title: Human periheral blood-derived monocytes and unstimulated as well as IL-4-stimulated differentiating macrophages

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
CD14+ monocytes were separated from human peripheral blood and exposed to IL-4 for 12 or 72 hours then subjected to microarray analysis
We used Affymetrix miRNA1.0 microarray to obtain global miRNA expression data of human monocytes, unstimulated and IL-4-stimulated differentiating macrophages.

overall_design: CD14+ monocytes were separated from human peripheral blood and exposed to IL-4 for 12 or 72 hours. The global miRNA expression patterns of human monocytes, unstimulated and IL-4-stimulated differentiating macrophages were analyzed on Affymetrix microarrays.

first: Zsolt

last: Czimmerer

first: Tamas

last: Varga

first: Mate

last: Kiss

first: Cesaré

middle: O

last: Vázquez

first: Quang

last: Doan-Xuan

first: Dominik

last: Rückerl

first: Sudhir

middle: G

last: Tattikota

first: Zsuzsanna

last: Nagy

first: Bence

last: Daniel

first: Attila

last: Horvath

first: Gergely

first: Eva

last: Varallyay

first: Matthew

last: Poy

first: Judith

middle: E

last: Allen

last: Bacso

first: Cei

last: Abreu-Goodger

first: Laszlo


title: SGK1 REGULATION BY miR-466g IN CORTICAL COLLECTING DUCT CELLS

status: Public on Apr 16 2016

city: Palo Altp

first: Mollie

middle: Elizabeth

last: Jacobs

state: CA

address: 3801 Miranda AVE

department: Medicine

country: USA

institute: Stanford University

summary:
To study the effects of aldosterone on miRNA in the kidney cortical collecting duct, polarized mpkCCDc14 cell were treated with aldosterone or vehicle.
A putative target for miR-466g was identified, the effect of modulating miR-466g levels on SGK1 levels was examined

overall_design: In this dataset we include paired vehicle or aldosterone-treated samples

first: Alan

middle: C

last: Pao


title: Gene expression profiles of yeast treated with YCl3 and Y2O3 nanoparticle

status: Public on Apr 27 2016

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

country: Japan

institute: Gifu University

summary: In this study, we attempted to compare among the stress of Y2O3 nanoparticle and YCl3 to yeast cells. Yttrium oxide (Y2O3) nanoparticle is used in widespread applications. It has been reported that Y2O3 nanoparticle showed toxic activities. However, we assumed that the most important toxic factor of nanoparticles was metal ion release. We tried to prove the toxicity of yttrium nanoparticles comes from yttrium ion. Therefore, we used YCl3 as a positive control for evaluation of effects of yttrium ion.

overall_design: Series contains four hybridization results from independent biological samples respectively in five conditions (Control; performed sep9 2014, Control; performed nov9 2015, treated YCl3 5 mg, treated Y2O3 nanoparticle 3 mg , treated Y2O3 nanoparticle 20 mg).

first: Youta

last: Mizuno

first: Junko

last: Takahashi

first: Masanori

last: Horie

first: Hitoshi

last: Iwahashi


title: Effect of NIK overexpression on Foxp3+CD4+ and Foxp3-CD4+ T cell subsets [Affymetrix]

status: Public on Apr 29 2016

city: Portland

first: Susan

last: Murray

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Molecular microbiology and immunology

institute: OHSU

summary:
We previously found that NF-kB inducing kinase (NIK) overexpression in T cells via CD4 promoter driven transgene induction caused lethal autoimmunity in mice. Autoimmunity was associated with increased conventional T cell effector function and decreased regulatory T cell (Foxp3+CD4+) suppression. The goal in this study was to elucidate global transcriptional changes in Foxp3+CD4+ and Foxp3-CD4+ T cells intrinsically caused by chronic NIK overexpression in these cell types.
Total RNA from FACS-sorted NIKtg and WT Foxp3RFP+CD4+ and Foxp3RFP-CD4+ harvested from NIKtg/CD4Cre/Foxp3RFP + WT/Thy1.1/Foxp3RFP mixed bone marrow chimeric mice, >8 weeks after bone marrow reconstitution.

overall_design: Fanny,Polesso

first: Minhazur

last: Sarker

first: Arian

last: Anderson

first: David

last: Parker

first: Chris

last: Harrington

first: Aimee

last: Potter

first: Julja

last: Burchard

first: Mark

last: Fisher


title: Yeast cells: Mutant M1 vs. the control with and without oxidative stress

status: Public on Mar 10 2016

city: Singapore

first: Hefang

last: Geng

address: 62 Nanyang Drive, School of Chemical & Biomedical Engineering, Nanyang Technological University

country: Singapore

institute: Nanyang Technological University

summary:
Transcription profiles of mutant M1 and the control in the absence/presence of 4mM H2O2
M1 is a mutated  Saccharomyces cerevisiae strain. It was obtained through transcriptional engineering of general transcription factor TFIIB. Encoded by SUA7, TFIIB is reported to regulate the expression of over 730 genes in Saccharomyces cerevisiae. M1 showed significant growth improvement compared with the control when challenged with 4mM H2O2. It also had resistance towards high osmotic pressure (1.5M NaCl).

overall_design: Two-condition experiment (no stress and 4mM H2O2 stress): M1 vs the control. Two biological replicates for M1 and the control under each condition.

first: Yang

last: Zhong

first: Rongrong

last: Jiang


title: Differentially expressed miRNAs between T29H and T29 cells

status: Public on Mar 06 2016

city: wenzhou

first: jianmin

last: wu

state: zhejiang

address: 268 xueyuan Road

country: China

institute: wenzhou medical university

summary:
miRNAs are small regulatory non-coding RNA molecules that influence a wide range of biological and pathological processes. Piling evidence has shown that miRNAs regulate the expression of various genes pivotal for tumor onset, progression and metastasis.
Here we compared the miRNA profiling between T29(human ovarian epithelial cell immortalized with SV40T/t antigens and the human telomerase catalytic subunit) and T29H (T29 transformed with the oncogenic H-RASv12) cell lines.

overall_design: T29H vs.T29

first: Jianmin

last: Wu

first: Yimin

last: Sun

first: Ki-Fu

last: Tang


title: miRNA expression data of shoot meristems of trifoliate orange

status: Public on Mar 04 2016

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

summary: In 1976, a spontaneous mutant derived from Poncirus trifoliata (L.) Raf with short juvenile phase, namely, precocious trifoliate orange, was found in Yichang, Hubei province, China. Compared with 6 to 8 years of the wild-type trifoliate orange, almost all of the seedlings germinated from precocious trifoliate orange only have 1 to 2 years’ juvenile period, and 20% seedlings even flowered in the year after germination. Therefore, precocious trifoliate orange is an ideal material for studying the role of miRNAs involved in citrus juvenile and adult developmental stages.  To characterize these miRNAs expressed at the juvenile and adult development stages of citrus, Affymetrix miRNA arrays were used to generate miRNA profiles of shoot meristems of trifoliate orange, the results revealed that some miRNAs were down-regulated expressed at adult stage compared with juvenile stage. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated.

overall_design: To investigate the expression patterns of these miRNAs at juvenile and adult stages of citrus, four independent precocious trifoliate orange RNA samples (March, June, December and April next year) were hybridized with miRNA microarray, respectively. The expression of miRNA was analyzed with the SAM software.

first: Jin-Zhi

last: Zhang

first: Xiao-Yan

last: Ai

first: Lei-Ming

first: Wen-Wu

last: Guo

first: Shu-Ang

last: Peng

first: Xiu-Xin

last: Deng

first: Chun-Gen

last: Hu


title: Genome-wide microRNA expression profiling in tunicamycin treated NIH3T3 cells

status: Public on Mar 22 2016

city: Charleston

first: John

middle: Alan

last: Diehl

state: SC

address: 86 Jonathan Lucas Street

institute: Medical University of South Carolina

summary: NIH 3T3 cells were challenged with tunicamycin for 2, 5 or 10h. MICRO-RNAs that are upregulated or down regulated were identified by micro-ARRAY.

overall_design: NIH 3T3 cell were challenged with 2ug/ml tunicamycin for 2, 5 or 10 hrs. Total RNA was purified using miRNeasy Mini Kit (QIAGEN). Microarray was carried out using GeneChip® miRNA Arrays (Affymetrix, CA) and results were analyzed using GENESPRING software.  ANOVA and T-tests were used to calculate fold change and p-values.  Spotfire (Somerville, MA) software was used to generate heat maps.

first: J

middle: A

first: Yiwen

last: Bu

first: Nilesh

last: Chitnis


title: Transcriptomic analysis of two ethanol-tolerant Saccharomyces cerevisiae clones obtained by evolutionary engineering

status: Public on Mar 01 2016

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

summary: Evolutionary engineering strategy was used for selection of ethanol-tolerant Saccharomyces cerevisiae clones under gradually increasing ethanol stress levels. Clones B2 and B8 were selected based on their higher ethanol-tolerance and higher ethanol production levels. Whole genome microarray analysis was used for identifying the gene expression levels of these two evolved clones compared to the reference strain.

overall_design: Two evolved ethanol-tolerant strains B2 and B8, which were selected by evolutionary engineering under gradually increasing ethanol stress, were used for whole genome transcriptomic analysis in comparison with the reference strain. Cells were grown in yeast minimal media until they reach a final OD600 of 1. Following total RNA isolation, gene expression levels were analyzed using One-color microarray-based gene expression analysis (Agilent Technologies). Experiments were done in triplicates.

first: B

last: Turanli-Yildiz

first: L

last: Benbadis

first: C

last: Alkım

first: T

last: Sezgin

first: A

last: Akşit

last: Gökçe

first: Y

last: Öztürk

middle: T

last: Baykal

first: Z

middle: P

last: Çakar

middle: M

last: François


title: INO80 promotes reassembly of promoter proximal nucleosomes.

status: Public on Mar 02 2016

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

summary: INO80 and SWR1 mediate the exchange of H2A.Z and H2A. The influence of H2A.Z on overall gene expression in yeast is limited. Here we analyzed the possible influence on stress induced transcription, which changes expression of a large proportion of all yeast genes.

overall_design: Yeast cells (wild type and htz1 mutant) were grown to exponential phase and treated with osmotic stress (0.4M NaCl) for 20 minutes or left untreated. Experiments were performed with 2 biological replicates.

first: Walter

last: Glaser

first: Martin

last: Radoph

first: Eva

last: Klopf

last: Schüller


title: Expression data from Nasopharyngeal carcinoma cell SUNE1

city: Guangzhou

first: Yang

middle: Meng

last: Zhao

address: Shiliugang Road

institute: Southern Medical University

summary: To investigate the effect of FOXO1 on miRNAs in Nasopharyngeal carcinoma, we used miRNA chip on SUNE1 cells after FOXO1 overexpression. This analysis identified 82 miRNAs which were markedly dysregulated in FOXO1 overexpressing cells.

