title: Investigating the effect of CodY mutation on the gene expression in Streptococcus suis serotype 2 SC19 strain.

status: Public on Apr 21 2015

city: shanghai

first: liping

last: feng

address: No. 3577 Jinke Rd., Shanghai

country: China

institute: Shanghai Laboratory Animal Research Center

summary: To investigate the effect of CodY mutation on the gene expression in Streptococcus suis serotype 2 SC19 strain, we have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by CodY mutation. DNA microarray analysis was performed using an Agilent custom-designed oligonucleotide microarray. Based upon the whole genome sequence of SC19 , specific 60-mer oligonucleotide probes were designed using eArray (https://earray.chem.agilent.com/earray/), to cover all annotated genes. Probes were printed seven times on microarray slides. Three biological replicates of total RNA from two wild type strains and from two codY mutant strains were amplified and labeled with Cy3-CTP using Low Input Quick Amp Labeling Kit, one-color(Agilent technologies, US), following the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy mini kit (Qiagen). After fragmentation, microarray slides were hybridized with 600 ng Cy3-labeled cRNA. Hybridization was performed at 65 °C for 17 h with rotation at 10 rpm. Microarray slides were washed and scanned by an Agilent Microarray Scanner (G2565BA). Those genes with greater than two-fold change ratios were regarded as differentially expressed genes.

overall_design: codY mutation induced gene expression in Streptococcus suis serotype 2 SC19 was detected in two wild type and two codY mutated strain of  Streptococcus suis serotype 2.

first: Weicheng

last: Bei

first: Liping

last: Feng


title: Vascular smooth muscle cell: control vs. exposed to nicotine

status: Public on Apr 15 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human aortic smooth muscle cells (HSMCs) comparing exposed with nicotine or not.

overall_design: Two-condition experiment, control vs. treated HSMCs by nicotine.

first: Akio

last: Nakamura

first: Shinji

last: Yoshiyama


title: Metabolic modeling of antibiotic and cytotoxic effects of the isoquinoline IQ-238 in S. aureus, S. epidermidis and human cells

status: Public on Apr 30 2015

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary: Isoquinolines (IQs) are natural substances with antibiotic potential. IQ-238 is a synthetic analog of the novel-type N,C-coupled naphtylisoquinoline (NIQ) alkaloid ancisheynine.  Gene expression data, cytotoxicity measurements and metabolic modelling is combined to assess the effects of the N,C-coupled naphtylisoquinoline (NIQ) compound IQ-238 on Staphylococcus aureus and man as a potential lead for novel antibiotics. It possesses a high activity against staphylococci but has low cytotoxicity in human cell lines. Genome annotation identified missed enzymes (validated by PCR) in the primary (e.g. nucleotide) metabolism of staphylococci. Gene expression changed after cultivation with IQ-238. Metabolic modelling did yield the adaptations of all central enzymes, including those not affected by significant gene expression changes. The data show that IQ-238 interferes with the carbohydrate metabolism in staphylococci.  The data suggest that IQ-238 is a promising lead for antibiotic therapy against S. aureus infections.

overall_design: HG001 WT strain exposed to GB-AP-238 in rich medium

first: Alexander

last: Cecil

first: Knut

last: Ohlsen

first: Thomas

last: Menzel

first: Patrice

last: François

first: Jacques

last: Schrenzel

first: Marcus

last: Dittrich

first: Chunguang

last: Liang

first: Jörg

last: Bernhardt

first: Tobias

middle: A

last: Oelschlaeger

first: Gerhard

last: Bringmann

first: Matthias

last: Unger

first: Leane

last: Lehmann

last: Dandekar


title: MicroRNA Expression Regulated by the HER2 Isoform HER2D16 in MCF-7 Breast Tumor Cells

status: Public on Apr 27 2015

city: New Orleans

first: Frank

middle: E

last: Jones

state: LA

address: 6400 Freret Street, 2000 Percival Stern Hall

department: Cell and Molecular Biology

country: USA

institute: Tulane University

summary: The oncogenic isoform of HER2, HER2D16, was stably overexpressed in the MCF-7 breast tumor cell line (MCF-7/HER2D16) and miR expresion profiles between MCF-7 cell lines expressing a vector control (MCF-7/pcDNA) were compared to the MCF-7/HER2D16 cell line.

overall_design: This experiment includes a total of 4 samples which are divided in to 2 groups, each with 2 biological repeats


title: Ginger and its component ameliorated trinitrobenzene sulfonic acid-induced colitis in mice via modulation of nuclear factor-κB activity and interleukin-1β signaling pathway

status: Public on Apr 28 2015

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: Colitis is the common pathological lesion of inflammatory bowel diseases, the major chronic inflammatory diseases of intestinal tracts in humans. In this study, we investigated the therapeutic effects of ginger extract and its component zingerone in mice with 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis. Mice were administered with TNBS and/or various amounts of ginger and zingerone by an intrarectal route. The severity of colitis was evaluated by colonic weight/length ratio, macroscopic lesion, and histological examination. The mechanisms of ginger and zingerone were further elucidated by DNA microarray, ex vivo imaging, and immunohistochemical staining. Our data showed that treatment with ginger extract and zingerone ameliorated TNBS-induced colonic inflammation and injury in a dose-dependent manner. Pathway analysis of ginger- and zingerone-regulated gene expression profiles showed that ginger and zingerone significantly regulated cytokine-related pathways. Network analysis showed that nuclear factor-κB (NF-κB) and interleukin-1β (IL-1β) were key molecules involved in the expression of ginger- and zingerone-affected genes. Ex vivo imaging and immunohistochemical staining further verified that ginger and zingerone suppressed TNBS-induced NF-κB activation and decreased the NF-κB and IL-1β protein levels in the colon. In conclusion, our data showed that ginger improved the TNBS-induced colitis in mice via modulation of NF-κB activity and IL-1β signaling pathway. Moreover, zingerone might be the active component of ginger responsible for the amelioration of colitis induced by TNBS.

overall_design: A total of 24 mice was randomly divided into four groups of six mice: mock, mice were given with 0.1 ml of 50% ethanol; TNBS, mice were given with 250 mg/kg TNBS in 0.1 ml of 50% ethanol; TNBS/ginger, mice were administered with mixtures containing 250 mg/kg TNBS and various amounts of ginger extract in 0.1 ml of 50% ethanol; TNBS/zingerone, mice were given with mixtures containing 250 mg/kg TNBS and various amounts of zingerone in 0.1 ml of 50% ethanol. Mice were sacrificed seven days later for histochemical staining, RNA extraction, and ex vivo imaging.

first: Tin-Yun

last: Ho

first: Hsin-Yi

last: Lo


title: Customized internal reference controls for improved assessment of circulating microRNAs in disease

city: Ottawa

first: Kenny

last: Schlosser

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

summary: Altered levels of circulating extracellular miRNA in plasma and serum have shown promise as non-invasive biomarkers of disease.  However, unlike the assessment of cellular miRNA levels for which there are accepted housekeeping genes, analogous reference controls for normalization of circulating miRNA are lacking.  The objective of this study was to devise an approach to both identify and validate circulating miRNA reference controls on a de novo basis, and evaluate the relative performance of these customized internal reference controls versus other strategies.  As a case example, 1066 different miRNAs were screened in plasma from pulmonary arterial hypertension patients and control subjects to identify an initial pool of miRNA candidates.

overall_design: PCR array profiling was performed on 4 treatment-naïve idiopathic pulmonary arterial hypertension (PAH) patients, 3 healthy control subjects and 1 non-PAH control subject

first: Lauralyn

last: McIntyre

first: R

middle: J

last: White

first: Duncan

last: Stewart


title: Profiling of copy-number variation in tumors from heterozygous and homozygous Tp53C273X knockout rats

status: Public on Apr 09 2015

city: Utrecht

first: Roel

last: Hermsen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

type: Genome variation profiling by genome tiling array

summary: We used Nimblegen HD aCGH to detect copy-number variants between tumor and ear control-DNA samples from heterozygous and homozygous Tp53C273X knockout rats

overall_design: Comparison of tumor DNA with ear control-DNA from the same animal

first: Marieke

last: Simonis


title: Vitamin D receptor (VDR) target genes in THP-1 monocytic leucemia cells

status: Public on Apr 26 2015

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: The biologically active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is a direct regulator of gene transcription, since it is the only high affinity natural ligand of the transcription factor vitamin D receptor (VDR). Transcriptome-wide analysis of THP-1 human monocyte-like cells had indicated more than 600 genes to be significantly (p < 0.05) regulated after a 4 h stimulation with 1,25(OH)2D3. In this study, we screened of the list of primary vitamin D targets for genes encoding for transcriptional regulators and selected those of the activating transcription factor NFE2 and the transcriptional repressor BCL6. Both genes are under the control of two VDR loci and are the only 1,25(OH)2D3 targets within their respective chromosomal domain. However, NFE2 mRNA was rapidly up-regulated, while the increase of BCL6 expression showed a slower rise. After 24 h incubation of THP-1 cells with 1,25(OH)2D3 more than 1,500 genes responded significantly (p < 0.001), of which 132 where more than 2-fold induced. Public chromatin immunoprecipitation-sequencing datasets suggested that the majority of these genes could be targets of NFE2 or BCL6. In time course experiments we displayed for representative gene examples the specific delayed response of secondary 1,25(OH)2D3 targets and confirmed for the respective chromosomal domains the genomic binding of NFE2, BCL6 and VDR. In conclusion, our study indicated that the physiological response of monocytes to 1,25(OH)2D3 involves the action of NFE2 and BCL6.

