Mar 04 2017

city: Ribeirao Preto

first: Aparecida

middle: Maria

last: Fontes

state: SP

address: Av. Bandeirantes, 3900

department: Medical School Ribeirao Preto - Genetics Department

institute: University of Sao Paulo

summary: The objective is to investigate epigenetic markers in medulloblastoma

overall_design: 5 medulloblastoma tissues; 4 medulloblastoma cell lines; 3 cerebellum control tissues and 3 primary cell culture of cerebellum

first: Ricardo

last: Silva

first: Daniel

middle: G

last: Pinheiro

first: Kuruvilla

last: Abraham

first: Hélio

last: Machado

first: Fernando

last: Ramalho

first: Daniela

last: Tirapelli

first: Carlos

last: Carlotti Jr

first: Zila

middle: L

last: Simoes

first: Cláudia

last: Wiezel

first: Aguinaldo

first: Dimas

middle: T

last: Covas


title: Using the Bovine SNP60k array to discover de novo copy number variations in aging bulls and fibroblasts

status: Public on Mar 03 2017

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

country: Canada

institute: University of Guelph

summary: We have identified de novo copy number variations (CNVs) generated in ageing bulls. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 vs. 111 or 49% vs. 51%, respectively). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent, as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 vs. 64). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.

overall_design: One array (24 samples) ran with 3 samples collected over 30 months from 8 bulls to investigate in vivo aging, another array ran 3 samples collected from Passage 5, 15 and 25 from 3 bovine fibroblast cultures.

first: Olutobi

last: Oluwole

first: Tom

last: Kroetsch

first: Allan

middle: W

last: King


title: miRNA expression profiling in the exosomes derived from human suspended red blood cell unit with leukocyte reduced

city: fuzhou

first: liping

last: fan

state: fujian

address: xinquan road NO.29 gulou district

department: blood transfusion

institute: fujian medical university union hospital

summary: Using the highly sensitive miRNA array, we screened 30 microRNAs abundant in the exosomes derived from human suspended red blood cell unit with leukocyte reduced

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, three samples from human suspended red blood cell unit with leukocyte reduced were used to acquire the miRNA expression profiling in the exosomes

first: Liping

last: Fan

first: Haobo

last: Huang


title: Expression data of 3 colorectal carcinoma cell lines with or without exposure to radiation

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

summary: To explore long non-coding RNA (lncRNA) associated with radiosensitivity in colorectal carcinoma cell lines, expression profiles of Lovo, RKO and SW480 cell lines with different levels of radiosensitivity were investigated on ArrayStar platform. A probe-remapping strategy was applied to aquire the accurate probe annotation. By comparing expression profiles of cells with exposure to radiation with those of control sample (cells without exposure), a list of lncRNAs associated with radiation response was compiled. GSEA was then performed to explore their biological functions.

overall_design: A six chip study using total RNA collected from three cell lines (Lovo, RKO and SW480) with or without exposure to 2Gy dose of radiation.

first: Xiaowen

last: Xu

first: Xiaomei

last: Hou

first: Zhen

last: Tan

first: Zhiqi

last: Yu

first: Chang

last: Zhang

first: Chuangang

last: Fu

first: Guangwen

last: Cao


title: Radiation effects on lung carcinogenesis in neonatal, juvenile, and adult Wistar rats after thoracic X-ray irradiation

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

summary: Studies of radiation exposed populations have shown that children are at greater overall risk of radiation-induced cancer, although there is considerable debate relating to heterogeneity of the effect in different tissues. Given public concern around increasing radiation doses received by children from advanced diagnostic imaging, and the use of radiotherapy to treat childhood cancers, understanding the relationship between age-at-exposure and radiation-induced cancer risk is a priority of radiation protection research.   Although tobacco smoking accounts for up to 90% of lung cancers in some countries, epidemiological studies and animal experiments show that exposure to ionizing radiation is also a risk factor for developing cancers of the lung. Female Wistar rats are susceptible to lung cancer upon thoracic X-ray irradiation, developing adenocarcinomas (AC) and squamous cell carcinomas (SCC) similar to those seen in humans, and have been used previously to evaluate the interaction of radiation and a chemical carcinogen in neonatal, juvenile and young adult rats. In the present study, the induction of lung tumors was analyzed in female Wistar rats exposed to increasing doses of thoracic X-rays as neonates, juveniles or adults, to allow the effect of age-at-exposure to be observed in the absence of interaction with smoking. Histology was used to compare tumor subtypes between groups, and genomic DNA copy number alterations in a number of tumors arising after exposure to radiation at different ages were examined.

overall_design: The experiment contains three individual rat lung adenocarcinomas from each of four groups (total 12 samples): one group of rats receiving no treatment (spontaneous adenocarcinomas) and three groups receiving X-ray irradiation (1-5 Gy) at either 1 week, 5 weeks or 15 weeks of age. Each tumour is represented by one array, with two arrays per slide, on a total of six array slides. It is not possible to know whether the adenocarcinomas from the irradiated rats are radiation-induced.

first: Yutaka

last: Yamada

middle: J


title: Improvement of antiproliferative activity of betulinic acid by fluorine substitution

city: Taichung

first: Ling-Chu

last: Chang

state: -- select state --

address: 6F, No. 350, Jingmao 1st Road, Beitun Dist.,

department: Center for Molecular Medicine

country: Taiwan

institute: China Medical University Hospital

summary: Gene expression profiling of betulinic acid and fluorinated betulinic acid-treated MCF-7 human breast cancer cells. We used Phalanx Biotech Human Whole Genome OneArray HOA6.2 Array to determine differential gene expression.