overall_design: Total RNA (6–7 mg) was isolated from FOXO1-overexpressing and control SUNE1 cells and Micro RNA Array was used to search the differential expression miRNAs

first: Mengyang

first: Weiyi

last: Fang


title: Clinical impact of a novel microRNA chemo-sensitivity predictor in gastroesophageal cancer

status: Public on Feb 18 2016

city: Aarhus C

first: Mette

last: Winther

address: Noerrebrogade 44, build. 5

department: Dept. of Experimental Clinical Oncology

country: Denmark

institute: Aarhus University Hospital

summary:
Background: miRNAs might be potentially useful biomarkers for prediction of response to chemotherapeutic agents, radiotherapy and survival. The aim of this retrospective study was to validate miRNA response predictors in a cohort of patients with gastroesophageal cancer in order to predict overall survival (OS) and disease-specific survival (DSS).
Material and methods: The study population encompassed 53 patients treated with curative intended for loco-regional gastroesophageal cancer. miRNA expression was quantified from pre-therapeutic and diagnostic, formalin-fixed, paraffin embedded tumor specimens using Affymetrix GeneChip miRNA 1.0 Array. Based on growth inhibition of the NCI60 panel in the presence of cisplatin, epirubicine and capecitabine, a miRNA based response predictor was developed. The Cox proportional hazards model was applied to assess the correlations of the response predictor with OS and DSS.
Results: A univariate analysis demonstrated a statistical significant improvement of OS for patients who had undergone surgical resection with prediction scores above the median prediction score (HR: 0.41 (95% CI: 0.17-0.96). Adjusting for surgery and stage, this predictor was identified to be independently associated with both OS (HR: 0.37 (95% CI: 0.16-0.87)) and DSS (HR: 0.32 (0.12-0.87)).
Conclusion: The miRNA profile predictive for sensitivity to cisplatin, epirubicine and capecitabine was shown to be independently associated with OS and DSS in patients with gastroesophageal cancer.

overall_design:
Tumor biopsies from 53 patients with gastroesophageal cancer
*** Submitter has provided limited clinical information.  Thus, this submission is incomplete. ***

first: Steen

last: Knudsen

first: Jesper

last: Dalgaard

first: Thomas

last: Jensen

first: Anker

last: Hansen

first: Peter

middle: B

first: Trine

last: Tramm

first: Jan

last: Alsner

first: Marianne

last: Nordsmark


title: MicroRNA and gene expression changes in human cerebral aneurysms [expression array]

status: Public on Feb 24 2016

city: Corvallis

first: David

middle: Anthony

last: Hendrix

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

summary: Cerebral Aneurysm tissues and superficial temporal arteries were compared through RNA-Seq to identify differentially expressed genes, and through microRNA microarray to identify differentially expressed microRNAs. Significant miR:gene pairs were identified for potential microRNA silencing regualtory effects.

overall_design: To study differentially expressed genes and microRNAs in cerebral aneurysms, we collected 7 cerebral aneurysm tisses and 10 superficial temporal artery (STA) tisses from 17 individuals. We performed RNA-Seq and microRNA microarray analysis on these samples, and compared them using STA as a control.

first: Kimon

last: Bekelis


title: Helicobacter pylori-induced changes in miRNA expression in human gastric epithelial cells

status: Public on Jan 18 2016

first: Jeremy

last: Barth

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: H. pylori infection of human gastric epithelial cells (GEC) represses H,K-ATPase alpha subunit (HK-alpha) gene transcription through NF-Kappa B p50 homodimer binding to HK-alpha promoter. The bacterial cagA and slt gene products have been implicated in HK-alpha repression, which facilitates gastric H. pylori colonization and may underlie transient clinical hypochlorhydria. We hypothesized that H. pylori also regulates H,K-ATPase expression post-transcriptionally by micro-RNA interaction with HK-alpha mRNA. Our microarray experiment examined the effect of infection by wildtype H. pylori infection or a delta-cagA H. pylori mutant on miRNA expression of human gastric cells (AGS). Our results indicate that H. pylori infection up-regulates GEC miRNAs that target the HK-alpha 3' UTR and block translation, and that CagA activity is implicated in the miRNA up-regulation.

overall_design: Three types of samples were generated for microarray analysis: 1) AGS cells infected with wildtype H. pylori; 2) AGS cells infected with cagA-deficient H. pylori; 3) a mock-infected sample, prepared as a control by combining total RNA from uninfected AGS cells with total RNA from wildtype H. pylori, with relative eukaryotic and prokaryotic RNA amounts matching those observed in infected samples, based on proportional ribosomal peak heights quantified by Bioanalyzer. Three experimental replicates were generated for each type of treatment.

first: Adam

middle: J

last: Smolka

middle: L


title: miR-182 modulates myocardial hypertrophic response induced by angiogenesis in heart (miRNA)

status: Public on Feb 17 2016

city: New Haven

first: Daniela

last: Tirziu

state: CT

address: 300 George Street

department: Internal Medicine/Cardiology

institute: Yale University School of Medicine

summary:
Angiogenesis induced by placental growth factor (PlGF) in heart promotes myocardial hypertrophy through the paracrine action of endothelium-derived nitric oxide which triggers the degradation of RGS4 and subsequent activation of the Akt/mTORC1 pathway in cardiomyocytes. However, whether alterations in miRNAs contribute to the development of hypertrophy is largely undetermined.
We found that miR-182 contributed to the hypertrophic response and activation of the Akt/mTORC1 pathway by suppressing the expression of Bcat2, Pink1, Adcy6, Foxo3.

overall_design: The expression of miRNAs and the effects of anti-miRs were investigated in the mouse model of myocardial angiogenesis induced by conditional, cardiac specific expression of PlGF. We also induced angiogenesis, but blocked hypertrophy by concomitant expression of PlGF and RGS4 (PlGF/RGS4 mice). Microarray profiling of miRNAs in LV myocardium was determined after 3 and 6 weeks of transgene expression.

last: Li


title: Gene expression change of M1 and BY-P41K-RPB7 in YPAD (OD600 reached 1) and after 12h Very High Gravity (VHG) fermentation

status: Public on Feb 12 2016

first: Zilong

last: Qiu

address: 62 Nanyang Drive

department: School of Chemical & Biomedical Engineering

summary: To further study the transcription profile of mutant M1 and its control (BY-P41K-RPB7), we have employed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in YPAD medium under OD600 reached 1 and after 12 VHG fermentation.

overall_design: Total cellular RNAs were extracted from both the mutant and the control using RNeasy® Mini Kit and RNase-Free DNase Set (Qiagen,Hilden, Germany) under the following two conditions: i) when cells reached early exponential phase (OD600 ~1.0) in YPAD; ii) after 12h VHG fermentation. RNA quality and integrity was verified by gel electrophoresis, as well as by measuring 260/230 ratios with a NanoDrop 1000 spectrophotometer (Thermo Scientific, MA, USA). Two biological replicates of each sample were sent to Genomax Technologies (Singapore) for DNA microarray assay using Yeast (V2) Gene Expression Microarray, 8×15K Microarrays (Agilent technologies, USA). The obtained data was analyzed by Agilent Genespring GX software and the p-values were calculated by unpaired Student t-test.

first: Qiu

last: Zilong


title: Toxicogenomic effects of sub-lethal exposures of organophosphates on mouse liver cells [miRNA Expression]

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: In order to examine the long term effects of the OPs, murine liver cells (BNL CL.2, ATCC® TIB-73) have been exposed to sub-lethal doses of three OPs: diisopropylfluorophosphate (DFP) representative of sarin and soman, O,S-diethyl methylphosphonothioate (OSD) serving as a simulant for VX, and paraoxon as an example of OP insecticides.  Dosing levels of these compounds was set at 20% of the IV LD50 for each, with a 4 hour exposure time.  Gene arrays and physiological tests were run at three time points following exposure; 2 hours, 2 days, and 2 weeks.  The physiological results showed little to no effect upon exposure to sub-lethal dose of OPs.  Gene expression and microRNA (miRNA) profiles using GeneChip Mouse Gene 1.0 ST arrays and miRNA arrays (Affymetrix, Santa Clara, CA) found that the OPs did alter expression of genes related to several systems previously implicated in OP exposure with no long term effects.  In addition, a significant number of sRNA/snRNA and ribosomal RNA were found to be affected suggesting the need for further study of the changes in these regulators.

overall_design: Three biological replicates of ;iver cells were exposed to three representative OPs and then harvested at three time points (2 hours, 72 hours, and two weeks) following exposure.  These time points were designed for a determination of both early and late effects as well as identification of persistent, chronic changes.  The RNAs from the collected cells were extracted and processed on commercial microarrays to determine the gene expression patterns and miRNA profiles associated with response to exposure to the OPs.

last: O’Shaughnessy

first: Anthony

last: Malanoski

first: Robert

last: Rubin

first: Nina

last: McAuliff


title: Low plasma levels of miR-451a, miR-223-3p, and miR-27a-3p predict adverse prognosis in myelodysplastic syndromes

status: Public on Jan 13 2016

city: Prague 2

first: Michaela

last: Dostalova Merkerova

address: U nemocnice 1

department: Department of Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

summary: We investigated the spectra of circulating miRNAs in plasma of myelodysplastic syndromes (MDS) patients. Peripheral blood plasma from MDS patients with different risk scores was used for Agilent miRNA expression microarray analysis to define miRNA profile and to find miRNAs with discriminatory levels for lower risk and higher risk MDS. Results were further validated using droplet digital PCR on a larger cohort, enabling absolute quantification of plasma miRNAs and defining miRNAs with prognostic value for the disease.

overall_design: We analyzed expression profile of circulating miRNAs in plasma from 21 individuals:  7 controls and 14 MDS patients.

first: Andrea

last: Hrustincova

first: Zdenek

last: Krejcik

first: Eva

last: Ratajova

first: Jaroslav

last: Cermak

first: Monika

last: Belickova


title: Establishment and miRNA expression characterization of a canine mammary gland tumor cell line

status: Public on Jan 01 2016

city: Tottori

first: Tomohiro

last: Osaki

state: Tottori

address: 4-101 Koyamachominami

department: Faculty of Agriculture

institute: Tottori University

summary: Canine mammary gland tumors (CMGTs) are the most common neoplasms in sexually intact female dogs. CMGTs have been suggested as a model for studying human breast cancer because of several similarities, including the relative age of onset, risk factors, incidence, histological and molecular features, biological behavior, metastatic pattern, and responses to therapy. In the present study, we established a new cell line, the SNP cell line, from a CMGT. A tumor formed in each NOD.CB17-Prkdcscid/J mouse at the site of subcutaneous SNP cell injection, with an average size at 7 days after inoculation of 49.9 mm3. SNP cells are characterized by proliferation in a tubulopapillary pattern. Moreover, we examined miRNA expression in the cultured cells and found that the expression values of miRNA-143 and miRNA-138a showed the greatest increase and decrease, respectively, of all miRNAs observed. These miRNAs might therefore play a significant role in the malignancy of SNP cells. SNP cells might serve as a model for future genetic analysis and clinical treatments of human breast tumors.

