title: MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule

status: Public on Jan 14 2015

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. Samples were compared between different localisations either within or around the tumor.
miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

overall_design: 6 microdissected hepatocellular carcinoma samples were compared to four different tumor localisations (LC: cirrhotic septa of the tumor-adjacent liver; LP: tumor-adjacent liver parenchyma;TC: fibrinous capsule of the tumor; TP: tumor parenchyma)

first: Jan

last: Peveling-Oberhag


title: Role of micro-RNAs in pathophysiology of diabetic cardiomyopathy.

status: Public on Dec 31 2014

city: Chandigarh

first: madhu

last: khullar

state: Chandigarh

address: Research Block-B

department: Experimental Medicine and Biotechnology

country: India

institute: Postgraduate Institute of Medical Education and Research

summary: Diabetic cardiomyopathy (DCM), occurs independent of Hypertension, Coronary artery disease, or any other known cardiac disease and is characterized by myocardial fibrosis, myocytes loss and hypertrophy. The molecular mechanisms leading to these diseased cardiac phenotype are still being elucidated. A small number of studies have demonstrated that altered expression of several microRNAs are associated with ischemia , mechanical overload, or cardiovascular biology; however, much work is still required to identify individual or group of  microRNAs and their role in the pathophysiology of diabetic cardiomyopathy. The aim of present study was to identify the expression of individual or group of microRNAs associated with myocytes hypertrophy and myocardial fibrosis during DCM. MicroRNAs expression profiles were studied in myocardium from High Fat diet and streptozotocin (STZ) induced diabetic (n=4) and non-diabetic (n=2) Wistar rats. All normalized and filtered microRNAs (n=780) processed for differential expression study using unpaired T-test in Gene spring in which unpaired comparison has been performed as test vs. control. After unpaired T-test, total 72 microRNAs were found to be significantly expressed with P-value ≤0.05. Differentially expression analysis was performed and at fold Change cut off ≥ 1.0, all 780 microRNA passed and 39 out of 780 microRNAs were differentially expressed on fold Change cut-off ≥1.5. These results indicate that during the development and progression of DCM, various microRNAs were differentially expressed and may participate in the regulation of various signaling pathways leading to myocytes hypertrophy, apoptosis and cardiac fibrosis.

overall_design: After the development and characterization of animal model of DCM, total RNA was isolated from left ventricular  tissue of Wistar rats, by RNeasy mini kit Qiagen and microRNA microarray of 6 individual samples (Control sample, n=2 and Test sample, n=4) were performed on Affymetrix microRNA 2.0 plateform. Further, each test samples were compared with mean of 2 control samples for differential microRNA expression and clustering analysis.

first: Madhu

last: Khullar

first: Akhilesh

last: Kumar

first: Satish

middle: K

last: Raut

first: Gurinder

middle: B

last: Singh

first: Vibhuti

last: Sharma

first: Anupam

last: Mittal

first: Amit

first: Rajni

first: Uma

last: Nahar

first: Rajendra

middle: P

last: Ola


title: Development and blind clinical validation of a microRNA based predictor of response to treatment with R-CHOEP in DLBCL

status: Public on Feb 20 2015

city: Hørsholm

first: Thomas

last: Jensen

address: Venlighedsvej 1

department: lab

country: Denmark

institute: MPI

summary:
microRNAs er are group of short noncoding RNAs that regulate gene expression at the posttranslational level. It has been shown that mirs are independent predictios of outcome in patients with diffuse large b cell lymphoma treated with r-chop.
Outcome in patients with dlbcl lymphoma treated with r-chop. Based on the measured GI50 in 60 human cell lines.

overall_design: 116 DLBCL samples

first: Steen

last: Knudsen

first: Christoffer

last: Hother

first: Kirsten

last: Grønbæk

first: Anker

last: Hansen

first: Wiktor

last: Mazin

first: Jesper

last: Dahlgaard

first: Mikael

last: Møller

first: Elizabeth

last: Ralfkjær

first: Peter

last: de Nully Brown


title: Sperm miRNA expression data from male C57BL/6J, C57BL/6J-ChrY^SJL, and C57BL/6J-ChrY^RF

status: Public on Jan 16 2015

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

country: USA

institute: University of Vermont

summary: The prevalence of some autoimmune diseases (AID) is greater in females compared with males, notwithstanding that disease severity is often greater in males. The reason for this sexual dimorphism (SD) is unknown, but may reflect negative selection of Y chromosome (ChrY) bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the SD in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in ChrY multicopy genes. Here, we test the hypothesis that CNV in ChrY multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice.  We show that C57BL/6J consomic strains of mice possessing an identical ChrX and CNV in ChrY multicopy genes exhibit a female biased sex-ratio and sperm head abnormalities, consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous ChrX:ChrY multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of miRNAs within the sperm nucleus. These findings provide evidence for a genetic mechanism at the level of the male gamete that contributes to the SD in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the SD in MS.

overall_design: miRNA expression was analyzed in epidydimal sperm pooled from 5 mice for each replicate per strain.

first: Emma

middle: H

last: Wall

first: Erin

middle: E

last: Osmanski

first: Julie

middle: A

last: Dragon

first: Naresha

last: Saligrama

first: James

middle: F

last: Zachary

first: Bernardo

last: Lemos

last: Blankenhorn

first: Cory

last: Teuscher


title: Increased CLL Proliferation upon IgM stimulation is Sustained by the Up-regulation of miR-132 and miR-212: a Combined miRNA and Gene Expression Profiling Analysis and Correlation with Disease Progression [miRNA expression]

status: Public on Feb 10 2015

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

summary: In order to investigate a potential involvement of miRNAs in BCR stimulation, in the present work we first evaluated their expression following IgM cross-linking in CLL cells, as well as in healthy B lymphocytes. Next, to infer putative miRNA targeting networks, we combined miRNA profiling results with gene expression and functional analyses

overall_design: miRNA expression profiling analysis by microarray analysis of CLL samples and pools of CD19+ cells derived from healthy donors.