overall_design: THP-1 cells were treated 24 h either with 0.1% ethanol (vehicle, control) or 1α,25(OH)2D3 (1,25D)

first: Sabine

last: Seuter

first: Carsten

last: Carlberg


title: Molecular Signature of Erythroblast Enucleation in Human Embryonic Stem Cells

status: Public on Apr 14 2015

city: Paris

first: Hélène

last: LAPILLONNE

address: 27 Rue de Chaligny

department: UMR_S938 CDR Saint-Antoine

country: France

institute: UPMC Univ Paris 06

summary:
While enucleation is a critical step in the terminal differentiation of human red blood cells, the molecular mechanisms underlying this unique process remain unclear. To investigate erythroblast enucleation, we studied the erythroid differentiation of human embryonic stem cells (hESCs), which provide a unique model for deeper understanding of the development and differentiation of multiple cell types. First, using a two-step protocol, we demonstrated that terminal erythroid differentiation from hESCs is directly dependent on the age of the embryoid bodies. Second, by choosing hESCs in two extreme conditions of erythroid culture, we obtained
an original differentiation model which allows one to study the mechanisms underlying the enucleation of erythroid cells by analyzing the gene and miRNA (miR) expression profiles of cells from these two culture conditions. Third, using an integrated analysis of mRNA and miR expression profiles, we identified five miRs potentially involved in erythroblast enucleation.
Finally, by selective knockdown of these five miRs we found miR-30a to be a regulator of erythroblast enucleation in hESCs.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We compared the miRNA expression profles of sample groupe A (EB9) to sample goupe B (EB20). Microarray analysis was performed in triplicate for both sample groups at each time point: Day0, cells at the level of embryoid body (A-D0, B-D0) and Day18 of erythroid culture(A-D18, B-D18).

first: Shaghayegh

last: ROUZBEH

first: Ladan

last: KOBARI

first: Marie

last: CAMBOT

first: Christelle

last: MAZURIER

first: Nicolas

last: HEBERT

first: Anne-Marie

last: FAUSSAT

first: Charles

last: DURAND

first: Luc

last: DOUAY

first: Helene


title: Essential role of miR-200c in regulating self-renewal of breast cancer stem cells initiating from the counter parts of mammary epithelium

city: chong qing

first: ming

middle: zhong

last: feng

address: Shapingba District Street Bridge

institute: Xinqiao Hospital

summary: To explore the roles of essential miRNAs in regulating self-renewal of breast cancer stem cells (BCSCs), which initiate from mammary epithelial stem cells (MaSCs). CD44+CD24-/low cells and MUC1-ESA+ cells were isolated by fluorescence-activated cell sorting (FACS) from breast cancer cell line MCF-7 and normal mammary epithelial cell line MCF-10A, and were verified as BCSCs and MaSCs by clonogenic assay and multipotential differentiation experiment in 2-dimensional (2-D) and 3-D cultures, respectively. Using microarray containing oligonucleotides corresponding to 509 miRNAs from human, mouse, and rat genomes. We obtained candidate miRNAs in regulating breast tumorigenesis. One representative miRNA (miR-200c) was proved to regulate stemness of BCSCs and MaSCs in vitro and in vivo by miR-200c agomir transfection. We validated that miR-200c negatively regulated PDCD10, an apoptosis regulator, in BCSCs and MaSCs.

overall_design: Our miRNA microarray includes 509 mature miRNA sequences were downloaded from the miRNA Registry. We designed eight short oligos possessing no homology with all existed RNA sequence and produced their corresponding synthetic miRNAs by in vitro transcription using Ambion’s miRNA Probe Construction kit. All miRNA probe sequences were designed to be complementary  to the full-length mature miRNA. The probe sequence were concatenated up to 40 nt and modified with 5 0 -amino-modifier C6. Oligonucleotide probes were synthesized and dissolved in EasyArray TM spotting solution at 40 mM concentration. Each probe was printed in triplicate using a SmartArray TM microarrayer. Arrays were scanned with a confocal LuxScan TM scanner (CapitalBio Corp.)Significance Analysis of Microarrays(SAM, version 2.1) was performed using two class-unpaired comparison in the SAM procedure.

first: Zhong-Ming

last: Feng

first: Jun

last: Qiu

first: Xie-Wan

last: Chen

first: Rong-Xia

last: Liao

first: Xing-Yun

first: Lu-Ping

last: Zhang

first: Xu

first: Yan

last: Li

first: Zhen-Tang

first: Jian-guo

last: Sun


title: RNA-Induced Silencing Complex-associated RNA in MRC-5 cells transfected with hcmv-miR-UL22A-5p

status: Public on Apr 08 2015

city: Edmonton

first: Luiz

middle: Filipe

last: Lisboa

state: AB

address: 6-020 Katz bldg

department: Medical Microbiology and Immunology

institute: University of Alberta

summary: Investigation of mRNA targets of the human cytomegalovirus miRNA UL22A-5p

overall_design: One 4-plex chip was hybridized with cDNA originating from either total RNA or from AGO2-associated RNA (i.e. RISC-associated RNA) from fibroblasts transfected 48 hours earlier with hcmv-miR-UL22A-5p mimic or with a negative control siRNA

first: L

middle: F

first: A

last: Humar


title: The transcriptomic profile of Pseudozyma aphidis during production of mannosylerythritol lipids

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

type: Expression profiling by high throughput sequencing

summary: Pseudozyma aphidis is one of the most productive microbial producers of mannosylerythritol lipids on vegetable oils with a unique product spectrum that contains all four main variants MEL-A, -B, -C and -D. Secretion of MEL is thereby accompanied by a morphologenetic switch from yeast to hyphal growth. To investigate the genetic characteristics of MEL secretion and dimorphic transition, we analyzed the transcriptome of P. aphidis during production of MEL after the morphologenetic switch. The analysis revealed that the strong activation of 4 of the 5 genes within the MEL-cluster is clearly dependent on the presence of a hydrophobic carbon source. Only the acetyltransferase mat1 is not induced. This may explain the heterogeneous mixture of MEL with different degree of acetylation. In parallel to the MEL-Cluster, we saw a significant induction of a large group of genes which are coding for cell wall modifying enzymes. These genes were mainly grouped in two large gene clusters typical for the concerted cellular switch. In addition, a group of transcription factors was activated which may be key regulator candidates for MEL-synthesis and cell development. The induction of nitrogen metabolism and assimilation processes for phosphate, iron and other nutrients draw a picture of further cellular requirements at this time point. As part of this work, we present the manually annotated and experimentally verified genome and transcriptome of P. aphidis DSM 70725 with a total number of 6942 genes. 82 % of the genes are othologs to Pseudozyma antarctica and 73 % orthologs to Ustilago maydis.

overall_design: Experimental annotation of transcriptional landscape combined with examination of gene expression on two different carbon sources.

first: M

last: Guenther

first: C

first: S

last: Lorenz

first: P

last: Stevens

first: E

last: Lindemann

first: T

last: Hirth

first: K

last: Sohn

last: Zibek

last: Rupp


title: Proteus mirabilis mrpJ microarrays

status: Public on Apr 13 2015

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary:
This series of microarrays compares gene expression by the bacterial pathogen Proteus mirabilis when the transcriptional regulator mrpJ is deleted or induced to levels found during experimental urinary tract infection.

The enteric bacterium Proteus mirabilis is associated with a significant number of catheter-associated urinary tract infections. Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for successful disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the mrp fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects a wide array of cellular processes beyond adherence and motility. Microarray analysis found that expression of mrpJ mimicking expression levels that occur during UTI leads to differential expression of 217 genes related to, among others, bacterial virulence, type VI secretion and metabolism. We probed the molecular mechanism of transcriptional regulation through MrpJ using reporter assays and chromatin immunoprecipitation (ChIP). Two virulence-associated target genes, the flagellar master regulator flhDC and mrp itself, appear to be regulated through a binding site proximal to the transcriptional start, complemented by a more distantly situated enhancer site. Furthermore, an mrpJ deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observe that mrpJ is widely conserved in a collection of recent clinical isolates, leading us to conclude that our results elucidate an unanticipated role of MrpJ as a global regulator of P. mirabilis virulence.

overall_design: Four biological replicates were analyzed for each set of arrays (P. mirabilis HI4320 wild type vs. ΔmrpJ, and vector pLX3607 vs. mrpJ plasmid pLX3805).


title: SUV420H2 over-expression affects on gene expression in human breast cancer MDA-MB-231 cells [MAA13355]

first: Satoshi

last: Kondo

summary: Analysis of breast cancer MDA-MB-231 cells stably over-expressing SUV420H2, a histone H4K20 methyltransferase. Several genes were significantly up- or down-regulated. Results provide insight into the molecular mechanism by which H4K20me3 contributes to gene expression.

overall_design: SUV420H2 stably over-expressing MDA-MB-231 cells were cloned. Then total RNA was extracted from the SUV420H2 over-expressing cells and the parental MDA-MB-231 cells.

first: Yoshimi

last: Shinchi

first: Miki

last: Hieda


title: miRNAs related to metastasis of Small Cell Lung Cancer

city: Wuhan

first: Rui

last: Zhou

state: Hubei

address: 湖北省武汉市江汉区唐家墩156号

department: Cancer Center

institute: Wuhan Union Hospital

summary: Relationship between miRNAs and SCLC have not been investigated thoroughly. Thus we design this expirment tying to find out the miRNAs involved in SCLC metastasis.

overall_design: We used 6 patients' serum samples,two-condition experiment. 3 of them were form extensive-stage SCLC patients, and another 3 were from limited-stage SCLC patients.


title: Morphological and molecular descriptors of the developmental cycle of Babesia divergens parasites in human erythrocytes

status: Public on Apr 10 2015

city: Pretoria

first: Ingrid

last: Rossouw

state: Gauteng

address: Lynnwoodroad

department: Genetics

country: South Africa

institute: University of Pretoria

summary: Human babesiosis, especially caused by the cattle derived Babesia divergens parasite, is on the increase, resulting in renewed attentiveness to this potentially life threatening emerging zoonotic disease. The molecular mechanisms underlying the pathophysiology and intra-erythrocytic development of these parasites are poorly understood. This impedes concerted efforts aimed at the discovery of novel anti-babesiacidal agents. By applying sensitive cell biological and molecular functional genomics tools, we describe the intra-erythrocytic development cycle of B. divergens parasites from immature, mono-nucleated ring forms to bi-nucleated paired piriforms and ultimately multi-nucleated tetrads that characterizes zoonotic Babesia spp. This is further correlated for the first time to nuclear content increases during intra-erythrocytic development progression, providing insight into the part of the life cycle that occurs during human infection. High-content temporal evaluation elucidated the contribution of the different stages to life cycle progression. Moreover, molecular descriptors indicate that B. divergens parasites employ physiological adaptation to in vitro cultivation. Additionally, differential expression is observed as the parasite equilibrates its developmental stages during its life cycle. Together, this information provides the first temporal evaluation of the functional transcriptome of B. divergens parasites; information that could be useful in identifying biological processes essential to parasite survival for future anti-babesiacidal discoveries.