overall_design: SNP cells or normal mammary gland tissue were freshly frozen within 30 minutes of harvesting or surgical excision and stored at -80 °C until further use for an Affymetrix® GeneChip® miRNA array. An Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.) was used to assess the quality of total RNA (1,000 ng). The biotin-labeled sample was prepared with a Flash TagTM Biotin HSR RNA Labeling Kit (Affymetrix, Inc.) according to the manufacturer’s protocol, and 21.5 µl of biotin-labeled sample was combined with 110.5 μl of Hybridization Master Mix. The array was incubated at 48 °C and 60 rpm for 18 hours in a GeneChip® Hybridization Oven 645 (Affymetrix, Inc.) according to the manufacturer’s protocol. A GeneChip® Fluidics Station 450 (Affymetrix, Inc.) was used to wash the array according to the manufacturer’s protocol before scanning with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) following the protocol in the Affymetrix® GeneChip® Command Console User Manual.

first: T

first: A

last: Sugiyama

first: K

last: Azuma

first: Y

last: Murahata

last: Tsuka

first: N

last: Ito

last: Imagawa

last: Okamoto


title: Expression data for human nasopharyngeal carcinoma cell line HK1 stimulated with EGF or TGF-β recombinant protein.

status: Public on Dec 17 2015

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary: As regulators in gene expression, microRNAs take part in most biological process including cell differentiation, apoptosis, cell cycle and epithelial-to-mesenchymal transition (EMT). In order to evaluate their roles during the growth factors-induced EMT process, microRNA expression profile changes induced by EGF or TGF-β treatment on nasopharyngeal carcinoma cell line HK-1 cells were analyzed by means of the Affymetrix genome wide microarray system.

overall_design: Human nasopharyngeal carcinoma cell line HK-1 was starved for 12 hours before stimulation with EGF (50 ng/mL) or TGF-β (10ng/ml) or Control (PBS) for 36 hours in RPMI-1640 medium (with 1% serum) to establish the in vitro model of EMT. Total RNA were extracted and detected by Affymetrix® GeneChip® miRNA Arrays.

first: Zailong

last: Qin

first: Wei

last: He

first: Guiyuan

last: Li


title: Systemic inflammation is associated with differential gene expression and airway neutrophilia in asthma

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

summary: Systemic inflammation is reported to be associated with neutrophilic airway inflammation in asthma, this study aimed to examine the molecular mechanisms of the neutrophilia that is associated with systemic inflammation, and hypothesized that asthma patients with systemic inflammation have a group of genes that are differentially expressed and are assciated with airway inflammation.

overall_design: 50 asthma patients were recruited and grouped as asthmatics with systemic inflammation (n=18) and asthamtics without systemic inflammation (n=16) accroding to the levels of serum CRP and IL-6. RNA was extracted from induced sputum and was reverse-transcribed into cDNA. Gene profiling was performed using Illumina Sentrix HumanRef-8 Version 2 Expression BeadChips, and genes that were differentially expressed between asthmatics with systemic inflammation and asthmatics without systemic inflammation were compared and valided using qPCR.

first: Katherine

first: Juan-juan

last: Fu


title: The homeobox transcription factor Nkx2-1 regulates microRNAs controlling downstream gene silencing in lung epithelial cells (microRNA)

status: Public on Dec 22 2015

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

institute: Boston University

summary: Cell-specific gene expression is achieved by a combination of mechanisms including transcriptional and post-transcriptional regulation. The transcription factor Nkx2-1, essential for lung cell differentiation, mainly acts in transcriptional activation but can directly or indirectly repress gene expression. microRNAs are a class of small non-coding RNA that control one of the major mechanisms of gene repression. To identify miRNAs regulated by Nkx2-1 that may mediate its repressing effects, we knocked-down Nkx2-1 in mouse lung epithelial cell lines and systematically identified targets by genome-wide miR and mRNA expression analyses. Nkx2-1 controls expression of miRs known to contribute to lung cell differentiation in development and disease and others not previously described. Amongst the significantly altered miRs, the mir-106a-363 cluster, miR-1195, miR-378, and miR-346 are directly correlated with the levels of Nkx2-1, whereas miR-200c/b, miR-221, and miR- 222 are inversely correlated. These miRNAs are expressed in embryonic lung at day E11.5, and/or E19.5 determined by in-situ hybridization. Expression of predicted targets of mir-1195, mir-346 and miR-200c and mir-221/222 were evaluated by mRNA expression microarrays in Nkx2-1 knockdown cells identifying those anti-correlated to the corresponding miRNA expression. Genes regulated by mir-1195, Cyp2s1 and Map3k2, by mir-346, Klf6, and miR-200c, Myb, Nfib, and Six1, were validated by qRT-PCR. Inhibition of mir-1195 confirms the inverse correlation of this miRNA with its putative targets Cyp2s1 and Map3k2. This miRNA-mRNA expression analysis identifies potential paths of Nkx2-1 mediated gene repression, and contributes to the understanding of gene regulation in lung epithelial differentiation and development.

overall_design: Nkx2-1 mRNA was knocked down in lung epithelial cells using a lentivirus expressing a shRNA targeting Nkx2-1 (n=3) and compared to empty vector controls (n=3).

first: Jean-Bosco

last: Tagne

first: Omar

middle: R

last: Mohtar

middle: D

first: Meenakshi

last: Lakshminarayanan

first: Jingshu

last: Huang

first: Anne

last: Hinds

first: Jining

last: Lu

first: Maria

middle: I

last: Ramirez


title: miRNA and mRNA profiles in the genetic hypercalciuric stone-forming (GHS) rat compared to normal SD rat

status: Public on Dec 01 2015

city: Wuhan

first: Yuchao

last: LU

state: Hubei

address: 1095# Jiefang Avenue

department: Urology

institute: Tongji Hospital of Tongji medical college, Huazhong University of Science &Technology

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

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

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series


title: The effect of the magnesium and copper supplementation in the transcriptional response of Saccharomyces cerevisiae JP1 under fermentation condition

status: Public on Dec 09 2015

city: Recife

first: Marcos

middle: Antonio

last: Morais

state: Pernambuco

address: Av. Moraes Rego, 1235

department: Department of Genetics

country: Brazil

institute: Federal University of Pernambuco

summary: In our previous work, we showed the positive effect of the magnesium and the negative effect of the copper on yeast fermentation performance. The magnesium increases the ethanol yield and a faster glucose consumption by the yeast, on the other hand, the copper provides an opposite effect in yeast under fermentation condition. Therefore, from this contrasting effect we performed the gene-wide expression analysis in the industrial yeast Saccharomyces cerevisiae JP1 under fermentation condition in order to reveal the gene expression profile upon magnesium and copper supplementation.

overall_design: Fermentation assays was performed with the industrial yeast S. cerevisiae JP1 in reference medium (mineral concentration balanced), in the medium supplemented with 500 mg/L of magnesium (Mg2+ medium) and in the medium supplemented with 1 mg/L of copper (Cu2+ medium).

first: Souza

last: Rafael

first: Silva

last: Rayssa

first: Pita

last: Will

first: Paiva

last: Sergio

first: Morais

last: Marcos


title: Nitric oxide regulates gene expression in cancers by controlling histone posttranslational modifications [miRNA-4_0]

status: Public on Nov 05 2015

city: Chicago

first: Douglas

last: Thomas

state: IL

address: 900 S Ashland Ave Room 3306

department: Medicinal Chemistry & Pharmacognosy

institute: University of Illinois at Chicago

summary: Dynamic changes in histone posttranslational modifications (PTMs) are important regulators of chromatin structure and gene transcription in both normal and disease settings. Herein, we describe a novel signaling mechanism of nitric oxide (•NO) by demonstrating its ability to modulate gene expression via alteration of histone PTMs. Having established that •NO exposure induced differential expression of approximately 6500 genes, we set out to determine if there was an epigenetic component to their regulation. •NO exposure led to alterations in the global levels of acetyl and methyl modifications at numerous lysine residues on core histones H3 and H4. Residues H3K9me2/ac were examined further and determined to have differential distribution at various loci throughout the genome in response to •NO. Changes in the enrichment levels of H3K9me2/ac at specific genes correlated with changes in the expression levels of their transcripts. Molecular mechanisms contributing to phenotypic outcomes in •NO-associated cancers remain to be well understood since traditional modes of •NO-signaling do not explain a large proportion of its impact on tumor cell behavior. Our results reveal that •NO drives a significant amount of gene expression changes epigenetically by changing the distribution of numerous histone marks.

overall_design: Cultured cells were treated with 500uM DETA/NO to examine the effects of a physiologically relevant •NO concentration on miRNA expression. A total of three untreated biological replicates and three •NO-treated biological replicates were harvested. The untreated samples served as control against which comparisons were made to elucidate •NO-mediated changes in the miRNA expression.

first: Divya

last: Vasudevan

first: Jason

last: Hickok

first: Rhea

middle: C

last: Bovee

first: Vy

last: Pham

first: Lin

last: Mantell

first: Neil

last: Bahroos

first: Pinal

last: Kanabar

first: Xing-Jun

last: Cao

first: Mark

last: Maienschein-Cline

first: Benjamin

last: Garcia


title: Comparison of miRNA expression in HT29-tsp53 cells cultured at the permissive and restrictive temperatures

status: Public on Jan 07 2016

city: Ottawa

first: Bruce

last: McKay

state: Ontario

address: 1125 Colonel By Dr.