first: S

last: Tavolaro

first: T


title: Mucosal miRNA expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)

status: Public on Jan 01 2015

city: Leuven

first: Jan

last: Van der Goten

address: Herestraat 49 bus 701

department: Clinical and Experimental Medicine

country: Belgium

institute: KU Leuven

summary: In this study, we investigated if miRNA expression in UC mucosa is altered and correlated our findings with mucosal mRNA expression. Integration of mRNA and miRNA expression profiling may allow the identification of functional links between dysregulated miRNAs and their predicted target mRNA.

overall_design: Colonic mucosal biopsies were obtained during endoscopy from 17 UC (10 active and 7 inactive) patients and 10 normal controls. Total RNA, including small RNA, was isolated from colonic mucosal biopsies, labelled and hybridized to Affymetrix Genechip miRNA 2.0 Arrays.

first: Leentje

last: Van Lommel

first: Marc

last: Ferrante

first: Gert

last: Van Assche

first: Paul

last: Rutgeerts

first: Frans

last: Schuit

first: Séverine

last: Vermeire

first: Ingrid

last: Arijs


title: miRNA expression data from xlpra2 and normal canine retinas

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

summary:
To identify miRNAs associated with retinal development and degeneration in dogs affected with xlpra2, an early-onset canine retinal degeneration caused by a microdeletion in RPGRORF15.
XLPRA2-mutant and normal retinas were selected at different ages for RNA extraction and hybridization on Affymetrix miRNA-specific microarrays.

overall_design: miRNA expression was analysed at three crucial ages for the xlpra2 disease: 3, 7, and 16 wks. Three xlpra2-mutant and four normal retinas (biological replicates) were analysed at both 3 and 16 wks of age, while 4 biological replicates per group (both xlpra2 and normal retinas) were analysed at 7 wks of age.

first: Karina

last: Guziewicz

first: Giulia

last: Pertica

first: William

last: Beltran

first: Gustavo

middle: D

last: Aguirre


title: Differential Expression of microRNAs following activated protein C treatment in a rat model of septic shock

status: Public on Dec 20 2014

city: Charlotte

first: Cathy

last: Moore

address: 1000 Blythe Blvd

institute: Carolinas Medical Center

summary: Sepsis induces systemic stress by augmenting inflammatory and pro-coagulant responses resulting in microvascular dysfunction and end organ failure, events modulated by the Protein C pathway. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene transcription yet their role in sepsis remains poorly defined. We hypothesized that aPC selectively alters the expression of specific miRNAs implicated in protection of hepatic function during septic shock. Male Sprague-Dawley rats underwent sham surgery or cecal ligation and puncture (CLP). Twenty-four later, animals were randomized and treated with aPC (1mg/kg) or vehicle (0.9% (w/v) saline) via an indwelling venous catheter at 12 hour intervals for 24 hours. Gene array was performed on hepatic RNA to determine miRNA expression, and predicted mRNA targets determined using a bioinformatics approach. Of 351 rat miRNAs examined by microarray hybridization, 17 were highly expressed during sepsis and restored to basal levels after aPC treatment. In silico analysis identified 9 miRNAs significantly regulating target genes of the focal adhesion pathway. These data suggest aPC treatment coordinates beneficial cytoprotective effects during sepsis by modulating miRNA expression. While translational effects remain to be fully elucidated in a clinical setting, we demonstrate herein the potential experimental and computational benefits for use of microRNA analysis in sepsis.

overall_design: 12 samples were analyzed. Microarray experiments were performed, in which liver tissue was harvested from variuous groups (Sham+Vehicle, Sham+aPC, CLP+Vehicle, CLP+aPC; n=3/group) and pooled.

middle: C


title: In vivo activation of a conserved microRNA program induces robust mammalian heart regeneration (array)

status: Public on Nov 20 2014

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Heart failure is a leading cause of mortality and morbidity in the developed world, partly because mammals lack the ability to regenerate heart tissue. Whether this is due to evolutionary loss of regenerative mechanisms present in other organisms or to an inability to activate such mechanisms is currently unclear. Here, we decipher mechanisms underlying heart regeneration in adult zebrafish and show that the molecular regulators of this response are conserved in mammals. We identified miR-99/100 and Let-7a/c, and their protein targets smarca5 and fntb, as critical regulators of cardiomyocyte dedifferentiation and heart regeneration in zebrafish. Although human and murine adult cardiomyocytes fail to elicit an endogenous regenerative response following myocardial infarction, we show that in vivo manipulation of this molecular machinery in mice results in cardiomyocyte dedifferentiation and improved heart functionality after injury. These data provide a proof-of-concept for identifying and activating conserved molecular programs to regenerate the damaged heart.

overall_design: Analysis of miRNA levels in regenerating zebrafish hearts

first: Aitor

first: Juan

last: Belmonte


title: Dissecting the genetics of cutaneous miRNA in a mouse model of autoimmune bullous disease

status: Public on Dec 18 2014

city: Lübeck

first: Saleh

middle: M.