overall_design:
Two-condition experiment, Untreated vs.Treated B. divergens parasites, cultured in human erythrocytes. Treatment with a piperidinyl-benzimidizalone analogue. Biological replicates: 3 untreated (control) replicates, 3 treated replicates.
The 6-sample dataset represents untreated(control) vs pooled_reference samples at various timepoints.

first: Lyn-Marie

last: Birkholtz

first: Christine

last: Maritz-Olivier

first: Jandeli

last: Niemand

first: Annel

last: Smit

first: Nicholas

last: Olivier

first: Riette

last: van Biljon


title: Enhancement of ER function by PI3K inhibition limits the antitumor effects of PI3K inhibitors in breast cancer

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

summary: Gene expression data of breast cancer samples before and after PI3K inhibition

overall_design: In the study presented here, we evaluated the expression profiles of a total of 105 unique genes in 6 breast cancer samples before and after PI3K-inhibitor therapy

first: Maurizio

last: Scaltriti


title: Transcriptomic profiling of Arabidopsis thaliana in response to combined stress treatment under altered GSH conditions.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: The Arabidopsis seeds of Col-0 and pad2.1 were grown for three weeks and were further placed in filter paper for 5 min at 4°C and then transferred to 1/2MS media with 30% PEG at 4°C for an additional 6 hours; the leaves were collected for RNA isolation. Trancriptomic profiling of the combined stress treated Col-0 and pad2.1 indicated downregulation of various abiotic and oxidative stress responsive genes in pad2.1 in response to combined stress treatment.

overall_design: Agilent one-color experiment,Organism: Arabidopsis thaliana ,Agilent Custom Arabidopsis 8x60k Microarray designed by Genotypic Technology Private Limited (AMADID: 48015)

first: Deepak

last: Kumar

first: R

last: Datta

first: A

last: Sultana

first: Sharmila

last: Chattopadhyay


title: mir775_1st-Role of the young microRNA to plants

status: Public on Apr 23 2015

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: ra12-08_mir775 - mir775_1st - Look for potential targets of miR775 at Arabidopsis thaliana by the analysis of the transcriptome of a mutant not producing any more the miRNA.

overall_design: 2 dye-swaps - gene knock out.

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Nicolas

last: Bouche

first: Marie-Laure

last: Martin-Magniette


title: Development of microRNA (miRNA) expression signatures for mouse glioma-initiating cells (GICs)

status: Public on Apr 07 2015

city: Toon

first: Daisuke

last: Yamashita

address: Shitsukawa

department: Neurosurgery

institute: Ehime University Graduate School of Medicine

summary: To identify a novel miRNA that is aberrantly expressed in GICs, we analyzed differences in miRNA expression between the mouse GICs, NSCL61 and OPCL61, showing characteristic features of cancer stem cell, and their parental cells by miRNA microarrays.

overall_design: neural stem cells, glioma-initiating cells (GICs) from neural stem cells, oligodendrocyte precursor cells, glioma-initiating cells (GICs) from oligodendrocyte precursor cells.

first: Toru

last: Kondo


title: Comparative Analysis of Gene Expression Profiles in Infective and Developing Larvae of Brugia malayi and Brugia pahangi

city: St. Louis

first: Michael

last: Heinz

state: MO

address: 4320 Forest Park Blvd.

institute: Washington University School of Medicine

summary: Comparative analysis of gene expression profiles provided novel insights into the genes that are transcriptionally active in infective and developing larvae of two closely related species. Species differences may indicate different metabolic adaptations that could affect host specificity, tissue tropism, and pathogenicity

sample_organism:
Brugia malayi
Brugia pahangi

platform_organism: Wolbachia endosymbiont strain TRS of Brugia malayi

overall_design:
Two biological replicates of infective (L3) or developing larval RNA used for hybridization, in duplicate, to examine the gene expression changes in Brugia larvae
Brugia malayi vector derived third stage larvae (Bm VL3); Brugia pahangi vector derived third stage larvae (Bp VL3); Brugia pahangi L3 cultured in vitro (Bp cL3); Brugia pahangi L3 derived from peritoneal cavity of infected gerbils (Bp ipL3); Brugia pahangi migrating L3 (Bp mL3) from  infected gerbils

first: Ramakrishna

last: Rao

first: Seth

middle: D

last: Crosby

first: Gary

last: Weil

first: Thomas

middle: R

last: Klei


title: CpG island methylation data from maternal venous blood and infant cord blood samples

status: Public on Apr 17 2015

city: Chapel Hill

first: Saideep

middle: Rao

last: Gona

state: NC

address: 135 Dauer Dr

department: Environmental Sciences and Engineering

institute: University of North Carolina at Chapel Hill

type: Methylation profiling by genome tiling array

summary:
The biological mechanism of cadmium's effects is poorly characterized. This data was generated in order to help better understand the epigenetic role that Cadmium plays.
We used the MIRA assay and the Affymetrix Human Promoter 1.0R Array in order to measure methylation levels in promoter regions.

overall_design: 34 samples corresponding to 17 mother-infant pairs were selected based upon measured levels of cadmium in the blood. Methylated DNA fragments were then isolated, amplified, and run on the Affymetrix Human Promoter 1.0R Array. Results were then summarized to CpG islands for each sample.

first: Alison

middle: P

last: Sanders

first: Lisa

last: Smeester

first: Daniel

last: Rojas

first: Tristan

last: Debussycher

middle: C

last: Wu

first: Fred

last: Wright

first: Yi-Hui

last: Zhou

first: Jessica

last: Laine

first: Julia

last: Rager

first: Geeta

middle: K

last: Swamy

first: Allison

last: Ashley-Koch

first: Marie

middle: L

last: Miranda

first: Rebecca

last: Fry


title: The G protein-coupled pH-sensing receptor OGR1 is a regulator of intestinal inflammation

status: Public on Apr 12 2015

city: Zurich

first: Cheryl

last: de Valliere

address: Steinwartstrasse 14

institute: University Hospital Zurich

summary: OGR1 is a pH sensing G protein-coupled receptor involved in intestinal homeostasis and inflammation. Up-regulation of genes, mediated by OGR1, in response to extracellular acidification were enriched for inflammation, immune response, actin cytoskeleton and cell adhesion pathways.

overall_design: Microarray profiling was performed to compare global gene expression of Ogr1 KO and WT residential peritoneal macrophages in response to an acidic pH shift (pH 6.7, 24 h)

last: de Vallière

first: Yu

last: Wang

first: Jyrki

last: Eloranta

first: Solange

last: Vidal

first: Ieuan

last: Clay

first: Marianne

last: Spalinger

first: Irina

last: Tcymbarevich

first: Anne

last: Terhalle

first: Marie-Gabrielle

last: Ludwig

last: Suply

first: Michael

last: Fried

last: Scharl

first: Gerd

last: Kullak-Ublick

first: Isabelle

last: Frey-Wagner

first: Klaus

last: Seuwen

first: Carsten

last: Wagner

first: Gerhard

last: Rogler


title: Identification of differentially expressed microRNAs in liver tissue of Hepatitis B virus (HBV) infected hepatocellular carcinoma (HCC)

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive and Liver Diseases

institute: Institute of Post Graduate Medical Education and Research

summary:
Global expression profiling of miRNAs in liver tissue of HBV infected HCC and chronic hepatitis B (CHB) with no fibrosis was evaluated. A total of 40 differentially expressed miRNAs were identified in HCC. Top 10 miRNAs are validated in more numbers of HCC tisuues by qRT PCR.
Finally six miRNAs (miR-15a, miR-16, miR-21,miR-29b-3p, miR-126, miR-142-3p, miR-193a-5p) showed similar expression pattern in both microarray and qRT PCR

overall_design: Differential expression analysis of microRNAs in HBV infected HCC (n=4) compared to CHB patients with no fibrosis (n=8) as control.

first: Amit

last: Ghosh

first: Alip

first: Saroj

last: Mohapatra


title: Transcriptome analysis of Streptococcus suis serotype 2 during infection in a murine air pouch model

status: Public on Apr 25 2015

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

summary: During infection in the air pouches, S. suis encounters changing environments and host factors. It is important for S. suis to modulate the gene expression in response to stimulants. Using DNA microarray analysis, we compared the transcriptome of S. suis obtained from the air pouches with that from working cultures.

overall_design: S. suis were injected into the air pouches. Mice were euthanized at 6 h post infection, and bacterial cells collected from the air pouches were used for RNA isolation. Total RNA was isolated using an SV total RNA isolation system (Promega). Total RNA isolated from S. suis grown in working cultures was used as control. RNA concentration and integrity was assessed by Agilent 2100 Bioanalyzer. Microarray experiments were repeated 4 times for both samples.

first: Weicheng

last: Bei


title: MiRNA expression profile in human CD34+/CD105- cells derived from the renal artery subsequent to long warm ischemia compared short warm ischemia

status: Public on Apr 29 2015

city: Boston

first: Andrew

middle: Michael

last: Siedlecki

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: MiRNA regulate the maintenance, differentiation and function of stem cells and progenitor cells. miRNA expression of progenitor cells located in the adventital layer of arterial vessels has not been characterized in either animal or human models.  Further it is unknown if local arterial miRNA expression profiles change after injury of end organs supplied blood by these arterial conduits.  CD34+/CD105- cells were extracted and analyzed for changes in miRNA expression after kidney specific ischemic injury.