department: Biology

country: Canada

institute: Carleton University

summary: The p53 tumour suppressor is a transcription factor that can regulate the expression of numerous genes encoding either proteins or microRNAs (miRNAs).  The predominant outcomes of a typical p53 response are the initiation of apoptotic cascades and the activation of cell cycle checkpoints.  HT29-tsp53 cells express a temperature sensitive variant of p53 and in the absence of exogenous DNA damage, these cells preferentially undergo G1 phase cell cycle arrest at the permissive temperature that correlates with increased expression of the cyclin-dependent kinase inhibitor p21WAF1.   Recent evidence also suggests that a variety of miRNAs can induce G1 arrest by inhibiting the expression of proteins like CDK4 and CDK6. Here we used oligonucleotide microarrays to identify p53-regulated miRNAs that are induced in these cells undergoing G1 arrest.  At the permissive temperature, the expression of several miRNAs was increased through a combination of either transcriptional or post-transcriptional regulation. In particular, miR-34a-5p, miR-143-3p and miR-145-5p were strongly induced and they reached levels comparable to that of reference miRNAs (miR-191 and miR-103).  Importantly, miR-34a-5p and miR-145-5p are known to silence the Cdk4 and/or Cdk6 G1 cyclin-dependent kinases (cdks).  Surprisingly, there was no p53-dependent decrease in the expression of either of these G1 cdks.  To search for other potential targets of p53-regulated miRNAs, p53-downregulated mRNAs were identified through parallel microarray analysis of mRNA expression.  Once again, there was no clear effect of p53 on the repression of mRNAs under these conditions despite a remarkable increase in p53-induced mRNA expression.  Therefore, despite a strong p53 transcriptional response, there was no clear evidence that p53-responsive miRNA contributed to gene silencing.  Taken together, the changes in cell cycle distribution in this cell line at the permissive temperature is likely attributable to transcriptional upregulation of the CDKN1A mRNA and p21WAF1 protein and not to the down regulation of CDK4 or CDK6 by p53-regulated miRNAs.

overall_design: Two independent experiments were performed with 2 samples in each experiment (1 control and 1 treatment condition).  In the control sample, RNA was isolated cells maintained at the restrictive temperature (37˚C). The treatment treated sample, was incubated for 16 hours at the permissive temperature  (32˚C).

first: Miguel

last: Cabrita

first: Erin

last: Vanzyl

first: Jeff

last: Hamill

first: Elysia

last: Pan

first: Kristen

last: Marcellus

first: Victoria

last: Tolls

last: Alonzi

first: Alyssa

last: Pastic

first: Teaghan

last: Rambo

first: Hadil

last: Sayed


title: Persistence of Smoking-induced Dysregulation of Small Airway Epithelium miRNA Expression Despite Smoking Cessation

status: Public on Nov 23 2015

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Rationale: Even after quitting smoking, the risk of the development of chronic obstructive pulmonary disease (COPD) and lung cancer remains significantly higher compared to never-smokers. Objectives: Based on the knowledge that COPD and most lung cancers start in the small airway epithelium (SAE), we hypothesized that smoking modulates miRNA expression in the SAE linked to the pathogenesis of smoking-induced airway disease, and that some of these changes persist after smoking cessation. Methods: SAE was collected from 10th to 12th order bronchi using fiberoptic bronchoscopy. Affymetrix miRNA 2.0 arrays were used to assess miRNA expression in the SAE from 10 healthy never-smokers and 10 healthy smokers, before and after they quit for 3 months. Smoking status was determined by urine nicotine and cotinine measurement. Results: There were significant differences in the expression of 34 miRNAs between healthy smokers and healthy never-smokers (p<0.01, fold-change >1.5), with functions associated with lung development, airway epithelium differentiation, inflammation and cancer. After quitting smoking for 3 months, 12 out of the 34 miRNAs did not return to normal levels, with Wnt/β-catenin signaling pathway the top enriched pathway of the target genes of the persistent deregulated miRNAs. Conclusions: In the context that many of these persistent smoking-dependent miRNAs are associated with differentiation, inflammation diseases or lung cancer, it is likely that persistent smoking-related changes in small airway epithelium miRNAs play a role in the subsequent development of these disorders.

overall_design: MicroRNA profiling identified 34 miRNAs up-regulated by cigarette smoking in human small airway epithelium. Even after quitting smoking for 3 months, 12 miRNAs didn’t return to normal level.

first: Guoqing

last: Wang

first: Rui

first: Jacqueline

last: Salit

first: Michelle

last: Staudt

first: Joumana

last: Ahmed

first: Tilley

middle: E

last: Ann

first: Yee-Levin

last: Jenny

first: Hollman

last: Charleen

first: Harvey

last: Ben-Gary

first: Kaner

last: Robert

first: Mezey

middle: G

last: Jason

first: Sridhar

last: Sriram

first: Pillai

last: Sreekumar

first: Hilton

last: Holly

first: Wolff

last: Gerhard

first: Bitter

last: Hans

first: Visvanathan

last: Sudha

first: Fine

last: Jay

first: Stevenson

middle: S

last: Chistopher

first: Ronald

last: Crystal


title: Daphnia miRNA expression data from Cadmium exposed and none-exposed samples

status: Public on Oct 15 2015

city: West Lafayette

first: SHUAI

last: CHEN

state: IN

address: 195 Marsteller Street

department: Forestry and Natural Resources

institute: PURDUE UNIVERSITY

summary: We used Affymetrix microarrays to profile the Dapnia pulex miRNA expression under Cadmium exposure and identified Cadmium-responsive miRNAs

overall_design: D. pulex were exposed to Cadmium concentration of 0 ppb (control), 20ppb(Cd-low) and 40ppb(Cd-high) for 48h.  Each treatment has three biological replicates for expression profile by Affymetrix microarray.

first: Shuai

last: Chen

first: Maria

last: Sepulveda

first: Krista

last: Nichols


title: Small nucleolar RNA and microRNA expression data from an MS patient's and a healthy control's PBMC cultures stimulated with phytohemagglutinin.

status: Public on Nov 03 2015

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

summary: Multiple sclerosis is a common inflammatory and degenerative disease that causes neurological disability. It affects young adults and its prevalence is higher in women. The most common form is manifested as a series of acute episodes of neurological disability (relapses) followed by a recovery phase (remission). Recently, non-coding RNAs have emerged as new players in transcriptome regulation, and in turn, they could have a significant role in MS pathogenesis. In this context, our aim was to investigate the involvement of microRNAs and snoRNAs in the relapse-remission dynamics of MS in peripheral blood leucocytes, to shed light on the molecular and regulatory mechanisms that underlie this complex process. With this approach, we found that a subset of small non-coding RNAs (sncRNA) is altered in relapse and remission, revealing unexpected opposite changes that are sex dependent. Furthermore, we found that a relapse-related miRNA signature regulated general metabolism processes in leucocytes, and miRNA altered in remission are involved in the regulation of innate immunity. We observed that sncRNA dysregulation is different in relapse and remission leading to differences in transcriptome regulation, and that this process is sex dependent. In conclusion, relapse and remission have a different molecular background in men and women.

overall_design: PBMC samples from a MS patient and a healthy control cultured with and without stimulation with phytohemagglutinin.

first: David

last: Otaegui


title: Analysis of altered miRNA expression profiles in the  genetic hypercalciuric stone-forming (GHS) rat compared to normal SD rat

first: Yuchao

last: LU

summary: Urolithiasis is a common disease to human beings, and idiopathic hypercalciuria (IH) is an important risk factor of calcium urolithiasis, previous studies strongly suggested that the decreased tubular Ca2+ reabsorption played a key role of hypercalciuria. However,the molecular mechanism of IH-urolithiasis formation is still not completely elucidated. GHS rat is regarded as an ideal animal model of calcium urolithiasis, reveals many identical pathophysiologic characteristics with IH patients . We analyzed miRNA expression profiles of the kidney of GHS rat  in order to find out the target genes and signaling pathways in the pathogenesis of IH.

overall_design: The colony of GHS rats were created by the selective breeding of male and female SD rats with the highest 24 hour urine excretions (doi: 10.3390/ijms160716313). In the 28 generation, GHS rats have stabilized excreted significant higher level of urine calcium than wild-type normal SD rats, and reveals many identical pathophysiologic characteristics with IH patients, such as normal serum Ca2+, hypercalciuria, elevated intestinal Ca2+ resorption and a tendency to lose calcium from the bone. This present study examined the miRNAs expression of three pairs of GHS rats’ kidneys with normal SD rats by microarrays.

last: Lu

first: Shaogang

last: Wang


title: The prognostic significance of the dynamic changes of miRNA expression in locally advanced BC during neo-adjuvant chemotherapy treatment

status: Public on Oct 31 2015

city: Muscat

first: Manal

middle: Humaid

last: Al Khanbashi

address: Al Khod

department: Medicine

country: Oman

institute: Sultan Qaboos University

summary:
Introduction: MicroRNAs (miRNAs) are small non-coding RNA that play a vital role in cancer progression. Neo-adjuvant chemotherapy (NAC) has become the standard of care for locally advanced breast cancer. The aim of this study was to evaluate miRNA alterations during NAC using multiple samples of tissue and serum to correlate miRNA expression with clinico-pathological features and patient outcomes.
Methods: Tissue and serum samples were collected from patients with locally advanced breast cancer undergoing NAC at four time points: time of diagnosis, after the first and fourth cycle of doxorubicin/cyclophosphamide treatment, and after the fourth cycle of docetaxel administration. First, we evaluated the miRNA expression profiles in tissue and correlated expression with clinico-pathological features. Then, a panel of four miRNAs (miR-451, miR-3200, miR-21, and miR-205) in serum samples was further validated using quantitative reverse-transcription polymerase chain reaction (RT-qPCR). The alterations in serum levels of miRNA, associations with clinical and pathological responses, correlation with clinico-pathological features, and survival outcomes were studied using Friedman, Mann-Whitney U, Spearman, Wilcoxon signed-ranks tests. P≤0.05 was considered statistically significant.
Results: We analyzed 32 tissue samples and 108 serum samples from 8 patients and 27 patients, respectively. MicroRNA expression profiling of tumor versus normal tissue revealed more than 100 differentially expressed miRNAs. Serum miR-451 levels were significantly decreased during treatment, and higher serum levels were associated with improved clinical and pathological responses and disease-free survival. The serum levels of miR-3200 declined during NAC, and higher serum levels were associated with lower residual breast cancer burden and relapse rates.
Conclusion: Variations in serum miRNA levels during NAC treatment may be therapeutically significant for predicting response and survival outcomes.

overall_design: Serum and tissue from a total of 27 consecutive patients diagnosed with locally advanced breast cancer undergoing NAC treatment were collected however microarray data were generated from tissue biopsy of 5 patients at four timepoints for both Normal and tumor. Additionally 3 tissue from only tumor at four timepoints and 6 patients at two timepoint T1 and T4

middle: H

last: Al-Khanbashi

first: Stefano

last: Caramuta

first: Weng-Onn

last: Lui

first: Adil

last: Al-Ajmi

first: Ibrahim

last: Al-Haddabi

first: Marwa

last: Al-Riyami

first: Mansour

last: Al-Moundhri


title: Differential expression of microRNAs in porcine placenta on gestational days 26 and 50

status: Public on Oct 01 2015

first: Ruize

last: Liu

address: No.1,Shizishan Street

department: College of Animal Science and Technology

institute: Huazhong Agriculture University

summary:
Affymetrix miRNA arrays were used to generate miRNA profiles in placenta of Meishan and Yorkshire pigs on stages of initiation (gestational day 26) and establishment (gestational day 50) of placental folds development. The study allowed for the determination of the miRNAs that were differentially expressed in porcine placenta on different gestational day.
This study will provide the information to better understanding of the role miRNAs in porcine placental development.