last: Ibrahim

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Dermatology

country: Germany

institute: Universität zu Lübeck

summary:
MicroRNAs (miRNAs) are small endogenous, non-coding RNAs that control genes at post-transcriptional level. They are essential for development and tissue differentiation, and altered miRNA expression patterns are linked to the pathogenesis of inflammation and cancer. There is evidence that miRNA expression is genetically controlled similar to the transcription of protein-coding genes and previous studies identified quantitative trait loci (QTL) for miRNA expression in the liver. So far, little attention has been paid to miRNA expression in the skin. Moreover, there is no data on epistatic control of miRNA expression.
In this study, we statistically linked cutaneous miRNA expression patterns to SNP (single nucleotide polymorphism) markers in an advanced murine intercross line (AIL) of three strains (BxD2, NZM and MRL) that are known to be prone to develop autoimmune diseases as well as the wild-derived strain CAST/EiJ.
In particular, we screened 100 murine samples for 609 different miRNAs and identified 42 eQTL controlling the expression of 38 cutaneous miRNAs. As a result, we identified two chromosomal hot-spots on chromosome 2 and 8 that control the expression of multiple miRNAs. Moreover, for eight miRNAs, an interacting effect of pairs of SNP was observed. Combining the constraints on genes from the statistical interaction of their loci and further using curated protein interaction networks narrowed down the number of candidate genes controlling miRNAs to a set of several genes. Among the resulting interaction pairs were the genes COMMD3 and COPS5 found to regulate the expression of miR-501-5p.
Independently, a network analysis based on co-expression of miRNAs was performed using WGCNA (weighted gene co-expression analysis) to identify clusters (modules) of co-expressed miRNAs. One of these modules significantly correlated with the onset and severity of epidermolysis bullosa acquisita, a cutaneous autoimmune skin blistering disease induced by autoantibodies to type VII collagen. The key miRNAs identified from this analysis were miR-379 and miR-223.This work shows strong evidence for a genetic control of cutaneous miRNA expression.

overall_design: 100 murine skin samples

first: Yask

last: Gupta

middle: M


title: array CGH analysis of the aur2-1 mutant

status: Public on Dec 22 2014

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

type: Genome variation profiling by genome tiling array

summary: The gDNA of wild type (WT, Col-0), aur2-1 mutant (AAa), and WT trisomy 2 (AAA) were labeled and hybridized with Affymetrix Arabidopsis Tilling 1.0R arrays. The ratio of signal intensity of chromosomes in trisomy (AAa and AAA) to diploid (Col-0) were analyzed. The results indicated that the aur2-1 mutant was a tertiary trisomy (2n + 2L.3S).

overall_design: Three samples (Wild type, WT, Col-0; aur2-1, AAa; WT trisomy 2, AAA) were analyzed.

first: Kuan-Lin


title: Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma [SNP arrays]

status: Public on Mar 30 2015

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

summary: We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma.

overall_design: Affymetrix 250K NspI SNP arrays were performed according to the manufacturer's directions on DNA extracted from frozen follicular lymphoma or transformed follicular lymphoma tumor specimens

first: Wing

last: Chan

first: Timothy

middle: W

last: McKeithan


title: Serum miRNA expression is associated with lung cancer in a case-control study and normalizes following surgical resection

status: Public on Dec 30 2014

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

institute: NIH/NIEHS

summary:
microRNAs are small, non-coding, single-stranded RNAs between 18-22 nucleotides long that regulate gene expression. Expression of microRNAs is altered in tumor compared to normal tissue; there is some evidence that these changes may be reflected in the serum of cancer cases compared to healthy individuals. Several case-control studies have found evidence of differential levels of serum miRNAs in early stage non-small cell lung cancer (NSCLC) patients but with little consensus on specific miRNAs. Similarly, it is unclear whether miRNAs that show differential levels in tumors are the same miRNAs that are found in serum, and whether surgical resection of tumors leads to normalization of serum miRNA levels in cases.
We used Affymetrix arrays to examine serum miRNA expression profiles in a small series of surgically resected non-small cell lung cancer cases to investigate circulating levels of miRNAs.

overall_design: We compared global miRNA expression patterns in from patients prior to surgery with levels from 24 controls matched for age, sex, and smoking status. Within the case-patient series, circulating miRNA levels prior to surgery and one and six months post-operatively.

first: Ashley

last: Godrey

first: Stella

last: Sieber

first: Neil

last: Hayes

first: Patricia

last: Rivera

first: Jack

last: Taylor


title: Differential expression of microRNAs in porcine endometrium

status: Public on Nov 19 2014

city: wuhan

first: su

last: lijie

state: Hubei

address: shizishan street

department: animal science college

country: China

institute: Huazhong (Central China) Agricultural University

summary: Affymetrix miRNA arrays were used to generate miRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation.  The study allowed for the determination of the miRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the miRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role miRNAs in the porcine endometrium during pregnancy.

overall_design: the endometrium 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: Lijie

last: Su

first: Mei

last: Yu


title: miRNA expression data from MCF-7 cells, overexpressing ANXA1

status: Public on Jan 05 2015

city: Singapore

first: Peter

last: Nissom

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

summary:
Annexin 1 (ANXA1), an endogenous anti-inflammatory protein which modulates cellular processes such as proliferation, differentiation and apoptosis has been implicated in cancer initiation and progression.  ANXA1 was previously shown to be regulated by hsa-miR-196a and promoted cell proliferation and anchorarge-dependent growth and suppressed apoptosis. However, whether ANXA1 itself regulates miRNA expression is unknown.  Therefore, in this study, we investigated the regulation of miRNA by ANXA1 in breast cancer cells.
Using microarray technology, 12 miRNAs were found to be significantly and consistently  downregulated in MCF-7 cells (MCF-V5) overexpressing ANXA1 overexpressing MCF-7 cells (MCF-V5).  Hsa-miR-26b* and hsa-miR-562 were chosen for further investigation.The data suggest that miR-26b* and miR-562 may play a role in ANXA1-induced migration and possibly angiogenesis by targeting NFKB and point towards a potential therapeutic target for breast cancer.