overall_design: CD34+/CD105- cells were isolated from renal artery after short warm ischemic time in living donor kidney explants and long warm ischemic time following radical nephrectomy for renal cell cancer

first: Paul

last: Pang


title: MiRNA expression profile in CD34+/CD105- cells derived from the renal artery after kidney specific ischemic injury.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: MiRNA expression profile in mouse CD34+/CD105- cells derived from the renal artery subsequent to renal ischemia/reperfusion injury

overall_design: CD34+/CD105- cells were isolated from mouse renal artery after microvascular clamping of renal arteries bilaterally


title: Response of Prochlorococcus to varying CO2:O2 ratios

city: Cambridge

first: Sallie

middle: W

last: Chisholm

address: 15 Vassar St., Bldg. 48-419

institute: MIT

summary: Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology.  In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials.  Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph.  We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both.  O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation.  Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts.  These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: Two biological replicates of timecourses under four conditions:  medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)

first: Sarah

last: Bagby


title: Real-time quantitative PCR analysis of human ependymal and ventral horn regions in adult control spinal cord

city: Toledo

first: Daniel

last: Garcia-Ovejero

state: Toledo

address: Finca La Peraleda s/n

department: Neurología Experimental

institute: Hospital Nacional de Parapléjicos (SESCAM)

summary: Adult human ependymal and ventral horn regions were obtained from postmortem frozen samples by Laser Capture Microdissection. Briefly, Cryostat 25 micron sections from were stained with toluidin blue and both regions microdissected and collected on eppendorf (n=4 for each region). Samples mRNA concentration and purity was assessed by electrophoresis (BioRad Experion HighSensitivity kit, USA). RQI values were lower than 6,5 in every case, so that purification was followed by 2 cycle amplification with a kit designed for highly degraded samples (ExpressArt® TRinucleotide mRNA Amplification Kit; #6299-A15, AmpTec, AMSBIO, UK). After amplification, mRNA concentration and purity was assessed both by electrophoresis (BioRad Experion StSens kit, USA) and by spectrophotometry (Nanodrop, Thermo Scientific, USA). We amplified 3.7-37 ng of total RNA, obtaining between 6 and 21 µg of mRNA after 2 rounds. After collecting samples and studying the RNA integrity and quantity, cDNA of samples was selected for gene expression assays using 384 wells Custom Taqman Low Density Arrays. We built arrays with genes belonging to a profile of stemness or ependymoma (see Garcia-Ovejero et al., 2015, BRAIN).

overall_design: Taqman based qPCR gene expression profiling.  Ependymal and ventral horn regions obtained by LCMD from four different individuals each were used to establish genes involved in stem cell niches or in ependymoma phenotype that are enriched in control human ependyma using ventral horn as a non-ependymary, non-neurogenic region. Samples were treated as stated in the summary. Equal amount of amplified RNA (aRNA; 25ng, corresponding approximately to 500ng total RNA) from each donor was used in Custom Designed Taqman Low Density Arrays. Every value is the resultant of duplicates at least, but most of them have been assayed 4 times.

first: Angel

last: Arevalo-Martin

first: Beatriz

last: Paniagua-Torija

first: Jose

last: Florensa-Vila

first: Isidro

last: Ferrer

first: Lukas

last: Grassner

first: Eduardo

last: Molina-Holgado


title: The CdaA Regulon in Streptoccus mutans

status: Public on Apr 06 2015

city: Chengdu

first: Yu-Qing

last: Li

address: No.14, Section 3, Renmin Road South

institute: State Key Laboratory of Oral Diseases, Sichuan University

summary: Nucleotide signaling pathways are found in all kingdoms of life and are utilized to coordinate a rapid response to changes in the environment. One more recently discovered signaling nucleotide is the secondary messenger cyclic diadenosine monophosphate (c-di-AMP), which is widely distributed among bacteria and is also found in several archaea. This cyclic nucleotide has been shown to involve in several important cellular processes, including maintenance of DNA integrity, cell wall metabolism, stress tolerance, transcription regulation and virulence. However, the mechanisms by which c-di-AMP modulates these physiological changes have remained largely unknown.In the present study, we identified and characterized a c-di-AMP synthase (CdaA) in S. mutans UA159. Furthermore, we investigated the role of CdaA in S. mutans cell physiology and global gene expression by utilizing cdaA gene in-frame deletion mutant. Our findings suggest that CdaA is an important global modulator of optimal growth and environmental adaption in this pathogen.

overall_design: Streptococcus mutans UA159 whole-genome arrays (8 x 15 K) were obtained from Agilent and included 1998 probes for S. mutans transcripts. For microarray analysis, S. mutans UA159 and S. mutans ΔcdaA cells were routinely grown at 37°C anaerobically (90% N2, 5% CO2, 5% H2) in brain heart infusion broth (BHI; Difco, Sparks, MD, USA) to an optical density at 600 nm (OD600) of 0.5. Four RNA samples isolated from four independent cultures of UA159 and cdaA mutant strains were hybridized to the arrays and analyzed.


title: Microarray analysis of apple buds during dormancy

city: Petrolina

first: Diogo

middle: Denardi

last: Porto

state: Pernambuco

address: BR428 road, Km 152

department: Embrapa Semiárido

country: Brazil

institute: EMBRAPA

summary: Closed terminal buds of apple trees (Malus x domestica Borkh, Royal Gala and Castel Gala varieties) grown in commercial orchards were harvested during autumn and winter and exposed to cold treatments

overall_design: 18 biological samples, consisting of 9 pairs of replicates, were analysed in dye-swap. Samples are whole closed terminal buds. Biological replicates are buds from 2 different harvest year subjected to similar cold treatments. Samples with contrasting dormancy status in the same harvest year were compared in 8 dye-swap. Most samples were hybridized more than once in different combinations

first: Maryline

last: Bruneau

first: Pâmela

last: Perini

first: Rafael

last: Anzanello

first: Jean-Pierre

last: Renou

first: Henrique

last: dos Santos

first: Flávio

middle: B

last: Fialho

first: Luís

last: Revers


title: ABP1-regulated gene expression in etiolated Arabidopsis seedlings

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary: The AUXIN BINDING PROTEIN 1 (ABP1) is an essential plant protein involved in the control of growth and development all along the plant life. This protein was initially identified on its capacity to bind the phytohormone auxin. Binding of auxin to ABP1 was shown to enhance cell expansion of leaf cells. Conversely, the functional inactivation of ABP1 was demonstrated to severely impair cell expansion in shoot tissues. To date, the mechanism by which ABP1 controls cell expansion is still poorly understood. ABP1 was reported to affect expression of various auxin regulated genes but little is known on broader effects of ABP1 on gene expression. Here we have investigated the role of ABP1 in the control of cell expansion using dark grown hypocotyls by analyzing changes in gene expression resulting from ABP1 inactivation.

overall_design: Experiments were performed using the control transgenic line Alc-GUS and the SS12K9, which express GUS and ABP1, respectively, in response to ethanol treatment. Three biological repeats were prepared. RNA samples were labelled with Cy5 and Cy3 as indicated below. Samples from the SS12K9 line were compared to the corresponding control line.

first: Sébastien

last: Paque

first: Catherine

last: Perrot-Rechenmann

first: Miguel

middle: A

last: Blázquez

last: Alabadí


title: WTAP-induced change in gene expresssion in cholangiocarcinoma cells

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Knock-down or overexpression of WTAP regulated migration and invasion of cholangiocarcinoma cells in vivo and vitro studies. To investigate the underlying mechanism for WTAP-regulated migration and invasion, the gene expression between the mock cells and the stable cells was compared

overall_design: Total RNA was purified from the mock cells and the stable cells overexpressing WTAP

first: Sae-Ock

last: Oh


title: Transcriptome of postnatal mouse heart

status: Public on Apr 04 2015

city: Hong Kong

first: Lee

middle: Kenneth

last: Ka Ho

address: Rm126, Lo Kwee Seong Integrated Biomedical Science Building, CUHK, Shatin, N.T.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The present study aimed at determining the differences in global mRNA expression between proliferating cardiomyocytes in the 2-day-old heart and growth arrested cardiomyocytes in 13-day-old heart of ICR mice.

overall_design: The transcriptomic profiles of the samples at the two time points(day 2 and day 13 of postnatal stage) were analyzed by direct comparison of the transcriptional level between the two groups of heart on the same custom 12×135K microarray (Roche NimbleGen)

first: Kenneth

middle: H

last: Lee

first: Jingyi

last: Gan


title: Human whole blood stimulated with Pam2Cys and lipoteichoic acid from Staphylococcus aureus wt and delta-lgt mutant

status: Public on Apr 05 2015

city: Konstanz

first: Sonja

last: von Aulock

address: POB M668

department: Biochemical Pharmacology

institute: University of Konstanz

summary:
Comparison of the immune response of human whole blood to lipoteichoic acid (LTA) derived from the Staphylococcus aureus SA113 delta-lgt mutant (lacks lipoproteins), LTA from S. aureus SA113 wt. and PAM2Cys, a lipoprotein analogue.

Background: Our goal was to expand our report that LTA from SA 113 wildtype (wt LTA) and delta-lgt (lgt LTA) induce equal amounts of TNF release by human whole blood (von Aulock et al., J Immunol, 2007). Therefore we traced the translational activation by both LTA in comparison to the synthetic diacylated lipoprotein Pam2Cys-SK4 in human whole blood on an immunology microarray comprising 1076 genes related to apoptosis and signal transduction, cell cycle, chemokines, cytokines and their receptors, extracellular matrix proteins, inflammation and complement system.