overall_design: The placneta form different gestational day and breed were collected. In order to determine the miRNA expression profile of these tissue, RNA was extracted, labeled and hybridized on an Affymetrix miRNA array.

first: Mei

last: Yu


title: Small nucleolar RNA and microRNA expression data from multiple sclerosis patients in relapse and remission.

overall_design: 24 multiple sclerosis patients with samples both in remission and relapse (2 samples for each patient; 48 blood samples in total) and 24 healthy controls were included in the study, for a total of 72 samples.


title: Expression data from Dicer and Ago2-knockdown HeLa cells

status: Public on Sep 30 2015

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

summary:
Dicer and Argonaute2 (Ago2) gene is involving in microRNA (miRNA) maturation. Knockdown of these genes has great impact on miRNA expression profiles.
We used microarrays to detail the miRNA expression profiles in Dicer- and Ago2-knockdown HeLa cells and demonstarted that the significant difference between Ago2-knockdown and Dicer- and Ago2-co-knockdown HeLa cells were not found.

overall_design: Hela-shDicer cells, which inducibly express shDicer by Dox treatment, were cultured in Dox-containing medium for 48 h, followed by transfection with siControl or siAgo2. After 48 h incubation, the cells were collected and the miRNA expression profiles were in the cells analyzed by the miRNA microarray analysis.

first: Fuminori

last: Sakurai

first: Hiroyuki

last: Mizuguchi


title: Integrated ordination of miRNA and mRNA expression profiles [miRNA]

status: Public on Oct 08 2015

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

summary: Several studies have shown that negative and positive miRNA-mRNA correlations are symmetrically distributed. While negative correlations are consistent with a faster degradation of miRNA targets, the presence of positive correlations suggests bidirectional interactions between the two classes of molecules. However, a comprehensive study of miRNA and mRNA correlations is lacking. A homogeneous map of miRNA and mRNA relationships was obtained by multidimensional scaling (MDS) applied to a single matrix including both heterologous (miRNA-mRNA) and homologous (miRNA-miRNA and mRNA-mRNA) correlations.

overall_design: Liver samples were obtained from 4 patients with HBV-associated acute liver failure (ALF), 10 liver donors and 7 subjects who underwent hepatic resection for liver angioma.

first: Fausto

last: Zamboni

first: Ashley

last: Tice

first: Patrizia

last: Farci


title: MicroRNA signatures of colonic adenomas according to histology

status: Public on Sep 29 2015

city: Portland

first: Amiee

middle: Bell

last: Potter

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

summary:
Adenomatous polyps adjacent to colorectal cancer (CRC) were found to exhibit two distinct microRNAs (miRs) patterns from normal mucosa to low- and separately, to high-grade dysplasia; presence in screen-detected adenoma of non-cancer patients is unknown.
Global miR expression was performed on biopsies obtained from 109 healthy patients undergoing screening/surveillance colonoscopy.  Included were normal mucosa (NM); hyperplastic polyp (HP); tubular adenoma (TA), tubulovillous adenoma, with or without, high-grade dysplasia (TVHG) and serrated-polyps; sessile serrated adenoma (SSA) and traditional serrated adenoma (TSA).  Logistic regression was used to model miRs predictive of histology and CRC risk.
We identified 99 miRs that differed across five histologic groups (FDR=0.05) and that accurately separated on histology (Concordance Index (CI)=0.96). In HPNM, miRs-145, -143, -107a, -23b, and -24 were upregulated whereas miRs-663, -1268, -320b, -1275, and -671 where overexpressed in TVHGs (FDR P<0 .05).  The expression of miR-145 and -30a showed high accuracy to separate low from high-risk polyps independent of serrated status (CI= 97.1%; AUC 93.4%). For TSAs, miR-125b and -199a were uniquely downregulated relative to HPNMs and miR-335 discriminated between non-serrated and serrated histology.
Histologically advanced polyps from non-cancer patients share miR alterations with those reported for CRC and high-grade adenoma adjacent to tumor including downregulation of immune regulatory miRs-125 and -199a in TSAs; polyp that frequently present with in situ carcinoma.  These data extend evidence that miR patterns of high-risk adenoma are detectable in subset of screen-detected adenoma for which measurement may be useful in in adenoma risk stratification.

overall_design: The statistical analysis included 113 samples allocated to one of five pathology groups. Samples desginated as normal mucosa and hyperplastic polyp (HPNM) were combined to serve as the controls. The remaining four pathologic groups included tubular adenoma (TA),  tululovillous adenoma with or without high grade dysplasia (TVHG), sessile serrated adenoma (SSA), and traditional serrated adenoma (TSA). The RNA was isolated from FFPE biopsy tissues obained from 109 human patients undergoing colonoscopy.  Therefore, study design included 113 human RNA samples with biological replicates for five conditions.

first: Vassiliki

last: Tsikitis

first: Motomi

last: Mori

first: Julie

middle: A

last: Buckmeier

first: Christina

last: Preece

last: Harrington

first: Angela

last: Bartley

first: Achyut

last: Battacharrya

first: Stanley

last: Hamilton

first: Peter

last: Lance

first: Patricia

last: Thompson


title: Expression data from cardiac stem cells (CSCs) with or without MSC-exosomes treatment

city: Suzhou

first: Junjie

last: Yang

address: 708 Renmin Road

institute: Institute for cardiovascular science of Soochow University

summary: Cardiac resident c-kit+ cells aroused much interest among the cardiologists at the beginning of the century. These cells are selfrenewing, clonogenic, and multipotent and possess the potential to differentiate into all cardiovascular lineages. However, one of the critical problems faced by c-kit+ cells is the poor engraftment and survival after transplantation. Therefore, researchers are focusing on developing next generation CSC products that will enhance the engraftment, survival, and regenerative capabilities of these cells. Considering this, we made a proposal that cardiac stem cells preconditioned with exosomes derived from bone marrow mesenchymal stem cells could survive and function better in a myocardial infarction model.

overall_design:
We isolated and characterized exosomes from MSCs and evaluated their effects on CSCs in vitro and in vivo.
We compared the miRNA expression profiling on CSCs with or without MSC-exosomes treatment.

first: Zhiwei

last: Zhang


title: SncRNA (microRNA & snoRNA) expression in leucocytes from multiple sclerosis relapse and remission and cultured peripheral blood mononuclear cells

first: Maider

last: Muñoz-Culla


title: Effect of mutant p53 R282W on miRNA expression

status: Public on Oct 10 2015

city: Shanghai

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

institute: Shanghai Institute for Digestive Diseases

summary:
The H1299 cells stably transfected with mutp53 R282W or the control vector were respectively analyzed by Affymetrix GeneChip miRNA 4.0 microarray with three biological replications.
The labeled RNA was consequently hybridized for sixteen hours to an Affymetrix GeneChip miRNA array according to the product manual. Microarrays were washed and stained in the Affymetrix Fluidics Station 450, and scanned on the Affymetrix G3000 GeneArray Scanner.

overall_design: Controlled experiments with 3 repeats for each condition.


title: Complexity and Specificity of the Neutrophil Transcriptome in Diverse Inflammatory States

status: Public on Sep 18 2015

city: Buffalo

first: kaiyu

last: Jiang

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

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

summary: In this study, we explored transcriptional complexity in human neutrophils, cells generally regarded as nonspecific in their functions and responses.  We studied distinct human disease phenotypes and found that, at the gene, gene isoform, and miRNA level, neutrophils exhibit considerable specificity in their transcriptomes.  These findings were particularly striking for isoform usage.  Thus, even cells whose responses are considered non-specific show tailoring of their transcriptional repertoire toward specific physiologic or pathologic contexts.  These findings have important implications for our understanding of the link between gene expression and disease phenotypes.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Total RNA was extracted from isolated neutrophils from patients with JIA, from  patients with cystic fibrosis and from healthy controls.

first: Kaiyu

first: Zihua

last: Hu

first: Mark

middle: B

last: Frank

first: Yanmin

last: Chen

first: James

middle: N

last: Jarvis


title: miRNA profile of microglial cells under oxygen-glucose deprivation

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

institute: Fudan University Shanghai Cancer Center

summary: Migroglia cells were exposed to oxygen-glucose deprivation (OGD) for 3 h. The miRNA was isolated and the expression profiles of OGD-activated cells were compared with the profiles of resting cells.

overall_design: Two samples were analysed. miRNAs that were differentially expressed (increased or decreased in expression by ≥1.5-fold) between theOGD-activated and resting  cells were identified.

first: Li


title: Global transcriptomic profiling of Desulfovibro vulgaris Hildenborough following transitions between sulfate respiration and syntrophy

status: Public on Sep 17 2015

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

summary: Managing tradeoffs through gene regulation is believed to be critical for the success of a generalist in a fluctuating resource environment. To investigate this hypothesis in depth, we imposed a fluctuating environment that required a representative community of the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Counterintuitively, the community rapidly collapsed and went extinct because extensive gene regulation during shifts drove precipitous decline in intracellular abundance of essential transcripts and proteins. We demonstrate that extensive gene regulation can be catastrophic for a generalist when resources fluctuate rapidly, and that the extinction phenomenon can be prevented by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Two strains were profiled at early and mid-log phase of growth during Sulfate Respiration and Syntrophy, and after transition between them. 2 biological replicates, 24 samples

first: Christina

last: Arens

first: Nitin

last: Baliga

first: Sergey

last: Stolyar


title: Human embryos commonly form abnormal nuclei during development: a mechanism of DNA damage, embryonic aneuploidy, and developmental arrest

status: Public on Sep 11 2015

first: Dieter

last: Egli

address: 116th St & Broadway

institute: Columbia University

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

summary: Nuclear abnormalities are commonly found in human IVF embryos and are associated with DNA damage, aneuploidy, and decreased developmental potential.

overall_design: Immunohistochemical, microscopic, and cytogenetic analysis of human IVF embryos at different developmental stages and morphologic grades.