overall_design: Breast cancer MCF-7 cells (MCF-V5) overexpressing ANXA1  were cultured for RNA extraction and hybridization on Affymetrix miRNA microarrays. These were compared against the control, which were MCF-7 cells (MCF-EV) carrying an empty expression vector. Expression analyses were carried out in triplicates

first: Durkesh

last: Anbalagan

first: Vijay

last: Pandey

first: Lau

last: Hoe

first: Pradeep

last: Bist

last: Lobie

first: Lina

last: Lim


title: Yeast translational profiling: rcm1 knockout vs. wild-type with oxidative stress

status: Public on Nov 07 2014

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: Rcm1 methylates ribosomal RNA at C2278 and a knockout of this gene induces structural alterations of rRNA and decreased translational fidelity. To test the influence of rcm1 knockout on the specific translation of mRNAs, we analysed the mRNA recruitment pattern into polysomes versus total cellular mRNAs under different oxidative stress conditions by microarrays. In order to estimate the efficiency of translation of individual mRNAs, we calculated the translational efficiency (TE) as ratio between signal intensity in the polysome fraction (‘translatome’) versus signal intensity in the total yeast cell lysate (‘transcriptome’) for each probeset on the array. Genes with at least 2-fold up- or downregulation at p < 0.05 were defined to be significantly translationally up- or downregulated.

overall_design: 2 genotypes (wild-type and rcm1 knockout), 3 oxidative stress treatments (0, 30 and 90 min H2O2), 2 biological replicates, common reference design with common reference pool = RNA pool of all 24 samples

first: Johannes

last: Grillari

first: Lore

last: Breitenbach-Koller

first: Sigrid

last: Pfeifenberger

first: Thomas

last: Mohr


title: micro RNA-379 couples glucocorticoid hormones to metabolic dysfunction in diabesity

status: Public on Oct 15 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
In metabolic control, GC signaling acts as a major counter-regulatory system against insulin action, and aberrantly elevated GC activity is tightly linked to major components of the so-called Metabolic Syndrome, including obesity, insulin resistance, hyperglycemia, and systemic dyslipidemia. Here we identify the hepatic induction of the conserved microRNA (miR)-379/410 genomic cluster as a key component of GC/GR-driven metabolic dysfunction in “diabesity”
Microarray data were utilized to screened for differentially regulated miRNAs between wt and db/db and between wt and GR Knockdown mice

overall_design: For wt vs. db/db: mice were fasted for 24 hours and refed for 6 hours; For GR-dependent miRNAs: mice were treated with rAAV delivering either control or GR-directed miRNA for the knockdown of the GR specifically in the liver.

first: Roldan

last: de Guia

first: Adam

middle: J

last: Rose

first: Anke

last: Sommerfeld

first: Oksana

last: Seibert

first: Daniela

last: Strzoda

first: Annika

last: Zota

first: Yvonne

last: Feuchter

first: Anja

last: Krones-Herzig

first: Norbert

last: Gretz

first: Geesje

last: Dallinga-Thie

first: Sven

last: Diederichs

first: Nora

last: Klöting

first: Matthias

last: Blüher

first: Mauricio

last: Diaz

first: Stephan

last: Herzig


title: MicroRNA expression profiles in 15 paired of gastric cancer tissues and gastric normal tissues

status: Public on Nov 10 2014

city: Changchun

first: XiaoTian

last: Zhang

state: Jilin

address: No.126 of Xinmin street, College of Basic Medicine, Jilin University.

institute: Jilin University

summary: In this dataset, we include the expression data obtained from gastric cancer tissues and gastric normal tissues to determine the differentially expressed microRNA in gastric cancer tissue.s

overall_design: Total RNA obtained from 30 tissues (15 paired of gastric cancer vs.normal tissues) was used for microarray analysis.

first: Xiaotian

first: Fan

last: Li


title: MicroRNA expression data from H1N1 influenza virus infected mouse lung

status: Public on Oct 21 2014

city: beijing

first: yanyan

last: bao

address: Dongzhimen South Street

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

summary:
Influenza A virus is a kind of single negative-stranded RNA virus which belongs to the Orthomyxoviridae family. It can cause localized outbreak or worldwide epidemic in a short time for its great contagiosity, fast spread speed and a wide range of host, and H1N1 influenza virus is a strong pathogenic subtype of influenza A virus. Influenza A virus infection has been shown to alter miRNA expression both in cultured cells and in animal models.
We used microRNA microarrays to detail the programme of microRNA expression and identified distinct classes of differentially regulated microRNAs during this process.

overall_design: Mice lungs infected with PR8 H1N1 influenza virus were separately selected for RNA extraction and hybridization on Affymetrix microRNA microarrays. We sought to obtain microRNAs expression level in different stages of infection. To that end, we selected two time-points: 2 days and 5 days.

first: Xiaolan

last: Cui

first: Yanyan

last: Bao


title: Allele specific RNA polymerase occupancy and gene expression analysis for  8 CEPH lymphoblastoid cell lines.

status: Public on Dec 31 2014

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

type: Genome binding/occupancy profiling by SNP array

summary: Allelic variation in gene expression is common in human genome. To understand genetic and epigenetic basis of allelic gene expression variation, we conducted allele specific RNA polymerase occupancy and allele specific gene expression analysis in CEPH lymphoblastoid cell lines.