Results and Discussion: The results show extensive overlaps of the clustered heat-maps of SA113 wt and lgt LTA, which are clearly different from those of Pam2Cys-SK4 stimulation. Only four of the 1076 genes were significantly differently regulated after stimulation with the LTAs, whereas stimulation with Pam2Cys-SK4 led to a significantly different regulation of 43 genes compared to SA 113 wt LTA and 39 compared to SA 113 lgt LTA. Mainly chemokines were upregulated by both LTA, which is consistent with our previous findings (von Aulock et al., Immunobiol, 2003) and different from stimulations with Pam2Cys-SK4. The gene array results support our protein data obtained from LTA-stimulated human whole blood and point to a significant concordance between the immunostimulatory activity of lgt and wt LTA preparations. In contrast, a distinct difference is observed between both LTA and the synthetic lipoprotein Pam2Cys-SK4. This supports the conclusion that the immunostimulatory activity of wt LTA in human whole blood is not determined by possible lipoprotein contaminations.

overall_design:
Human whole blood incubations were done with 4 healthy donor volunteers. 10 µg/ml of wt or lgt LTA or Pam2Cys-SK4 were used to stimulate whole blood diluted 1:5 in RPMI 1640 for 7 h.
After the incubation samples were resuspended by gentle shaking, centrifuged at 400 x g for 2 min, and supernatants were removed and stored at -80°C for cytokine measurement. The remaining cell pellet was resuspended and transferred to a 15 ml centrifugation tube (Greiner Bio-One) on ice. 5 ml erythrocyte lysis buffer (EL buffer, Qiagen, Hilden, Germany) was added to each sample and incubated for 10 min on ice. Samples were briefly vortexed twice during this time. The samples were centrifuged at 400 x g for 10 min at 4°C and the supernatant was discarded. The remaining leukocyte pellet was washed twice with PBS and stored at -80°C until RNA preparation. After RNA preparation, the microarray analysis was done by testing each stimulus against its unstimulated control for each individual blood donor.

first: Christoph

last: Rockel

first: Stefanie

last: Sigel

first: Christian

last: Draing

first: Oliver

last: Dehus

first: Thomas

last: Hartung

first: Sebastian

last: Bunk

first: Susanne

last: Deininger

first: Artur

last: Ulmer

first: Markus

last: Pfitzenmaier

first: Friedrich

last: Götz

first: Corinna

last: Hermann

first: Marina

last: Borisova


title: Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells (miRNA)

status: Public on Apr 02 2015

city: Solna

first: Penny

last: Nymark

state: Stockholm

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: Understanding toxicity pathways of engineered nanomaterials (ENM) has recently been brought forward as a key step in 21st century ENM risk assessment. Molecular mechanisms linked to phenotypic end points is a step towards the development of toxicity tests based on key events, which may allow for grouping of ENM according to their mechanisms of action. This study identified molecular mechanisms underlying mitochondrial dysfunction in human bronchial epithelial BEAS 2B cells following exposure to one of the most studied multi-walled carbon nanotubes (MWCNTs; Mitsui-7). Asbestos was used as a positive control and a non-carcinogenic glass wool material was included as a negative fibre control. Decreased mitochondrial membrane potential (MMP↓) was observed for MWCNTs at a biologically relevant dose (0.25 μg/cm2) and for asbestos at 2 μg/cm2, but not for glass wool. Extensive temporal transcriptomic and microRNA expression analyses identified a 330-gene signature related to MWCNT- and asbestos-induced MMP↓. Fourty-nine of the MMP↓-associated genes showed highly similar expression patterns over time (six time points) and the majority was found to be regulated by two transcription factors strongly involved in mitochondrial homeostasis, APP and NRF1. In addition, four miRNAs were associated with MMP↓ and one of them, miR-1275, was found to negatively correlate with a large part of the MMP↓-associated genes. Cellular processes such as gluconeogenesis, glucose metabolism, mitochondrial LC-fatty acid β-oxidation and spindle microtubule function were enriched among the MMP↓-associated genes and miRNAs. These results are expected to be useful in the identification of key events in ENM-related toxicity pathways for the development of molecular screening techniques.

overall_design: BEAS 2B cells were exposed to 0.25 and 2 μg/cm2 of MWCNT, asbestos and glass wool (MMVF10) for 1, 4, 6, 12, 24 and 48 hours. Three independent experiments were performed to obtain a total of 3 replicates for each experimental condition. Non-exposed cells for each time point were used as controls. Three samples failed to give adequate quality RNA and a total of 123 samples were hybridized to Agilent miRNA arrays.

first: Peter

last: Wijshoff

first: Rachel

last: Cavill

first: Marcel

last: van Herwijnen

first: Maarten

last: Coonen

first: Sandra

last: Claessen

first: Julia

last: Catalán

first: Hannu

last: Norppa

first: Jos

last: Kleinjans

first: Jacob

middle: J

last: Briedé


title: mRNA expression of brain endothelial cells

city: Tokyo

first: Naoomi

last: Tominaga

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research institute

summary: To investigate the mRNA expression after extracellular vesicles or miRNA treatement, global gene expression analysis was performed in endothelial cells after the transfection of N.C. or miR-181c and or after the addition of extracellular vesicles from cancer cells.

overall_design: mRNA expression in brain endothelial cells was collected from negative control or miR-181c treatment and or after the addition of extracellular vesicles from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.

first: Nobuyoshi

last: Kosaka


title: Grassland ecosystem responses to elevated CO2 are contingent on nitrogen conditions

status: Public on Apr 03 2015

city: Beijing

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

country: China

institute: Tsinghua University

summary: To study whether and how soil nitrogen conditions affect the ecological effects of long-term elevated CO2 on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. Under the aN condition, a majority of microbial function genes, as measured by GeoChip 4.0, were increased in relative abundance or remained unchanged by eCO2. Under the eN condition, most of functional genes associated with carbon, nitrogen and sulfur cycling, energy processes, organic remediation and stress responses were decreased or remained unchanged by eCO2, while genes associated with antibiotics and metal resistance were increased. The eCO2 effects on fungi and archaea were largely similar under both nitrogen conditions, but differed substantially for bacteria. Coupling of microbial carbon or nitrogen cycling genes, represented by positive percentage and density of gene interaction in association networks, was higher under the aN condition. In accordance, changes of soil CO2 flux, net N mineralization, ammonification and nitrification was higher under the aN condition. Collectively, these results demonstrated that eCO2 effects are contingent on nitrogen conditions, underscoring the difficulty toward predictive modeling of soil ecosystem and ecoprocesses under future climate scenarios and necessitating more detailed studies.

overall_design: Fourty eight samples were collected for four different carbon and nitrogen treatment levels (aCaN,eCaN,aCeN and eCeN) ; Twelve replicates in every elevation

first: Yunfeng

last: Yang


title: Transgenic GS1a poplar under different nitrate nutrition level.

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: Transcriptional profile of leaves from poplar plants transformed with a pine GS1a gene under two different nitrate nutrition level (50mM and 10mM).

overall_design: Two conditions: nitrate nutrition (50mM and 10 mM) and genotype (GS1a transgenic poplar vs WT poplar)

first: Vanessa

last: Castro-Rodríguez

first: Ángel

last: García-Gutiérrez

first: Javier

last: Canales

first: Edward

middle: G

last: Kirby

first: Concepción

last: Ávila

first: Francisco

last: Cánovas


title: ARF6 bi-directionally regulates the dendritic spine formation depending on neuronal maturation and activity

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: Recent studies reported contradictory results regarding the role of ADP-ribosylation factor 6 (ARF6), a small GTPase known to regulate actin cytoskeleton, in dendritic spine development and maintenance. We readdress this question, and found that ARF6 either positively or negatively regulates dendritic spine formation depending on neuronal maturation and activity. ARF6 activation facilitates filopodia to spines transition, increasing the spine formation in developing neurons while it decreases spine density in matured neurons. Consistently, genome-wide microarray analysis revealed that Arf6 activation in developing and matured neurons leads to opposite expression patterns of a subset of genes that are involved in neuronal morphology.

overall_design: To readdress effects of ARF6-T157A on spine formation in both developing and matured neurons, we have generated the Sindbis virus for ARF6-T157A-6xHis and performed its infection into rat hippocampal neuron culture at 10 DIV (days in vitro) for developing stage and 17 DIV for mature stage, and maintained for additional 48 h. Infected neurons were washed twice with PBS and were frozen at -70C for storage. Samples were lysed and RNA isolation was carried out using the RNA-spin total RNA extraction kit (iNtRON Biotechnology, Sungnam, Kyungki-Do, South Korea). Then, genome-wide microarray analysis was performed. Microarray analysis revealed that Arf6 activation in developing and matured neurons leads to opposite expression patterns of a subset of genes that are involved in neuronal morphology.

first: Yoonju

first: Sang

middle: E

last: Lee

first: Joohyun

last: Park

first: Bo

middle: Y

first: Daehee

last: Hwang

first: Sunghoe

last: Chang


title: Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells

first: Penny

last: Nymark

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


title: Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells (Affymetrix)

overall_design: BEAS 2B cells were exposed to 0.25 and 2 μg/cm2 of MWCNT, asbestos and glass wool (MMVF10) for 1, 4, 6, 12, 24 and 48 hours. Three independent experiments were performed to obtain a total of 3 replicates for each experimental condition. Non-exposed cells for each time point were used as controls. Three samples failed to give adequate quality RNA and a total of 123 samples were hybridized to Affymetrix GeneChip U133 Plus 24-array plates.


title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [HybMap microarray]

status: Public on Apr 01 2015

city: Salt Lake City

first: Timothy

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

type: Expression profiling by genome tiling array

summary: ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures.

overall_design:
Total RNA expression was determined by the HybMap protocol, hybridization of total RNA to genomic tiling microarray followed by detection with an anti-RNA-DNA-hybrid antibody. Total RNA was isolated from three independent biological replicates of each strain, including wild type (YBC1894), rsc2ts (YBC1111), isw1 null (YBC1416), ioc3 null (YBC2693), isw1 null rsc2ts (YBC3227), and ioc3 null rsc2ts (YBC3228).

Please note that each sample consists of three replicates (i.e. three raw data files) and the sample data table contains combined quantile normalized data of the replicates.

first: Alisha

last: Schlichter

first: Bradley

middle: R

last: Cairns


title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-chip]

type: Genome binding/occupancy profiling by genome tiling array

overall_design:
Genomic localization of RSC and ISW1a complexes were measured by chromatin immunoprecipitation followed by genome-wide microarray hybridization. Two independent biological replicates of two strains, Rsc8-9xMyc (YBC2882) and Ioc3-13xMyc (YBC2883), each grown in two different media, rich glucose media (YPD) or minimal synthetic glucose (SD) media. Each sample consists of one chromatin immunoprecipitate and one input chromatin control.