first: Daniel

last: Kort

first: Gloryn

last: Chia

first: Nathan

last: Treff

first: Akemi

middle: J

last: Tanaka

first: Lauren

last: Vensand

first: Stephanie

last: Micucci

first: Robert

last: Prosser

middle: V

last: Sauer


title: Genome-wide copy number profiling of 18 gastric cancer cell lines using 500K SNP arrays

status: Public on Aug 04 2015

city: Singapore

first: Muthulakshmi

last: Muthuswami

address: 8 College Road

department: Cancer and Stem cell Biology

institute: Duke NUS Graduate Medical School

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

summary: The genomic loci with copy number alterations are known to harbor cancer genes. We investigated a comprehensive panel of gastric cancer cell lines for their genome-wide copy number alterations. Eighteen gastric cancer cell lines were profiled using Affymetrix 500K SNP arrays. For copy number calculation, seven independent normal blood samples were profiled together. The copy numbers were calculated genome-wide, in these cell lines with high resolution and reveal the cell line specific amplification and copy number changes.

overall_design: 18 gastric cancer cell lines were profiled using high resolution 500k SNP arrays from Affymetrix. 7 Independent normal blood samples were profiled and used for copy number calculation.

first: Ming

last: Hui

first: Jeanie

last: Wu

first: Ganesan

last: Kumaresan

first: Patrick

last: Tan


title: Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [mouse NSC miRNA 2.0]

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the mouse neural stem cell miRNA 2.0 GeneChip data only but is part of a larger SuperSeries (GSE71579).

overall_design: A total of 14 miRNA 2.0 GeneChips were run on small RNA purified from the mouse neural stem cell samples.

first: Cherry

last: Ignacio

first: Steven

last: Hicks

last: Burke

first: Lambert

last: Lewis

first: Zsuzsa

last: Szombathyne-Meszaros


title: microRNA and snoRNA expression profile in the solitary colorectal cancer

status: Public on Aug 01 2015

city: Chengdu

first: Wen-Jian

last: Meng

state: Sichuan Province

address: No. 37, Guoxue Street

department: Department of Gastrointestinal Surgery

institute: West China Hospital, Sichuan University

summary: We evaluated the profile of miRNA and snoRNA expression in 7 solitary CRC and matched normal colorectal tissues using the Affymetrix GeneChip miRNA 1.0 array. We found that global dysregulated miRNAs and snoRNAs between cancer tissue and normal mucosa in solitary CRC. Our findings firstly implicates that dysregulation of snoRNAs and miRNA may play important role in the cancinogenesis and present therapeutic targets for solitary CRC.

overall_design: Examination of microRNA and snoRNA expression in cancer and matched normal tissues of solitary CRC

first: W

first: L

last: Yang

first: Q

last: Ma

first: Z

middle: Q

last: Wang

first: C

first: Y

middle: Y

last: Yu

last: Li

last: Zhou

first: X

middle: F

last: Sun


title: Expression data from hyperoxaluric rats

status: Public on Aug 18 2015

city: Wuhan

first: Jiang

last: Hongyang

address: No. 1095 Jie Fang Avenue

institute: Tongji Hospital, Huazhong University of Science and Technology

summary: Calcium oxalate stones account for over 80% of urinary stones, while the molecular mechanism of its formation is still not completely elucidated. The incidence of hyperoxaluria in calcium oxalate stone formation ranks only second to hypercalciuria. It plays an important role in the pathophysiological process of stone formation. We analyzed miRNA expression profiles between experimental hyperoxaluric rats and normal rats in order to find out the target genes and signaling pathways in the pathogenesis of hyperoxaluria.

overall_design: We feed ethylene glycol (EG) and ammonium chloride (AC) to male experimental hyperoxaluric rats (T group) and age-matched male rats selected as control group (C group). The oxalate concentration in 24-hour urine of each experimental rat was measured and the three highest were selected for microarray test. MicroRNA microarray was applied to evaluate the expression difference between the two groups and screen miRNA that were above 2- or below 0.5-fold change.

first: Hongyang

last: Jiang

first: Zhuo

last: Liu


title: Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [rat miRNA 2.0]

last: Middleton

summary: We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the rat miRNA 2.0 GeneChip data only but is part of a larger SuperSeries (GSE71579).

overall_design: A total of 38 miRNA 2.0 GeneChips were run on small RNA purified from the rat blood serum samples.

middle: D

first: Patrick


title: Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations [Affymetrix]

status: Public on Aug 20 2015

first: Angel

last: Rubio

state: GUIPÚZCOA

address: Paseo Mikeletegi, Nº 48

department: Bioinformatics

institute: CEIT

summary: Background: The development of a more refined prognostic methodology for early non-small cell lung cancer (NSCLC) is an unmet clinical need. An accurate prognostic tool might help to select patients at early stages for adjuvant therapies.  Results: A new integrated bioinformatics searching strategy, that combines gene copy number alterations and expression, together with clinical parameters was applied to derive two prognostic genomic signatures. The proposed methodology combines data from patients with and without clinical data with a priori information on the ability of a gene to be a prognostic marker. Two initial candidate sets of 513 and 150 genes for lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC), respectively, were generated by identifying genes which have both: a) significant correlation between copy number and gene expression, and b) significant prognostic value at the gene expression level in external databases. From these candidates, two panels of 7 (ADC) and 5 (SCC) genes were further identified via semi-supervised learning. These panels, together with clinical data (stage, age and sex), were used to construct the ADC and SCC hazard scores combining clinical and genomic data. The signatures were validated in two independent datasets (n=73 for ADC, n=97 for SCC), confirming that the prognostic value of both clinical-genomic models is robust, statistically significant (P=0.008 for ADC and P=0.019 for SCC) and outperforms both the clinical models (P=0.060 for ADC and P=0.121 for SCC) and the genomic models applied separately (P=0.350 for ADC and P=0.269 for SCC).  Conclusion: The present work provides a methodology to generate a robust signature using copy number data that can be potentially used to any cancer. Using it, we found new prognostic scores based on DNA s that, jointly with clinical information, are able to predict overall survival (OS) in patients with early-stage ADC and SCC.

overall_design: Copy number analysis of Affymetrix 500K SNP arrays was performed in autosomal chromosomes for 39 early stage Non-Small Cell Lung Cancer (NSCLC) patients

first: Luis

last: Montuenga


title: MicroRNAs of the RPE are essential for RPE differentiation and photoreceptor maturation (microRNA)

status: Public on Jun 16 2015

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: Dysfunction of the retinal pigmented epithelium (RPE) results in degeneration of photoreceptors and vision loss and is correlated with common blinding disorders in humans. Although many protein-coding genes are known to be expressed in RPEs and important for their development and maintenance, virtually nothing is known about the in vivo roles of non-protein coding transcripts in RPEs. The expression patterns of microRNAs (miRNAs) have been analyzed in a variety of ocular tissues, and few were implicated to play role in RPE based on studies in cell lines. Herein, through RPE specific conditional mutagenesis of Dicer1 or DGCR8, the importance of miRNA for RPE differentiation was uncovered. Interestingly, miRNAs were found to be dispensable for maintaining the RPE fate and survival, and yet they are essential for acquisition of important RPE properties such as the expression of genes involved in the visual cycle pathway, pigmentation and cell adhesion. Importantly miRNAs of the RPE were found to be required for maturation of the adjacent photoreceptors, specifically for the morphogenesis of the outer segments. The profiles of miRNA and mRNA altered in the Dicer1 deficient RPE point to a key role of miR-204 in regulation of RPE differentiation program in vivo and uncovers the importance of additional novel RPE miRNAs. The study exposes the combined regulatory activity of miRNAs of the RPE, which is required for RPE differentiation and for the development of the adjacent neuroretina.

overall_design: Effect of Dicer 1 deficiency on RPE miRNA and mRNA.

first: Reut

last: Ohana

first: Benjamin

last: Weiman-Kelman

first: Shaul

last: Raviv

first: Ernst

last: Tamm

first: Ariel

last: Rinon

first: Dvir

last: Netanely

first: Ron

last: Shamir

first: Arie

last: S Salomon

first: Ruth

last: Ashery-Padan


title: Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: MicroRNAs of the RPE are essential for RPE differentiation and photoreceptor maturation

platform_organism:
Mus musculus
synthetic construct


title: miRNA regulation in diabetes associated impaired wound healing

status: Public on Jun 09 2015

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
Circulating miRNAs constitute a novel class of disease biomarkers, which are altered in diabetes but the effect of diabetes associated inflammation as seen in chronic wounds is unknown.
We here compared the miRNA pattern in diabetic patients in presence or absence of chronic wound with PAD.

overall_design: The clinical plasma samples were obtained from Heart and Diabetes centre, NRW and compared for plasma miRNA levels in 2 pools of 17 T2DM+PAD+Wound patients vs 2 pools from 20 T2DM controls

first: Seema

last: Dangwal

first: Thomas

last: Thum


title: MicroRNA profiling by array of human urinary sediments from IgAN patients

status: Public on Jun 02 2015

city: Beijing

first: Nannan

last: Wang

address: Fuxing Road NO.28

department: Department of Nephrology

institute: Chinese PLA General Hospital, Chinese PLA Institute of Nephrology,National Clinical Research Center for Kidney Diseases

summary: We have performed a microRNA expression analysis in urine sediments from 18 IgAN patients, 6 healthy subjects and 8 disease controls(including 4 membranous nephropathy patients and 4 minimal change disease patients). Pathologic diagnosis of all IgAN patients was included in grades I–V by light microscopy according to the grading system of Lee et al. And we have identified a set of deregulated microRNAs with potential diagnostic value to identify patients with IgAN.

overall_design: Using microarray-based technology, We have performed a microRNA expression analysis in urine sediments from 18 IgAN patients(IgAN Group), 4 membranous nephropathy patients(MN Group), 4 minimal change disease patients(MCD Group) and 6 healthy subjects（HC Group). The IgAN Group was comprised of 6 IgAN I-II Grade patients, 6 IgAN III Grade patients and 6 IgAN IV-V Grade patients according to the grading system of Lee et al. And we have identified a set of deregulated microRNAs with potential diagnostic value to identify patients with IgAN.

first: N

first: X

middle: M

last: Chen

first: G

last: Cai

first: R

last: Bu


title: Differentially expressed miRNAs in H2AX knockdown cells undergoing apoptosis

status: Public on Apr 25 2015

first: Chengrong

last: Lu

address: Fucheng road 30

department: Aviation Medicine Research lab

institute: General Hospital of Air Force

summary:
H2AX has been characterized as a novel tumor suppressor protein. Difficiency of H2AX will result in apoptotic inhibition of cancer cells. However, how H2AX epigenetically regulates apoptosis of cancer cells is still unclear
To reveal the miRNA expression regulated by H2AX and involved in apoptosis, the microarray profiling analysis was employed to identify differentially expressed miRNAs in H2AX knockdown lung cancer cells and control ones after apoptotic induction. H2AX was knockdown by miRNA interfering system in human lung cancer originated cell A549 and the stable cell line named P1, while the control stable cell line named C. Genes with greater than 1.5-fold change and P-value ＜0.05 were identified as differentially expressed genes between C and P1 cells both with apoptosis induction.