overall_design: DNAs, RNAs and chromatin lysates were isolated at the same culturing condition across 8 cell lines. DNA analysis were performed following the standard Affymetrix SNP array protocol. RNAs were amplified using Affymetrix amplified double strand cDNA synthesis kit. DNAs from RNApolymerase ChIP were amplified using SIGMA WGA kit. Amplified cDNAs and ChIP DNAs were fragmented labelled and hybridized on Nsp/Sty arrays following the standard protocol.

first: Mitsutaka

last: Kadota

first: Sheryl

last: Gere

first: Robert

last: Clifford

first: Chunhua

last: Yan

first: Michael

last: Edmonson

first: Richard

last: Finney

first: Daoud

last: Meerzaman

first: Barbara

last: Dunn

last: Hu

first: Chaoyu

last: Wang

first: Phillip

middle: R

last: Taylor

first: Kenneth

last: Buetow

first: Maxwell

last: Lee


title: Expression of miRNAs in human ex-vivo CD8+ T cell subsets

status: Public on Oct 24 2014

city: Auckland

first: Vicky

last: Fan

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: University of Auckland

summary:
The aim was to assess miRNA expression in 3 human ex-vivo CD8+ T cell subsets which span from antigen inexperienced  cells (Naïve) to early memory cells (central memory, Tcm) and later stage memory cells (effector memory, Tem)
CD8+ T cells  were sorted on a FACS Aria II machine. N = naïve = CD8+, CCR7+, CD45RA+, CD45RO-, Tcm = central memory =  CD8+, CCR7+, CD45RA-, CD45RO-,Tem= effector memory =  CD8+, CCR7-, CD45RA-, CD45RO+

overall_design: PBMC were isolated from 3 healthy human donors and  sorted by FACS into 3 CD8+ T cell subsets. Total RNA was purified using the miRVANA kit (Ambion)

first: Hilary

last: Sheppard

first: Rod

last: Dunbar


title: miRNAs were significantly regulated by myocardin and ERα

status: Public on Oct 01 2014

city: Wuhan

first: da

middle: lin

last: lu

address: Wuhan university of science and tecnology

institute: Wuhan university of science and technology

summary: Using microarray, we compared miRNAs expression profiles of MDA-MB-231 cells transfected with myocardin and empty vector (pcDNA3.1) and found that 25 miRNAs were significantly changed in myocardin-transfected groups (17 up-regulated and 9 down-regulated miRNAs). Moreover, we showed that 18 of 25 miRNAs significantly regulated by myocardin were inhibited by ERα in MDA-MB-231 cells. In addition,through a microarray approach, we identify the subset of miRNAs modulated by ERα in MDA-MB-231 cells. Our results determined that ERα may function as tumor-promoter through down-regulating expression of 3 miRNAs (miR-26b, miR-146a and miR-331-3p) in MDA-MB-231 cells.

overall_design: There are 4 samples in this experiment (pcDNA3.1-transfected, myocardin-transfected, ERα-transfected, myocardin plus ERα co-transfecteded groups) and each sample was replicated 3 times. The vector-pcDNA3.1 was used as control.

first: Dalin

last: Lu

first: Xinghua

last: Liao

first: Tongcun

last: Zhang


title: Proinflammatory effect of Pseudomonas aeruginosa hook protein FlgE on human corneal epithelial cells

status: Public on Oct 08 2014

city: Suzhou

first: Yiqiang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: Recombinant protein of Pseudomonas aeruginosa hook protein FlgE was added to cultured human corneal epithelial cell line for 4 hours and the mRNA expression profiling was performed using Agilent 8*60K array and dual labeling.

overall_design: Three triplicates were included for FlgE treatment and PBS control respectively, thus producing three pairs of samples for array, namely E1PBS1, E2PBS2, E3PBS3.

last: WANG

first: Dandan

last: LIN


title: Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk [miRNA]

city: Chang sha

first: shishi

last: min

state: Hunan

address: Lu shan  road

department: College of life sciences

institute: Hunan Normal University

summary: In this study, we analyzed transcriptome gene expression microarray, epigenomic miRNA microarray and methylome sequencing data simultaneously in PBMs from 5 high hip BMD subjects and 5 low hip BMD subjects. Through integrating the transcriptomic and epigenomic data, firstly we identified BMD-related genetic factors, including 9 protein coding genes and 2 miRNAs, of which 3 genes (FAM50A, ZNF473 and TMEM55B) and one miRNA (hsa-mir-4291) showed the consistent association evidence from both gene expression and methylation data, and 3 genes (TMEM55B, RNF40 and ALDOA) were confirmed in the meta-analysis of 7 GWAS samples and GEnetic Factors for OSteoporosis consortium (GEFOS-2) GWAS results. Secondly in network analysis we identified an interaction network module with 12 genes and 11 miRNAs including AKT1, STAT3, STAT5A, FLT3, hsa-mir-141 and hsa-mir-34a which have been associated with BMD in previous studies. This module revealed the crosstalk among miRNAs, mRNAs and DNA methylation and showed four potential regulatory patterns of gene expression to influence the BMD status, including regulation by gene methylation, by miRNA and its methylation, by transcription factors and co-regulation by miRNA and gene methylation. In conclusion, the integration of multiple layers of omics can yield more in-depth results than analysis of individual omics data respectively. Integrative analysis from transcriptomics and epigenomic data improves our ability to identify causal genetic factors, and more importantly uncover functional regulation pattern of multi-omics for osteoporosis etiology.