Please note that each sample consists of two replicates (i.e. two raw data files) and the sample data table contains combined quantile normalized data of the replicates.


title: Reprogramming of primary human Philadelphia chromosome-positive B cell acute lymphoblastic leukemia cells into nonleukemic macrophages

city: Stanford

first: Christopher

last: Dove

address: Room 3005, 265 Campus Drive, 3rd Floor

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: BCR–ABL1+ precursor B-cell acute lymphoblastic leukemia (BCR– ABL1+ B-ALL) is an aggressive hematopoietic neoplasm characterized by a block in differentiation due in part to the somatic loss of transcription factors required for B-cell development. We hypothesized that overcoming this differentiation block by forcing cells to reprogram to the myeloid lineage would reduce the leukemogenicity of these cells. We found that primary human BCR–ABL1+ B-ALL cells could be induced to reprogram into macrophage-like cells by exposure to myeloid differentiation-promoting cytokines in vitro or by transient expression of the myeloid transcription factor C/EBPα or PU.1. The resultant cells were clonally related to the primary leukemic blasts but resembled normal macrophages in appearance, immunophenotype, gene expression, and function. Most importantly, these macrophage-like cells were unable to establish disease in xenograft hosts, indicating that lineage reprogramming eliminates the leukemogenicity of BCR–ABL1+ B-ALL cells, and suggesting a previously unidentified therapeutic strategy for this disease. Finally, we determined that myeloid reprogramming may occur to some degree in human patients by identifying primary CD14+ monocytes/ macrophages in BCR–ABL1+ B-ALL patient samples that possess the BCR–ABL1+ translocation and clonally recombined VDJ regions.

overall_design: We obtained the expression profiles of 5 human B-ALL samples using Afymmetrix U133A2 microarrays. Blasts were either analyzed without culture, or cultured in the presence of myeloid cytokines and sorted into CD14+ and CD19+ populations.

first: J

middle: S

last: McClellan


title: In depth characterization of the activity of a novel synthetic macrocyclic antifungal compound

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

institute: University of Lausanne and University Hospital Center

summary: The systemic infections by peptogenous fungi member of the genera Candida and Aspergillus represent a serious threat for public health. During previous research we have successfully identified a family of compounds active against different Candida spp. including strains resistant to antifungal drugs currently on the market. We have further refined our knowledge on this field by identifying a possible molecular target that could justify the activity of these compounds. The research of the mode of action of the compounds object of this manuscript was supported also by fluorescent microscopy of labeled derivatives. Transcriptional data indicates that one of the macrocyclic antifungal induces a drug response involving ATP binding cassette transporters. Moreover the data show that the macrocyclic antifungal decrease expression of cell wall biosynthesis genes. Moreover, the quality of the compounds and their potential was tested in vivo revealing a promising profile in particular against fungal infection caused by resistant strains

overall_design: Gene expression was measured in Candida albians CAF2-1 exposed to the macrocyclic compound FR59 at 3 µM at two time points (15 min and 45 min), The one-color system was used. Three independent experiments were performed using non-exposed cells, 15 min and 45 min exposed cells.

first: Patrick

last: Vandeputte


title: Bedaquiline-induced transcriptional response of Mycobacterium smegmatis mc2 155

city: Dunedin

first: Jennifer

last: Robson

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Transcriptional profiling of M. smegmatis mc2155 grown on Hartmans de Bont (HdB) supplemented with 0.2% glycerol and 0.05% Tween80 challenged with 2 μg/ml Bedaquiline and Dimethyl sulfoxide (DMSO)

overall_design: Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.

first: Gregory

middle: M

last: Cook


title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [nucleosome occupancy]

overall_design:
Genome-wide nucleosome occupancy maps in wild-type, mutant RSC, and mutant ISW1 strains were generated by hybridization of mononucleosomal DNA to microarrays. Strains carrying Sth1 degron and either pGal-UBR1 (YBC2191) or ubr1 null (YBC2192) represent RSC null and RSC wildtype, respectively. Strains carrying Sth1 degron isw1 null and either pGal-UBR1 (YBC2467) or ubr1 null (YBC2468) represent RSC null isw1 null and RSC wildtype isw1 null, respectively. Mononucleosomes were isolated from three independent biological replicates from each genotype.

Please note that each sample consists of three replicates (i.e. three raw data files) and the sample data table contains combined quantile normalized data of the replicates.


title: Compare HSCs between WT and Merit40-/- mice

city: Philadelphia

first: Wei

last: Tong

state: PA

address: 316A Abramson Bldg., 3615 Civic Center Blvd.

department: Pediatrics

institute: Children's Hospital of Philadelphia, and University of Pennsylvania School of Medicine

summary: The adaptor protein MERIT40 is a core subunit of deubiquitinating (DUB) complexes that specifically cleave Lysine63-polyubiquitin chains. We found that MERIT40 is an important negative regulator of hematopoietic stem cell (HSC) homeostasis, quiescence and self-renewal. This study aims to investigate the molecular mechanism by which MERIT40 regulates HSC expansion and cell cycle. We performed expression profiling of bone marrow CD150+CD48-LSK LT-HSCs from WT and Merit40-/- mice. Results identify select MERIT40-mediated pathways with potential involvement in HSC cell cycle regulation.

overall_design: CD150+CD48-LSK HSCs were double sorted from WT and Merit40-/- mice at young age. RNA was isolated using miRNeasy kit from QIAGEN and processed using the NuGEN Pico kit. The microarray analysis was performed at the PENN Molecular Profiling/Genomics Facility using GeneChip Mouse Gene 2.0ST array (Affymetrix).

first: Krasimira

last: Rozenova

first: Jing

last: Jiang

first: Ryan

last: Donaghy

first: Bernadette

last: Aressy

first: Roger

last: Greenberg


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Sperm Epimutations Promotes Genetic Mutations [MeDIP-Chip]

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation.  This involves the germline transmission of epigenetic information between generations.  Exposure specific sperm epimutations have been previously observed.  The current study was designed to investigate the potential role genetic mutations have in the process, using copy number variations (CNV).  In the first (F1) generation following exposure negligible CNV were identified, but in the transgenerational F3 generation a significant increase in CNV were identified in the sperm.  The genome-wide differential DNA methylation regions (epimutations) were correlated with the genome locations of the CNV.  Observations indicate the environmental induction of the epigenetic transgenerational inheritance of sperm epimutations promotes genome instability such that genetic CNV mutations are acquired in later generations.  A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes.

overall_design: Sperm DNA was isolated from F1 and F3 generation rats that were ancestrally exposed to vinclozolin and dimethyl sulfoxide (vehicle) control. Equal concentrations of DNA from sperm samples from groups of three individuals were used to produce three different DNA pools per lineage. Three different comparative (CNV vs CNV) hybridization experiments were performed (2 array set) for each experiment vinclozolin versus control lineage, with each array including hybridizations from DNA pools from these different experiments. Also, two different comparative (MeDIP vs. MeDIP) hybridization experiments were performed for vinclozolin lineage versus control, with each array set encompassing DNA samples from 6 animals (3 each from vinclozolin and control). These sperm DNA samples were distinct from those used for the MeDIP-Chip analysis and those used for Copy number variation (CNV) analysis. Then, the genome-wide differential DNA methylation regions (epimutations) were correlated with the genome locations of the CNV.

first: Carlos

last: Guerrero-Bosagna

first: M

last: Haque


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Sperm Epimutations Promotes Genetic Mutations

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

overall_design: Refer to individual Series


title: Epigenetic analysis of genomic DNA isolated from whole blood of normal and leukemia individuals

city: Seoul

first: Kee-Beom

last: Kim

address: Heusokdong

institute: Chung-Ang University

summary: DNA methylation profiling of whole blood using Illumina's Infinium HumanMehtylation27 Beadchip array.

overall_design: The dataset encompasses profiles of 4 normal and 8 leukemia samples individuals. Bisulfite converted DNA from 12 samples were hybridized to the Illumina Infinium HumanMehtylation27 Beadchip

first: Sulji

last: Choi

first: Sang-Beom

last: Seo


title: Cow mammary nutrigenomics

city: Saint-genes-champanelle

first: Anne

last: de la Foye

address: INRA-UMRH

institute: INRA

summary: Twelve midlactation cows received 4 diets differing in forage-to-concentrate ration (High (HF) versus Low (LF) forage supplemented or not with lipids (HF with whole intact rapeseeds (HF-RS) and LF with sunflower oil (LF-SO))

overall_design:
12 cows got into 4 groups, each cow was received 4 different diets in a latin square design
Green*txt and Red_*txt raw data files contain Cy3 and Cy5 signal intensities, respectively.

first: C

last: Leroux

first: Y

last: Faulconnier

first: A

first: J

last: Domagalski

last: Rouel

last: Chilliard


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Sperm Epimutations Promotes Genetic Mutations [CGH]

overall_design:
Sperm DNA was isolated from F1 and F3 generation rats that were ancestrally exposed to vinclozolin and dimethyl sulfoxide (vehicle) control. Equal concentrations of DNA from sperm samples from groups of three individuals were used to produce three different DNA pools per lineage. Three different comparative (CNV vs CNV) hybridization experiments were performed (2 array set) for each experiment vinclozolin versus control lineage, with each array including hybridizations from DNA pools from these different experiments. Also, two different comparative (MeDIP vs. MeDIP) hybridization experiments were performed for vinclozolin lineage versus control, with each array set encompassing DNA samples from 6 animals (3 each from vinclozolin and control). These sperm DNA samples were distinct from those used for the MeDIP-Chip analysis and those used for Copy number variation (CNV) analysis. Then, the genome-wide differential DNA methylation regions (epimutations) were correlated with the genome locations of the CNV.