overall_design: The two groups including control (C) and H2AX knockdown lung cancer cells (P1) were harvested 48 h after VP-16 treatment. Three independent experiments were performed for each group.


title: Inactivation of the exosome ribonuclease DIS3 triggers the pluripotency factor LIN28B, repressing let-7 miRNAs and unleashing MYC and RAS.

status: Public on Jun 12 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Somatic mutations affecting DIS3, the catalytic component of the RNA exosome, have been found in up to 18% of patients affected by the hematological cancer multiple myeloma. Here we show that DIS3 targets and degrades the pluripotency factor LIN28B. In cancer cells, DIS3 inactivation leads to enhanced LIN28B expression, thus disrupting the let-7 miRNAs tumor suppressor network and ultimately increasing protein levels of crucial oncogenes such as MYC and RAS. DIS3 represents the catalytic component of the exosome. The exosome is required for cell viability and targets several RNA species, including pre-mRNAs, pre-tRNAs, pre-rRNAs, snRNAs and snoRNAs. To gain insight on the macular wiring underlying DIS3 activity in mammalian cells, we comprehensively evaluated expression profiles, including miRNAs, in various cell lines, upon DIS3 knockdown.

overall_design: This series of microarray experiments contains the miRNA expression profiles of independent replicates of RPMI-8226, KMS12-BM multiple myeloma cell lines and HEK-293T cells, knocked-down with a scrambled or hDIS3 sh4 and collected 72 hours after infection. 500 nanograms of total RNA were processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample. The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0, following the Affymetrix manufacturer's instructions.

first: Simona

last: Segalla

first: Silvia

last: Pivetti

first: Erica

middle: C

last: Giuliani

first: Malgorzata

last: Chudzik

first: Federico

last: Lazzaro

first: Viviana

last: Volta

first: Katia

last: Todoerti

first: Dejan

last: Lazarevic

first: Giovanna

last: Musco

first: Marco

last: Muzi-Falconi

first: Antonino

last: Neri

first: Stefano

last: Biffo

first: Giovanni

last: Tonon


status: Public on Apr 28 2015

city: Xi'an

first: Lin

last: Shi

state: Shaanxi

address: Yanta West Road No 76

department: Department of Immunology and Microbiology

institute: Xi'an Jiaotong University Health Science Center

summary: To reveal microRNAs expression differences in cumulus cells between polycystic ovary syndrome (PCOS) and non-PCOS women. miRNAs expression profile of the cumulus cell samples with PCOS and non-PCOS were determined by Affymetrix miRNA 2.0.

overall_design: Six pooled RNAs from CC samples (three PCOS and three non-PCOS pooled RNAs) were separately analyzed on 6 GeneChip miRNA 2.0 Array (miRBase V15)


title: Emergence of a developmental stage-dependent human liver disease signature demonstrated by directed differentiation of alpha-1 antitrypsin deficient iPS cells [miRNA-2_0]

status: Public on Apr 15 2015

city: Boston

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: We monitored 9 pluripotent stem cell lines across three time points of hepatic directed differentiation, representing 3 developmental stages: undifferentiated (T0), definitive endoderm (T5), and early hepatocyte (T24). ESCs (n=3) and patient-derived normal (n=3) or PiZZ (n=3) iPSCs were analyzed in the undifferentiated state (T0), after differentiation to definitive endoderm (T5), and upon reaching hepatic stage (T24) for a total of 27 samples.  We sought to test the hypothesis that a single transgene-free iPSC clone from each donor could be used to detect disease-specific differences between the normal cohort and the PiZZ cohort, anticipating that this difference would emerge only at a developmental stage in which the mutant AAT gene is expressed. Cells were sorted before analysis at T0 and T5 after antibody staining for TRA1-80+/SSEA3+ (T0) or C-kit+/CXCR4+ (T5) cells.

overall_design: ESCs (n=3) and patient-derived normal (n=3) or PiZZ (n=3) iPSCs were analyzed in the undifferentiated state (T0), after differentiation to definitive endoderm (T5), and upon reaching hepatic stage (T24) for a total of 27 samples.  Cells were sorted before analysis at T0 and T5 after antibody staining for TRA1-80+/SSEA3+ (T0) or C-kit+/CXCR4+ (T5) cells. RNA was extracted at each stage, biotin labeled, and hybridized to either Affymetrix GeneChip Human Gene 1.0 ST or miRNA 2.0 arrays. For methylation analysis, gDNA was sorted from the same 27 samples before undergoing bisulfite conversion. Bisulfite converted DNA was then amplified and purified prior to overnight hybridization to Illumina’s Infinium HumanMethylation 450 BeadChips.  Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.

first: Andrew

last: Wilson

first: Darrell

last: Kotton


title: miRNA expression profiles from neurogenic differentiation of mesenchymal stem cells under conditioned microenvironments

status: Public on Apr 30 2015

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

summary:
Background:   Studies suggested that mesenchymal stem cells (MSCs) have intrinsic neurogenic potential and can be differentiated into neural stem cell/ neural progenitor cells (NPCs) under specific microenvironment. Manipulation of growth factors is one of the popular method to achieve trans-lineage differentiation of MSCs. Synergistic effect of epidermal growth factor (EGF) and fibroblast growth factor 2 (bFGF) have been widely identified as basic requirement for neural differentiation to take place. Insulin-like growth factor 1 (IGF-1) also known as somatomedin C is an important growth promoting protein during embryonic development which control numerous cellular responses and biological systems. Our recent study has found that the combination of EGF, bFGF and IGF-1 could significantly improved the growth and survivability of MSCs-derived NPCs. Therefore, to understand the genomic mechanism underlying the differentiation in vitro, we have studied the miRNAs profile of MSCs-derived NPCs under IGF-1 influenced conditioned microenvironments.
Objectives:   To evaluate the effects of IGF-1 in trans-lineage differentiation of MSCs, we have induced MSCs into neural lineage in 3 groups; Group A (positive control) - EGF+bFGF, Group B (Treatment) - EGF+bFGF+IGF-1, and Group C (negative control/ untreated). To unravel the role of regulatory miRNAs involved in the early differentiation, we have performed detailed miRNA profiling for MSCs-derived NPCs at three time intervals (day 1, day 3 and day 5). The data has explored crucial miRNAs involved in early differentiation of MSCs into NPCs.

overall_design: Stage specific MSCs-derived NPCs at Passage 1 were collected for total RNA extraction at three time-points (D1, D3 and D5) and hybridization on Affymetrix miRNA geneChip 2.0 arrays. Each experiment were repeated three times independently (Exp 1, Exp 2 and Exp 3). Group A served as positive control (EGF+bFGF), Group B as treatment (EGF+bFGF+IGF-1) and Group C without growth factor as negative control.

first: Tee

last: Huat

first: Jafri

last: Abdullah

first: Hasnan

last: Jaafar

first: Fauziah

last: Idris


title: Separated and combined effects of the over-expression of a plant defensin and of a 20 mM Zn treatment on yeast.

status: Public on Mar 31 2015

city: Montpellier

first: Pierre

last: BERTHOMIEU

address: Place Viala

department: UMR BPMP

institute: Montpellier SupAgro

summary: The expression of plant defensins in Saccharomyces cerevisiae has been shown to increase tolerance to Zn of yeast (Mirouze et al., 2006; Shahzad et al., 2013). The present transcriptomic approach has been conducted to uncover the mechanism underlying this phenotype. WT yeast was compared to yeast expressing the AhPFF1.1b plant defensin when grown in both control medium and medium supplemented with 20 mM ZnSO4.

overall_design: 4 conditions with 2 biological replicates compared: control yeast (BY4741) grown on control medium, control yeast grown in the presence of 20 mM ZnSO4, yeast expressing the AhPDF1.1b defensin grown in control medium, yeast expressing the AhPDF1.1b defensin grown in the presence of 20 mM ZnSO4

first: Oriane

last: Mith

first: Isabelle

last: Sanchez

last: Delobel

first: Bruno

last: Blondin

first: Laurence

last: Marquès

last: Berthomieu


title: Impact of Gene Dosage on Gene Expression, Biological Processes and Survival in Cervical Cancer: a Genome-Wide Follow-Up Study [Mapping250K; copy number]

status: Public on Jun 04 2015

city: MEXICO CITY

first: INGRID

last: MEDINA MARTINEZ

state: CUAUHTEMOC

address: DR. BALMIS 148

department: MEDICINA GENOMICA

country: Mexico

institute: HOSPITAL GENERAL DE MEXICO OD

summary: The contribution of copy number (CN)-altered genes in cervical carcinogenesis is unknown owing to a lack of correlation with gene expression. We mapped CN-altered genes in 31 cervical cancers (CCs), and investigated the expression of 21,000 genes in 55 CCs using microarrays. Biological processes associated with genes deregulated by gene dosage and the relationship between gene dosage and patient survival were investigated. CN-altered genome (CN-AG) percentages varied widely among tumors from 0% to 32.2% (mean = 8.1 ± 8.9). Tumors were classified as low (mean = 0.5 ± 0.6, n = 11), medium (mean = 5.4 ± 2.4, n = 10), or high (mean = 19.2 ± 6.6, n = 10) CN. The highest %CN-AG was found in 3q, which contributed an average of 55% of all CN alterations. Genome-wide, only 5.3% of CN-altered genes were deregulated by gene dosage; by contrast, the rate in fully duplicated 3q was twice as high. Amplification of 3q explained 23.6% of deregulated genes in whole tumors (r2 = 0.236, p = 0.006; analysis of variance), including those in 3q and other chromosomes. A total of 862 genes were deregulated exclusively in high-CN tumors, but only 22.9% were CN altered. This result suggests that the remaining genes are not deregulated directly by gene dosage but by mechanisms induced in trans by CN-altered genes. Anaphase-promoting complex/cyclosome (APC/C)-dependent proteasome proteolysis, glycolysis, and apoptosis were upregulated, whereas cell adhesion and angiogenesis were downregulated exclusively in high-CN tumors. The high %CN-AG and upregulated gene expression profiles of APC/C-proteasome-dependent proteolysis and glycolysis were associated with poor patient survival, although only the first 2 correlations were statistically significant (p < 0.05, log-rank test). The data suggest that inhibitors of APC/C-dependent proteasome proteolysis and glycolysis may be useful treatments in these patients.

overall_design:
In this study 31 tumors and 25 reference controls were used for analysis of copy number alterations using the 500K microarray. The results obtained from 500K array analysis were validated in 15 of the 31 tumors with a higher density microarray (Cytoscan HD). For the analysis of gene expression 55 cervical tumors (27 of them belong to the group of 31 tumors analyzed for copy number) and 17 controls were used.