first: Jigang

first: Lijun

last: Tan

first: Chen

last: Xu

first: Hao

last: He

first: Qing

last: Tian

first: Yu

last: Zhou

first: Chuan

last: Qiu

first: Xiang

last: Chen

first: Hong

last: Deng


title: MicroRNAs Involved in Aging of the Lateral Wall of the Cochlear Duct

first: David

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

summary:
Age-related hearing loss is a progressive sensorineural hearing loss that occurs as people get older. Degeneration of the organ of Corti and atrophy of the lateral wall of the cochlear duct (or scala media) in the inner ear are the two primary causes. MicroRNAs (miRNAs), a class of short non-coding RNAs that regulate the expression of mRNA/protein targets, are important regulators of cellular senescence and aging.
We examined the change of miRNA gene expression profiles in the lateral wall of the cochlear duct in two mouse strains during aging

overall_design: The totoal RNA was extracted from the lateral wall of cochlear duct from CBA/J and C57BL/6J mice at different ages. The expression profile of miRNAs was examined by miR microarray GeneChip.

first: Qian

first: Huizhan

middle: Z

last: Liu

first: Garrett

last: Soukup


title: Effects of SFP1 deletion and Sfp1p prionization on transcription in Saccharomyces cerevisiae

status: Public on Sep 23 2014

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

summary: Sfp1p is known to form the [ISP+] prion in Saccharomyces cerevisiae. Interestingly enough, the consequences and phenotypes of Sfp1p prionization and its absence are quite different. In order to understand the origin of this difference, we compared transcription profiles of an [ISP+], sfp1delta strains against the control strain (SFP1 [isp-]).

overall_design: 3 strains (an [ISP+], [isp-] and sfp1delta derivative of 25-25-2V-P3982, Peterhoff genetic collection), each in quadruplicate (4 biological replicates).

first: Tatyana

last: Rogoza

first: Elina

last: Radchenko

last: Lipaeva

first: Ludmila

last: Mironova

first: Sophie

last: Lamarre

first: Lidwine

last: Trouilh


title: Differential expression of mature miRNAs in P19 cells during neuronal differentiation and by Rbfox3 depletion.

status: Public on Sep 21 2014

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: To investigate whether Rbfox3 could alter the expression level of miRNAs during neuronal differentiation of P19 cells, we performed miRNA microarray analysis using the RNAs extracted from untreated (undifferentiated) P19-GFP, RA-treated (neuronally differentiated) P19-GFP, or RA-treated P19-T2 cells.

overall_design: Total 9 samples were analyzed. We compared expression levels of P19-GFP (-) vs P19-GFP (+) vs P19-T2 (+) to identify miRNAs which had changes in expression levels with p < 0.01. From this  miRNA list, we compared among P19-GFP (-) vs P19-GFP (+) vs P19-T2 (+) to identify the miRNAs which appeared to correlate with Rbfox3 expression.

first: Keekwang

last: kim

first: Jun

last: Zhu

first: Robert

middle: S

last: Adelstein

first: Sachiyo

last: Kawamoto


title: Expression of miRNAs in breast tumor from very youn women (<36) and women above 65 years old

status: Public on Sep 12 2014

city: Valencia

first: Gloria

last: Ribas

state: Valencia

address: Blasco Ibañez, 17

department: Medical Oncology and Hematology Unit

country: Spain

institute: INCLIVA Biomedical Research Institute

summary: miRNA expression from breast tumor tissue obtained from two groups of breast cancer (BC) patients: one group formed by women younger than 36 years and the other group by women older than 65 years.

overall_design: We selected breast tumor tissue samples from 21 women under 36 years old and 12 women above 65 years old, without BRCA mutation and without metastases. We selected a pool of samples in which all the subtypes were representated, in young patients as well as in older patients, to avoid expression biass. We add three samples from breast tissue of cancer-free women to minimize the age-related expression biass. Our aim was to compare miRNA expression between young women and older women, considering normal tissue as a reference.

first: Maria

last: Peña-Chilet

middle: T

last: Martínez

first: Jose

last: Pérez-Fidalgo

first: Ana

last: Lluch

last: Bosch

first: Joan

last: Climent

first: Octavio

last: Burgues

first: Jaime

last: Ferrer

first: Bea

last: Martinez-Delgado

first: Edu

last: Tormo

first: Pilar

last: Eroles

first: Lorena

last: Peiro-Chova


title: Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity [miRNA data]

status: Public on Sep 10 2014

city: Wellington

first: David

last: Rowlands

state: Wellington

address: 63 Wallace St Mt Cook

department: Institute of Food, Nutrition and Human Health

institute: Massey University

summary: Analysis of skeletal muscle miRNA expression from type 2 diabetic volunteers before and after 16 weeks of chronic exercise training (two groups, one undergoing aerobic ecercise and the other resistance training exercise)

overall_design: A biopsy was collected from the right Vastus Lateralis under local anaesthesia and RNA was isolated from muscle (~10 mg) using mirVana™ Kit , Low molecular weight RNA was biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit. 21.5 µl of high-quality biotin-labeled miRNA sample was hybridized to Affymetrix Gene-Chip® miRNA 2.0, stained on  Affymetrix Fluidics station 400 and scanned with a Hewlett Packard G2500A gene Array Scanner. Affymetrix® miRNA QC Tool v 1.1.1.0 was used for the data summarization, normalization, and microarray quality control.