overall_design: Samples were collected from betulinic acid and fluorinated betulinic acid-treated MCF-7 cells.

first: Jizhen

last: Li

first: Kan-Yen

last: Hsieh

first: Pei-Ling

last: Hsu

first: Susan

last: Morris-Natschke

first: Masuo

last: Goto

first: Kuo-Hsiung

last: Lee


title: Agave strain vs wine strain

status: Public on Mar 01 2017

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

country: Spain

institute: Centro Superior de Investigaciones Científicas

summary: We studied transcriptional responses comparing an Agave strain ITD00185 with a wine strain T73 in a synthetic agave must

overall_design: Two strains with two time points each; three replicates for each strain and time point

first: Miguel

last: Díaz-Campillo

last: Pérez-Torrado

first: Laura

last: Pérez-Través

first: Amparo

last: Querol


title: Expression data from C. elegans treated with anatase TiO2 nanoparticles

city: Hsinchu

first: Chun-Chih

last: Hu

address: 101, Sec. 2, Kuang-Fu Road

department: Materials Science and Engineering

institute: National Tsing Hua University

summary:
The nematode C. elegans was exposed to TiO2 nanoparticles (NPs) to evaluate the ecotoxicity of TiO2 nanoparticles.
We used the DNA microarray method to understand changes in gene expression after the exposure to TIO2 NPs. We identified various genes involved in metal detoxification as well as in regulating worm development.

overall_design: We employ the model organism C. elegans (with a fully sequenced genome) to effectively study the toxicology of TiO2 NPs (i. e., anatase) under dark conditions.

first: Chun-Chuh

first: Gong-Her

last: Wu


title: Senescent carcinoma associated fibroblasts up-regulate interleukin 8 to enhance pancreatic cancer progression

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

summary: Comparison of the gene expression profile of senescent versus non-senescent cancer associated fibroblasts. The hypothesis tested is that senescent CAFs secrete higher levels of cytokines that promote cancer progression.

overall_design: Total RNA was obtained from control as well as senescent pancreatic cancer associated fibroblasts

first: C

middle: Q

last: Zhu

first: Tao

last: Wang


title: XVE AMY3C-EY induction in SAM

city: Taipei

first: Jychian

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

institute: Academia Sinica

summary: To study the molecular basis for chlorotic and reticulate phenotypes, we took advantage of a time course experiment on XVE AMY3C-EY plants designed for microarray analysis.

overall_design: Twenty μM 17-β-estradiol was applied on meristems of  plants for this experiment, and plants were harvested at 1, 3, 6 hr after treatment. Plants without treatment were regarded as samples of treatment for 0 hr. Besides the time course experiment, treatment of 17-β-estradiol on XVE single transformant SAM was served as a negative control. Samples from thirty plants were collected to extract RNA for further analysis of microarray.

first: Hsin-Yao

last: Huang


title: The gene expression of wild-type worms and kin-1(ok338) mutant worms exposing Salmonella entericaSL1344 at 24 hours

city: Kunming

first: Yi

last: Xiao

state: Yunnan

address: CuiHu north road.2

department: Yunnan University

institute: State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan

summary: PKA/KIN-1 pathway is required for innate immunity in C. elegans, however, the downstream signaling is largely unclear. To gain further insight into mechanism underlying the promoted immunity of PKA/KIN-1 pathway, we performed genome microarrays of wild-type and kin-1(ok338) worms infection by Salmonella entericSL1344, compared with the controls wild-type fed E.coli OP50

overall_design: The gene expression in wild-type worms and kin-1(ok338) mutant worms after exposure Salmonella entericaSL1344 at 24 hours. all experiments were performed three times independently.

first: Fang

last: Liu


title: The Arabidopsis N-acetylornithine deacetylase controls ornithine biosynthesis via a linear pathway with downstream effects on polyamine levels.

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

institute: University of Verona

summary: Arabidopsis thaliana At4g17830 codes for a protein showing sequence similarity with the Escherichia coli N-acetylornithine deacetylase (EcArgE), an enzyme implicated in the linear ornithine (Orn) biosynthetic pathway. In plants, N-acetylornithine deacetylase (NAOD) activity has yet to be demonstrated; however, At4g17830-silenced and mutant (atnaod) plants display an impaired reproductive phenotype and altered foliar levels of Orn and polyamines (PAs). Here, we showed the direct connection between At4g17830 function and Orn biosynthesis, giving the biochemical demonstration that At4g17830 codes for a NAOD. These results are the first experimental proof that Orn can be produced in Arabidopsis via a linear pathway. In this study, to identify the role of AtNAOD in reproductive organs, we carried out a transcriptomic analysis on atnaod mutant and wild-type flowers. In the atnaod mutant, the most relevant effects were the reduced expression of cysteine-rich peptide–coding genes, known to regulate male–female crosstalk during reproduction, and variation in the expression of genes involved in nitrogen:carbon (N:C) status. The atnaod mutant also exhibited increased levels of sucrose and altered sensitivity to glucose. We hypothesise that AtNAOD participates in Orn and PA homeostasis, contributing to maintain an optimal N:C balance during reproductive development.

overall_design: atnaod mutant and wild-type plants fertilised flowers (stage 15) were compared. Three independent biological replicates were conducted for both atnaod mutant and wild-type plants. Each biological sample consists of approximately 100 harvested fertilised flowers collected from a population of 17-20 plants.

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