This submission represents CNV component of study.


title: Oncogenic Fusion Protein EWS-FLI1 is a Network Hub that Regulates Alternative Splicing

status: Public on Mar 31 2015

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary:
The synthesis and processing of mRNA, from transcription to translation initiation, often requires splicing of intragenic material. The final mRNA composition varies based upon proteins that modulate splice site selection. EWS-FLI1 is an Ewing sarcoma (ES) oncogene with an interactome that we demonstrate to have multiple partners in spliceosomal complexes. We evaluate EWS-FLI1 upon post-transcriptional gene regulation using both exon array and RNA-seq. Genes that potentially regulate oncogenesis including CLK1, CASP3, PPFIBP1, and TERT validate as alternatively spliced by EWS-FLI1. EWS-FLI1 also alters splicing by directly binding to known splicing factors including DDX5, hnRNPK, and PRPF6. Reduction of EWS-FLI1 produces an isoform of g-TERT that has increased telomerase activity compared to WT TERT. The small molecule YK-4-279 is an inhibitor of EWS-FLI1 oncogenic function that disrupts specific protein interactions including DDX5 and RNA helicase A (RHA) that alters RNA splicing ratios. As such, YK-4-279 validates the splicing mechanism of EWS-FLI1 showing alternatively spliced gene patterns that significantly overlap with EWS-FLI1 reduction and WT human mesenchymal stem cells. Exon array analysis of 75 ES patient samples show similar isoform expression patterns to cell line models expressing EWS-FLI1, supporting the clinical relevance of our findings. These experiments establish systemic alternative splicing as an oncogenic process modulated by EWS-FLI1. EWS-FLI1 modulation of mRNA splicing may provide insight into the contribution of splicing towards oncogenesis, and reciprocally, EWS-FLI1 interactions with splicing proteins may inform the splicing code.
Alternative splicing of RNA allows a limited number of coding regions in the human genome to produce proteins with diverse functionality. Alternative splicing has also been implicated as an oncogenic process. Identifying aspects of cancer cells that differentiate them from non-cancer cells remains an ongoing challenge and our research suggests that alternatively spliced mRNA and subsequent protein isoforms will provide new anti-cancer targets. We determined that the key oncogene of Ewing sarcoma (ES), EWS-FLI1, regulates alternative splicing in multiple cell line models. These experiments establish oncogenic aspects of splicing which are specific to cancer cells and thereby illuminate potentially oncogenic splicing shifts as well as provide a useful stratification mechanism for ES patients.

overall_design: We analyzed three models of EWS-FLI1 using Affymetrix GeneChip Human Exon 1.0 ST microarray: (i) Ewing's sarcoma TC32 wild-type cells expressing EWS-FLI1, and TC32 cells where EWS-FLI1 was reduced with a lentiviral shRNA; (ii) A673i, which has a doxycycline-inducible shRNA to reduce EWS-FLI1 expression, and wild-type EWS-FLI1 to screen for alternative splicing as measured by exon-specific expression changes; and (iii) human mesenchymal stem cells (hMSC), a putative cell of origin of Ewing's sarcoma, exogenously expressing EWS-FLI1, and hMSC wild-type cells without EWS-FLI1. Three biological replicates were included for each condition. The Bioconductor package "oligo" in the R programming language was used for normalization and background correction. Analysis was carried out using only core probesets, as defined by the manufacturer.

first: Saravana

middle: P

last: Selvanathan

middle: T

first: Jeffrey

last: Toretsky


title: Epigenomic profiling in visceral white adipose tissue of offspring of mice exposed to late gestational sleep fragmentation

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

summary: Background: Late gestational sleep fragmentation (LG-SF) is one of the major perturbations associated with sleep apnea and other sleep disorders during pregnancy. Objectives: To investigate the effects of late LG-SF on the epigenome of visceral white adipose tissue (VWAT) in the offspring. Methods: Time-pregnant mice were exposed to LG-SF or control sleep (LG-SC) conditions during the last 6 days of gestation. We performed large-scale DNA methylation analyses using MeDIP coupled to microarrays (MeDIP-chip) in VWAT of 24-week-old LG-SF and LG-SC offspring (n=8 mice/group). Univariate multiple-testing adjusted statistical analyses were applied to identify differentially methylated regions (DMRs) between the groups. DMRs were mapped to their corresponding genes, and tested for potential overlaps with biological pathways and gene networks. Results: We detected 2148 DMRs between LG-SF and LG-SC groups (p< 0.0001, MAT algorithm). A large proportion of the DMR-associated genes have reported functions that are altered in obesity and metabolic syndrome. Overrepresented pathways and gene networks were related to metabolic regulation and inflammatory response. Conclusions: Our findings show a major role for epigenomic regulation of pathways associated to metabolic processes and inflammatory response in VWAT. Furthermore, LG-SF-induced epigenetic alterations appear to increase the susceptibility to obesity and metabolic syndrome in the offspring.

overall_design: 16 mouse VWAT samples were analyzed by MeDIP coupled to microarray analysis: Offspring of mothers exposed to late-gestational sleep fragmentation (n=8, LG-SF group) and offspring of mothers mouse exposed to normal sleep conditions (n=8, LG-SC group)

first: Abdelnaby

last: Khalyfa

first: Riyue

last: Bao

first: Jorge

last: Andrade

first: David

last: Gozal


title: Control of the E. coli SOS regulon expression by intracellular dNTP pool changes

city: Warszawa

first: Iwona

last: Fijalkowska

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

summary: We studied SOS mutator effect mediated by recA730 and changes in the dNTP pool. We found that established dNTP pool changes resulting from deficiencies in the ndk or dcd genes,  had a strongly suppressive effect on the recA730 mutator effect. To investigate whether the observed reduction in SOS mutator effect is due to lowered expression of the entire SOS regulon, we performed microarray analysis of gene expression profiles in each of the single ndk, dcd, and recA730 strains, as well as the double recA730 ndk and recA730 dcd strains.

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

overall_design: Comparison of transcriptomes of the bacterium Escherichia coli six strains: wt, dcd, ndk, recA730, recA730 dcd and recA730 ndk. All strains were derivatives of the MC4100 strain, carrying a sulA366 allele (Δ(argF-lac)169 sulA366). dcd and ndk alleles used were dcd::kan and ndk::cam, respectively. Strains were compared in pairs: wt vs dcd, wt vs ndk, wt vs recA730, recA730 vs recA730 dcd and recA730 vs recA730 ndk. Two or three biological replicates for each strain  were used. Each biological replicate had two technical replicates with dye swapping.

first: Katarzyna

last: Masłowska

first: Karolina

last: Makiela-Dzbenska

last: Fijałkowska

first: Roel

last: Schaaper


title: MicroRNA regulation and its effects on cellular transcriptome in Human Immnodeficiency Virus-1 (type-1) infected individuals with distinct viral load and CD4 cells

city: Pittsburgh

first: Velpandi

last: Ayyavoo

address: 130 Desoto street, University

country: USA

institute: Velpandi Ayyavoo

summary: Human PBMCs were isolated from donors' blood. We used Taqman low density arrays to examine the differences in microRNA expression in the PBMCs of HIV seronegative individuals and individuals infected with low and high viral load.

overall_design: qRT PCR. PBMCs from donors were used. Equal amounts of total RNA were used for microRNA profiling.

last: Duskova

first: Pruthvi

last: Nagilla

first: Hai-Son

last: Le

first: Priyadarshini

last: Iyer

first: Anbupalam

last: Thalamuthu

first: Jeremy

last: Martinson

first: Ziv

last: Bar-Joseph

first: William

last: Buchanan

first: Charles

last: Rinaldo


title: Increased level of glutathione contributes to stress tolerances and global translational changes in Arabidopsis

status: Public on Mar 28 2015

city: Taipei

first: Tsan-Piao

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

summary: Polysomal profiling results showed that global translation was enhanced in roots after 8 h and in shoots after 24 h of GSH treatment. By performing transcriptomic analyses of steady-state and polysome-bound mRNAs in GSH-treated plants, we reveal that GSH has more a greatersubstantial impact on translational change.

overall_design: GSH-induced gene expression in Arabidopsis roots and shoots was measured seperately at 8 and 24 hours after exposure to 100 μM GSH. Two independent experiments were performed at each time (8 or 24 hours).


title: RNA expression profiling for Paf1 complex mutant strains [mRNA]

status: Public on Mar 25 2015

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory.

overall_design: Total RNA extracted from wild-type and mutant strains to compare global expression. At least 2 biological replicates for each sample were performed.

last: Kowalik

first: Yukiko

last: Shimada

first: Michael

last: Stadler

first: Batki

last: Julia

first: Marc

last: Bühler

first: Stephane

last: Thiry


title: nautilus null vs. wild type miRNA

city: Bethesda

first: Anandarao

last: Ravulapalli

state: maryland

address: 9000 Rockville Pike

department: LBMB

institute: NCI

summary:
To determine if the Drosophila MyoD homolog, nautilus, was activating any miRNA loci, similar to vertebrate MyoD, we compared the miRNA expression profiles between wild-type (w1118) and nautilus null embryos during the window of maximum nautilus expression (6-8hr AEL), using LNA arrays specifically designed to quantify miRNA levels in Drosophila (Exiqon).
Expression levels for mir-309, mir-3, mir-286, mir-4, mir-5, and mir-6 from the 8-miR cluster, were significantly decreased in nautilus null embryos. It suggests that the intergenic 8-miR cluster, encoding eight miRNAs, is regulated by nautilus.

overall_design: Two-condition experiment, wild type (w1118)  vs. mutant (nautilus null). Biological replicates: 3 wild type, 3 mutants, independently isolated.

first: Wei

last: Qin

first: Bruce

last: Paterson


title: 8-miR cluster deletion affects mef2  levels in Drosophila melanogaster

summary: Loss of nautilus (MyoD) gene function results in a variable phenotype affecting muscle formation in embryos and larvae, larval movement, pupal eclosion, egg deposition, adult mobility and survival. 8-miR cluster deletion disrupts muscle formation in the embryo while affecting protein production from the nautilus, dMef2 ,  regulators of  the muscle transcriptional network.  We propose the complex phenotype in the nautilus null is due to the disruption of the regulatory interactions provided by the 8-miR cluster.  The results demonstrate that nautilus is an integral regulator of the miRNA circuitry buffering the transcriptional network directing muscle development.

overall_design: Two-condition experiment, wild type (w1118)  vs. mutant (8-miR cluster null). Biological replicates: 3 wild type, 3 mutants, independently isolated. One of the biological replicate was dye swaped to avoid dye bias.


title: High EMT signature score of invasive non-small cell lung cancer (NSCLC) cells correlates with NFĸB driven colony-stimulating factor 2 (CSF2/GM-CSF) secretion by neighboring stromal fibroblasts

status: Public on Mar 16 2015

city: Vienna

first: Andreas

last: Wernitznig

address: Dr.-Boehringer-Gasse 5-11

department: Oncology - Pharmacology

country: Austria

institute: Boehringer Ingelheim

summary:
We established co-cultures of invasive or non-invasive NSCLC cell lines and various types of fibroblasts (FBs) to more precisely characterize the molecular mechanism of tumor-stroma crosstalk in lung cancer
Differential expression analysis of the respective mono- and co-cultures revealed an upregulation of NFκB-related genes exclusively in co-cultures with Calu-1. Cytokine Array- and ELISA-based characterization of the “cytokine fingerprints” identified CSF2 (GM-CSF), CXCL1, CXCL6, VEGF, IL6, RANTES and IL8 as being specifically upregulated in various co-cultures

overall_design: 66 samples were analyzed. Epithelial Cancer Cell lines (Calu-1, HCI-H1437) and fibroblasts (HDF, WI-38, CAFs, and NFs) were cultivated in monoculture and in co-culture and hybridized on Affymetrix Exon Chips.