first: Mamta

last: Giri


title: State Transitions in the TORC1 Signaling Pathway and Information Processing in S. cerevisiae

status: Public on Jul 29 2014

city: Tucson

first: James

last: Hughes Hallett

state: AZ

address: 1007 E. Lowell Street

department: Molecular and Cellular Biology

institute: University of Arizona

summary: TOR kinase complex I (TORC1) is a key regulator of cell growth and metabolism in all eukaryotes. Previous studies in yeast have shown that three GTPases, Gtr1, Gtr2 and Rho1, bind TORC1 in nitrogen and amino acid starvation conditions to block phosphorylation of the S6 kinase Sch9 and activate protein phosphatase 2A (PP2A). This leads to down-regulation of 450 Sch9-dependent protein and ribosome synthesis genes, and up-regulation of 100 PP2A-dependent nitrogen assimilation and amino acid synthesis genes. Here, using bandshift assays and microarray measurements, we show that the TORC1 pathway also populates three other stress/starvation states. First, in glucose starvation conditions, the AMP activated protein kinase (AMPK/Snf1) and at least one other factor, push the TORC1 pathway into an off state where Sch9- branch signaling and PP2A-branch signaling are both inhibited. Remarkably, the TORC1 pathway remains in the glucose starvation (PP2A off) state even when cells are simultaneously starved for nitrogen and glucose. Second, in osmotic stress, the MAPK Hog1/p38 drives the TORC1 pathway into a different Sch9 off, PP2A off state, where PP2A-branch signaling can still be activated by nitrogen starvation. Third, in oxidative stress and heat stress, TORC1-Sch9 signaling is blocked while weak PP2A-branch signaling occurs. Together, our data show that the TORC1 pathway acts an information-processing hub, activating different genes in different conditions to ensure that available energy is allocated to drive growth, amino acid synthesis or a stress response, depending on the needs of the cell.

overall_design: 2-color microarray dataset. Experiments interrogate the immediate response of wild-type (ACY044) and mutant strains (ACY142 and ACY509) to log growth; stress, including heatshock (42C), oxidative (0.4mM H2O2), and osmotic stress (0.375M KCl); and starvation conditions, including nitrogen, amino acid, and glucose starvation. Cells in mid-log growth were subjected to stress and/or starvation and/or the TOR inhibitor rapamycin for 20 minutes. Taken together, these microarrays support a model where the TORC1 pathway acts an information-processing hub. We find that condition dependent gene expression programs are activated hierarchically to allocate available energy for growth, amino acid synthesis, or a stress response, depending on the needs of the cell.  All yeast strains are of W303 background, MatA. Mutant strains were made using standard techniques (homologous recombination).

last: Hughes-Hallett

first: Xiangxia

last: Luo

first: Andrew

last: Capaldi


title: Expression data from activated NK cells

status: Public on Sep 09 2014

city: montpellier

first: martin

last: villalba

address: CHU Montpellier Hôpital Saint-Eloi 80, av. Augustin Fliche.

department: INSERM U1040

country: France

institute: Institut for Research in Biotherapy of Montpellier

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series

first: Martin

last: Villalba

first: Julian

last: Pardo


title: miRNA Expression data from WASF3 overexpressing stable T47D cells and control cells

status: Public on Aug 19 2014

city: Augusta

first: yong

last: teng

address: 1120 15th Street

institute: Medical College of Georgia

summary:
We recently showed that inactivation of the WASF3/WAVE3 gene in breast cancer cells results in loss of cell motility and invasion in vitro and metastasis in vivo. To obtain a better understanding of molecular mechanisms of action of WASF3, we have established the stable  WASF3 overexpressing T47D cells using lentiviral infect system.
We used miRNA microarrays to detail the global programme of miRNA expression after overexpression of  WASF3 and identified distinct classes of up or down-regulated metastmir associated with breast cancer cell migration and motility invasion

overall_design: total RNA including small RNA was extracted from WASF3 overexpressing  and empty vector transfected T47D cells, then labeled RNAs were hybridized on GeneChip miRNA Array. To identify altered miRNA expression patterns before or after overexpression of WASF3, we compared average miRNA expression levels between WASF3 overexpressing and control T47D cells.

first: Y

last: Teng

first: J

middle: K

last: Cowell


title: Expression data from activated NK cells [miRNA]

summary:
Natural Killer (NK) cells present natural cytotoxicity against tumor cells, although their activity is increased after activation.NK cell activation depends on a complex intracellular signaling process mediated by activating and inhibitory receptors and the functional outcome depends on the integration of the activating and inhibitory signals received. Soluble cytokines and/or ligands on target cells bind the NK cell receptors, and hence, influence the final NK cell response: attack versus ignorance.
We used microarrays to detail the global programme of gene expression underlying NK cell activation by IL-2, a MHC-I-deficient target cell (K562)+IL-2 and an EBV-target cell (R69).

overall_design: PBLs from 4 different donors were activated by 100 U/ml IL-2; K562+IL-2 or R69 cells. After 5 days we obtained RNA and miRNA from naïve NK cells or from NK cells activated with the above mentioned stimuli, with more than 90% of purity. The 16 RNA samples were used to generate cDNA libraries that were hybridized on Human Gene 1.1ST arrays (Affymetrix) and analyzed with the Affymetrix Gene Chip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).