Please note that the sample R397 in the CytoScanHD_Array set corresponds to the R392 sample in the other data sets (due to an error in file name).

Please note that there is no processed data for the control samples and only one cnchp file for each pair of .CEL files (STY and NSP). Therefore, the 'CN4.cnchp' processed data files are linked to the Series records and the processed data file is indicated in the description field of the corresponding sample records.

first: Ingrid

last: Martinez

first: Jaime

last: Berumen


title: The microRNA expression profile in donation after cardiac death (DCD) livers and its ability to identify primary non function

status: Public on Apr 09 2015

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

country: United Kingdom

institute: kings college hospital

summary:
The microRNA expression profile in donation after cardiac death (DCD) livers its ability to identify primary non function
DCD livers are a marginal organ and their usein transplantation is associated with a higher risk of primary non function (PNF), or early graft dysfunction (EGD).

overall_design: We compared a three groups of DCD livers defined as PNF (n=7) retransplanted within a week, good functional outcome (n=7) AST < 1000IU/L and EGD (n=9) AST>2500IU/L . RNA was extracted from archived histology samples and miRNA expression was analysed using the affymetrix Genechip miRNA 2.0 assays.

first: Shirin

middle: E

last: Khorsandi

first: Siamak

last: Salehi

first: Wayel

last: Jassem

first: Hector

last: Melendez

first: Andreas

last: Prachalias

first: Parthi

last: Srinivasan

first: Nigel

last: Heaton


title: A unifying gene signature for adenoid cystic cancer identifies parallel MYB-dependent and MYB-independent therapeutic targets (microRNA)

status: Public on Mar 13 2015

city: Houston

first: Nicholas

last: Navin

state: tx

address: 6767Bertner AVE

country: USA

institute: UT MD Anderson

summary: MYB activation is proposed to underlie development of adenoid cystic cancer (ACC), an aggressive salivary gland tumor with no effective systemic treatments. To discover druggable targets for ACC, we performed global mRNA/miRNA analyses of 12 ACC with matched normal tissues, and compared these data with 14 mucoepidermoid carcinomas (MEC) and 11 salivary adenocarcinomas (ADC). We detected a unique ACC gene signature of 1160 mRNAs and 22 miRNAs. MYB was the top-scoring gene (18-fold induction), however we observed the same signature in ACC without detectable MYB gene rearrangements. We also found 4 ACC tumors (1 among our 12 cases and 3 from public databases) with negligible MYB expression that retained the same ACC mRNA signature including over-expression of extracellular matrix (ECM) genes. Integration of this signature with somatic mutational analyses suggests that NOTCH1 and RUNX1 participate with MYB to activate ECM elements including the VCAN/HAPLN1 complex. We observed that forced MYB-NFIB expression in human salivary gland cells alters cell morphology and cell adhesion in vitro and depletion of VCAN blocked tumor cell growth of a short-term ACC tumor culture. In summary, we identified a unique ACC signature with parallel MYB-dependent and independent biomarkers and identified VCAN/HAPLN1 complexes as a potential target.

overall_design: A total 12 human salivary gland adenoid cystic cancer (ACC) tumors and 12 mathced normal adjacent tissues. The 12 tumor samples contains 8 MYB-NFIB fusion positive tumor samples and 4 MYB-NFIB fusion negative samples. This is a microRNA chip expression assay.

first: Ruli

last: Gao

first: Chunxia

last: Cao

first: Min

last: Zhang

first: Lopez

last: Maria-Cecilia

first: Yuanqing

last: Yan

first: Zirong

last: Chen

first: Yoshitsugu

last: Mitani

first: Li

first: Maria

last: Zajac-Kaye

first: Bin

last: Liu

first: Lizi

last: Wu

first: Rolf

last: Renne

first: Henry

last: Baker

first: Adel

last: El-Naggar

first: Frederic

last: Kaye


title: Concurrent whole-genome haplotyping and copy number profiling of single cells (Affymetrix)

status: Public on May 15 2015

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

summary: Methods for haplotyping and DNA copy number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required that substantially distorts the frequency and composition of the cell’s alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP-genotypes (AA, AB, BB), and DNA copy number profiling remains difficult as true DNA copy number aberrations have to be discriminated from WGA-artifacts. Here, we developed a single-cell genome analysis method that reconstructs genome-wide haplotype architectures as well as the copy-number and segregational origin of those haplotypes by deciphering WGA-distorted SNP B-allele fractions, using a process we coin haplarithmisis. We demonstrate clinical precision of the method on single cells biopsied from human embryos to diagnose disease alleles genome wide, we advance and facilitate the detection of numerical and structural chromosomal anomalies in single cells, and can distinguish meiotic from mitotic segregation errors in a single assay.

overall_design: The samples of a reference family were applied for optimisation of single-cell genotyping using Affymetrix SNP-arrays prior to downstream analysis. Specifically, the reference family delivers genomic DNA samples isolated from peripheral blood of two siblings 'S1' and 'S2', the mother and father of these siblings, as well as of the maternal grandmother and grandfather. Of individuals ‘S1’ and ‘S2’, six EBV-transformed lymphoblastoid single cells were isolated of which three were whole-genome amplified using MDA and three using PicoPlex. These WGA-products were hybridized to Affymetrix NspI 250K SNP-arrays following the protocol as recommended by the company. Subsequently, the SNP-probe signals were interpreted by different genotyping algorithms (see data processing). Based on overall performance, it was decided to use the Dynamic Model (DM) for interpreting Affymetrix SNP-probe signals of single cells.

first: Eftychia

last: Dimitriadou

first: Ligia

last: Mateiu

first: Cindy

last: Melotte

first: Niels

last: Van der Aa

first: Parveen

last: Kumar

first: Rakhi

last: Das

first: Koen

last: Theunis

first: Jiqiu

last: Cheng

first: Eric

last: Legius

first: Yves

last: Moreau

first: Sophie

last: Debrock

first: Thomas

last: D'Hooghe

first: Pieter

last: Verdyck

first: Martine

last: DeRycke

first: Karen

last: Sermon

first: Joris

middle: R

last: Vermeesch

first: Thierry

last: Voet


title: Expression data from the Lateral Habenula (LHb) and the Medial Habenula (MHb) of the mouse (C57BL/6) brain after nicotine self-administration (microRNA)

status: Public on Mar 04 2015

city: Seongbuk-gu, Seoul

first: Heh-In

last: Im

address: 5, Hwarang-ro 14-gil

country: South Korea

institute: Korea Institute of Science and Technology

summary:
After intarvenouse catheter surgery, nicotine self-administration using an operant self-administration chamber, was conducted for 44 days with various doses of nicotine solution.
Age-matched mice were used for control. After the self-administration, the Lateral Habenual (LHb) and the Medial Habenula (MHb) of the mouse brain were collected.

overall_design: We used microarrays to detail the microRNA expression profile of the Lateral Habenual (LHb) and the Medial Habenula (MHb) after the nicotine self-administration.

first: Sangjoon

last: Lee


title: Expression data from ethanol and saline exposed mice [miRNA]

status: Public on Mar 07 2015

city: Toronto

last: Chater-Diehl

state: ON

address: 686 Bay St.

institute: SickKids Research Institute

summary: Mouse models of Fetal Alcohol Spectrum Disorder can be used to assess molecular changes underlying the disorder. Neonatal ethanol exposure in mice can be used to model third trimester ethanol exposure in humans.

overall_design: Mice were injected with 2.5 g/kg twice on each of posnatal days 4 and 7. Mice were allowed to reach postnatal day 70, at which time whole-hippocampus was isolated and snap frozen. Tissue was thawed and RNA was isolated. RNA run on affymetrix gene expression array according to standard protocol.  Each array was a pool of three mice, for a total n=9 ethanol-exposed and 9 control mice. All mice were male.

last: Diehl

first: Shiva

last: Singh


title: MicroRNA profiling in HEK293T cells after NDV infection

status: Public on Feb 07 2015

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

summary: Mammals have highly evolved receptors for sensing invading viral pathogens. RLRs comprise of one such family of receptors involved in sensing RNA viruses. The antiviral signaling cascade is tightly regulatedd by various post transcriptional modifications however the post transcriptional regulation by microRNAs is not well understood. We performed miRNA profiling to identify miRNAs induced by virus infections with potential role in regulating RLR signaling cascade.

overall_design: We infected HEK293T cells with NDV-LasoTa strain for 6h. Total small RNA was isolated and hybridised on the Affymetrix miRNA Gene Chip 4.0. We sought to identify novel miRNAs targeting the antiviral signaling.

first: Harshad

last: Ingle

first: Sushil

first: Ashwin

last: Raut

first: Anamika

last: Mishra

first: Takeshi

last: Kameyama

first: Akinori

last: Takaoka

first: Shizuo

last: Akira


title: Collaborative Cross founder strain lung miRNA expression after allergen challenge

status: Public on Mar 01 2015

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

summary: The goal of this project was to identify strain-dependent expression of miRNAs in lung tissue from Collaborative Cross founder strains that were sensitized and challenged with house dust mite allergen (Der p 1).

overall_design: We analyzed whole lung RNAs from the eight Collaborative Cross founder strains (n=4/strain, all males) using Affymetrix miRNA 2.0 arrays


title: Rat Life Cycle Kidney miRNA Expression Data

status: Public on Jan 10 2015

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

summary: Kidney miRNA expression was examined in F344 rats at 2, 5, 6, 8, 15, 21, 78, and 104 weeks of age in both sexes using Agilent miRNA microarrays. 311 miRNAs were found to be expressed in at least one age and sex. Filtering criteria of ≥1.5 fold change and ANOVA (FDR <5%) revealed 174 differentially expressed miRNAs in the kidney; 173 and 34 miRNAs exhibiting age and sex effects, respectively. Principal component analysis revealed age effects predominated over sex effects, with 2 week miRNA expression being much different from other ages. No significant sexually dimorphic miRNA expression was observed from 5 to 8 weeks, while the most differential expression (13 miRNAs) was observed at 21 weeks. Potential target genes of these differentially expressed miRNAs were identified. Pathway analysis was used to investigate the possible roles of these target genes in age- and sex-specific differences.

overall_design: Untreated male and female F344 rats from 2, 5, 6, 8, 15, 21, 78, and 104 weeks of age (n=5) were sacrificed by CO2 asphyxiation, whole kidneys collected and homogenized, total RNA, including small RNA fraction, was used for miRNA expression arrays (Agilent).

first: Joshua

last: Kwekel