first: Albin

last: Rudisch

first: Matthew

last: Dewhurst

first: Luminita

last: Horga

first: Nina

last: Kramer

first: Nathalie

last: Harrer

first: Meng

last: Dong

first: Heiko

last: van der Kuip

last: Bernthaler

first: Helmut

last: Dolznig

first: Wolfgang

last: Sommergruber


title: Ectopic expression of mir-3 affects mef2 and tinman levels

summary: Loss of nautilus (MyoD) gene function results in a variable phenotype affecting muscle formation in embryos and larvae, larval movement, pupal eclosion, egg deposition, adult mobility and survival. mir-3 over expression  disrupts muscle formation in the embryo while affecting protein production from the dMef2 and tinman genes, global regulators of  the muscle transcriptional network.  We propose the complex phenotype in the nautilus null is due to the disruption of the regulatory interactions provided by the 8-miR cluster.  The results demonstrate that nautilus is an integral regulator of the miRNA circuitry buffering the transcriptional network directing muscle development.

overall_design: Two-condition experiment, wild type (w1118)  vs. mutant (mir-3 ectopic expressionl). Biological replicates: 3 wild type, 3 mutants, independently isolated. One of the biological replicate was dye swaped to avoid dye bias.


title: A secreted effector protein of Ustilago maydis guides maize leaf cells to form tumors

status: Public on Mar 09 2015

city: Marburg

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Strasse 10

department: Department of Organismic Interactions

institute: Max Planck Institute for Terrestrial Microbiology

summary: Zea mays transcriptome profiling of infected seedlings by the Ustilago maydis wildtype and the seedling specific effector mutant demonstrated the variation of gene expression in the mutant and the classes of genes that are absent in the mutant as compared to the wildtype U. maydis SG200 strain. Two dye competitive hybridizations were performed on Agilent Oligo arrays.

overall_design: Comparison were done 1) with mock and infected samples at 6dpi. 2) between the two 6dpi infected samples with wildtype and the secreted effector mutant

first: Amey

last: Redkar


title: Adult Needles timelapse and whorl - Los Reales 2012

status: Public on Feb 27 2015

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

institute: Universidad de Málaga

summary:
Transcriptional profiling of Pinus pinaster adult needles in a complete year. The needles were isolated by year emergence (whorl) in four groups. 0 (2012), 1 (2011), 2 (2010) and 3 (2009).
The samples were harvested at 1245 m of altitude at Los Reales de Sierra Bermeja (Spain) (30S X:303.095 Y:4.039.618) one time per month.

overall_design: Reference design. 6 biological replicates that were pooled two by two resulting in 3 samples for the hybridization. The common reference samples was a pool of RNA samples from January. The reference sample was labeled with Cy5 and the test samples with Cy3.

first: Javier

last: Canales

first: Carmen

last: Muñoz

first: Jose

last: Granados

first: M

last: Pascual

first: Concha

last: Ávila

first: María

middle: L

last: García-Martín

first: Francisco

last: Cánovas


title: Bisphenol A disrupts HNF4α-regulated gene networks linking to prostate preneoplasia in Noble rats

status: Public on Mar 07 2015

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Exposure of humans to bisphenol A (BPA) is widespread and continuous. We previously showed that perinatal exposure to BPA increased prostate cancer risk in adult rats. Yet the effects of protracted, exposure to BPA during adulthood have not been studied.  In this study, we subjected Noble rats to 32 weeks of co-treatment with testosterone (T) and BPA (low- or high-dose) or T and 17β-estradiol (E2) via Silastic capsule implants. Circulating T levels were comparable in all treatment groups, whereas the levels of free BPA were elevated in the groups that received T+low BPA (1.06 ± 0.05 ng/ml, P<0.05) and T+high BPA (10.37 ± 0.43 ng/ml, P<0.01) when compared with those in controls (0.1 ± 0.05 ng/ml). T+low/high BPA induced prostatic hyperplasia, low-grade prostatic intraepithelial neoplasia (PIN), and intraepithelial infiltration of T-lymphocytes only in the lateral prostates (LPs), whereas T+E2 induced high-grade PIN in this prostatic lobe. Genome-wide transcriptome analysis identified differential changes in the LPs of T+BPA and T+E2 treatments, with aberrant expression of multiple genes in the regulatory network controlled by the transcription factor hepatic nuclear factor 4α (HNF4α) specifically in BPA- but not E2-treated LPs. These findings suggest that the adult rat prostate is susceptible to transcriptomic reprogramming by BPA associated with the development of prostate pathology in a manner distinct from that of E2. The relevance of these data to the previous report demonstrating an association between high urinary levels of BPA and prostate cancer needs to be studied further.

overall_design: Rat lateral prostates were collected from untreated control and treated groups [Testosterone (T) + Estradiol (E2), T + low dose Bisphenol A (low BPA) and T + high BPA] for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify transcriptional signature of BPA exposures in the lateral prostate gland.

first: Neville

middle: N

last: Tam

first: Hung-Ming

last: Lam

first: Jing

last: Chen

first: Shuk-Mei

last: Ho


title: T-cell activation and early gene response in dogs

status: Public on Mar 23 2015

city: The University of Sydney

first: Peter

last: Williamson

state: NSW

address: Rm 552 RMC Gunn Building B19

department: Faculty of Veterinary Science

country: Australia

institute: University of Sydney

summary: T-cells play a crucial role in canine immunoregulation and defence against invading pathogens. Proliferation is fundamental to T-cell differentiation, homeostasis and immune response. Initiation of proliferation following receptor mediated stimuli requires a temporally programmed gene response that can be identified as immediate-early, mid- and late phases. The immediate-early response genes in T-cell activation engage the cell cycle machinery and promote subsequent gene activation events. Genes involved in this immediate-early response in dogs are yet to be identified. The present study was undertaken to characterize the early T-cell gene response in dogs to improve understanding of the genetic mechanisms regulating immune function. Gene expression profiles were characterized using canine gene expression microarrays and quantitative reverse transcription PCR (qRT-PCR), and paired samples from eleven dogs. Significant functional annotation clusters were identified following stimulation with phytohemagluttinin (PHA) (5μg/ml), including the Toll-like receptor signaling pathway and phosphorylation pathways. Using strict statistical criteria, 13 individual genes were found to be differentially expressed, nine of which have ontologies that relate to proliferation and cell cycle control. These included, prostaglandin-endoperoxide synthase 2 (PTGS2/COX2), early growth response 1 (EGR1), growth arrest and DNA damage-inducible gene (GADD45B), phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), V-FOS FBJ murine osteosarcoma viral oncogene homolog (FOS), early growth response 2 (EGR2), hemogen (HEMGN), polo-like kinase 2 (PLK2) and polo-like kinase 3 (PLK3). Differential gene expression was re-examined using qRT-PCR, which confirmed that EGR1, EGR2, PMAIP1, PTGS2, FOS and GADD45B were significantly upregulated in stimulated cells and ALAS2 downregulated. PTGS2 and EGR1 showed the highest levels of response in these dogs. Both of these genes are involved in cell cycle regulation. This study provides a comprehensive analysis of the early T-cell gene response to activation in dogs.

overall_design: Blood was collected from 11 healthy dogs and the leukocyte fraction was isolated by gradient centrifugation. Cells were divided into two aliquots both were incubated for 4 hours, one in the presence of 5μg/ml of PHA, a mitogen for T-cell activation, the other served as non-stimulated control cells. RNA was isolated from from a total of 22 samples 11 stimulated and 11 non-stimulated controls and hybridized to an Affymetrix® Canine Gene 1.0 ST Array. One non-stimulated sample (SM4) failed to amplify and so is not included.

first: Sally

last: Mortlock

first: Jerry

last: Wei


title: Transcriptomic analyses of three wine yeast strains duting their response to nitrogen availability

status: Public on Mar 01 2015

city: Burjassot

middle: E.

last: Perez-Ortin

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: A time-course transcriptomic experiment was performed in three geographically different wine yeast strains in order to test differences in gene expression as response to different nitrogen availability

overall_design:
mRNA amounts for different wine yeast strains at different nitrogen availability was determined along the fermentation of a syntethic must. mRNA determinations were made at different fermentation stages (12, 24, 36 and 96 h after innoculation)
Please note that there are two replicates per each stage (i.e. two raw data files per each sample; R1.txt and R2.txt) and the data were combined to generate the normalized data for each stage (i.e. sample).

first: José

last: Pérez-Ortín

last: García-Martínez

first: Alexandra

last: Mendes-Ferreira

first: Catarina

middle: D

last: Rodrigues-Barbosa


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

status: Public on Jan 31 2015

city: Kyoto-shi, Sakyo-ku

first: Mayumi

last: Yoshida

state: Kyoto-fu

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University

summary: Transcriptome analysis of the effect of RECTAS on fibroblast cells derived from a familial dysautonomia patient.

overall_design: We analyzed fibroblast derived from FD patient (3 control (treated with 0.1% DMSO) and 3 treated (treated with 2 µM RECTAS)) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Naoyuki

last: Kataoka

first: Kenjyo

last: Miyauchi

first: Kenji

last: Ohe

first: Kei

last: Iida

first: Suguru

first: Takayuki

last: Nojima

first: Yukiko

last: Okuno

first: Hiroshi

last: Onogi

first: Tomomi

last: Usui

first: Akihide

last: Takeuchi

first: Takamitsu

last: Hosoya

first: Tsutomu

last: Suzuki

first: Masatoshi

last: Hagiwara


title: LIX75 vs H37Rv under Log phase growth (± 5 mM Nitrate), and during hypoxic growth (48 h)

status: Public on Feb 09 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Transcription analysis of ΔnarL mutant (LIX75) versus wild type H37Rv during aerobic growth in absence or presence of 5 mM Nitrate, and during hypoxic growth. This will elucidate the regulatory role of NarL response regulator duirng aerobic growth in absence of presence of exogenous nitrate supplemen and during hypoxic growth conditions and help identify genes that require NarL for expression under the three experimental conditions.

overall_design: Two color Experiment,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADIDAMADID-23057)

first: Vandana

last: Malhotra

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last: Duncan

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middle: K

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first: Josephine

last: Clark-Curtiss