title: Phenobarbital Induces Cell Cycle Transcriptional Responses in Mouse Liver Humanized for Constitutive Androstane and Pregnane X Receptors (miRNA)

status: Public on Aug 24 2014

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: The constitutive androstane receptor (CAR) and the pregnane X receptor (PXR) are closely related nuclear receptors involved in drug metabolism and play important roles in the mechanism of phenobarbital (PB)-induced rodent nongenotoxic hepatocarcino- genesis. Here, we have used a humanized CAR/PXR mouse model to examine potential species differences in receptor-dependent mechanisms underlying liver tissue molecular responses to PB. Early and late transcriptomic responses to sustained PB exposure were investigated in liver tissue from double knock-out CAR and PXR (CARKO -PXRKO ), double humanized CAR and PXR (CARh - PXRh), and wild-type C57BL/6 mice. Wild-type and CARh-PXRh mouse livers exhibited temporally and quantitatively similar tran- scriptional responses during 91 days of PB exposure including the sustained induction of the xenobiotic response gene Cyp2b10, the Wnt signaling inhibitor Wisp1, and noncoding RNA biomarkers from the Dlk1-Dio3 locus. Transient induction of DNA replication (Hells, Mcm6, and Esco2) and mitotic genes (Ccnb2, Cdc20, and Cdk1) and the proliferation-related nuclear antigen Mki67 were ob- served with peak expression occurring between 1 and 7 days PB ex- posure. All these transcriptional responses were absent in CARKO- PXRKO mouse livers and largely reversible in wild-type and CARh - PXRh mouse livers following 91 days of PB exposure and a subse- quent 4-week recovery period. Furthermore, PB-mediated upregu- lation of the noncoding RNA Meg3, which has recently been associ- ated with cellular pluripotency, exhibited a similar dose response and perivenous hepatocyte-specific localization in both wild-type and CARh-PXRh mice. Thus, mouse livers coexpressing human CAR and PXR support both the xenobiotic metabolizing and the proliferative transcriptional responses following exposure to PB.

overall_design: 13-week oral (drinking water) investigative phenobarbital study in male C57BL/6 wild type, CAR/PXR knockout and humanized CAR/PXR mice with a 4 week recovery period

first: Raphaelle

last: Luisier

first: Harri

last: Lempiäinen

first: Nina

last: Scherbichler

first: Albert

last: Braeuning

first: Miriam

last: Geissler

first: Valerie

last: Dubost

first: Arne

last: Müller

first: Nico

last: Scheer

first: Salah-Dine

last: Chibout

first: Hisanori

last: Hara

first: Frank

last: Picard

first: Diethilde

last: Theil

first: Philippe

last: Couttet

first: Antonio

last: Vitobello

first: Olivier

last: Grenet

first: Bettina

last: Grasl-Kraupp

first: Heidrun

last: Ellinger-Ziegelbauer

first: John

middle: P

last: Thomson

first: Richard

last: Meehan

first: Clifford

last: Elcombe

first: Colin

last: Henderson

first: C

last: Wolf

first: Michael

last: Schwarz

first: Pierre

last: Moulin

first: Rémi

last: Terranova

middle: G


title: miRNA expression data from skeletal muscle stem cells

status: Public on Aug 01 2014

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

country: Japan

institute: Fujita Health University

summary:
It has been shown recently that non-coding RNAs including miRNAs are involved in the development of skeletal muscle progenitors and to maintain the quiescent condition of adult skeletal muscle stem cells.
To identify the difference among developing skeletal muscle-committed progenitors or stem cells detected by Pax3-GFP; MyoD-primed RFP expressions, miRNA microarray was performed.

overall_design: Pax3-GFP; MyoD-RFP positive cells were selected at several developmental stages for miRNA extraction and hybridization on Affymetrix

first: Takuya

last: Yamamoto


title: miRNA profiling in HEV71-infected SH-SY5Y cells

status: Public on Jul 31 2014

city: Beijing

first: li

last: juan

address: East Street Fengtai District

institute: Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary:
MicroRNA (miRNA) has been highlighted in pathogen-host interactions, however, little is known about roles of miRNAs in neurological pathogenesis of human enterovirus 71 (HEV71) infections.
In this study, the comprehensive miRNA expression profiling in HEV71-infected human neuroblastoma SH-SY5Y cells were performed to identify cellular miRNAs response to HEV71. A total of 69 miRNAs were differentially expressed in HEV71-infected SH-SY5Y cells compared to non-infected cells. These findings provide new information on the miRNA and mRNA profiles in HEV71 infection, which may serve as a basis for further investigation into the biological functions of miRNAs in the neurological pathogenesis of HEV71 infections.

overall_design: Human neuroblastoma SH-SY5Y cells were infected with HEV71. After infection, the cells were harvested and extracted total RNA for miRNA profiling by hybridization on Affymetrix microarrays. A total of 69 miRNAs were differentially expressed inHEV71-infected SH-SY5Y cells compared to non-infected cells.

first: LiJuan

last: Xu

first: ChengFeng

last: Qin


title: Feasibility of global microRNA analysis from fine-needle biopsy FFPE material in patients with hepatocellular carcinoma treated with sorafenib

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. micro RNA expression were correlated to clinical outcome and sorafenib-therapy.
miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

overall_design: 20 microdissected hepatocellular carcinoma samples with detailed clinical data

first: Jan

last: Peveling


title: miRNA expression profiling in testis of mouse inter-subspecific hybrids

status: Public on Jun 01 2014

city: Prague

first: Petr

last: Simecek

state: Not Applicable

address: Vídeňská 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

summary: MiRNA expression profiling on 14.5 day old testis from sterile (PWD x B6)F1, (PWK x B6)F1 and fertile (B6 x PWD)F1 inter-subspecific hybrids were performed to study the genome wide variation in miRNA expression between different inter-subspecific hybrids during meiosis.

overall_design: The total RNA (120 ng) samples were extracted from 14.5 days juvenile testes (pool of 4 samples), converted to cDNA using the Affymetrix 3 IVT Express Kit and hybridized to Affymetrix Mouse miRNA Gene 1.0ST GeneChips (core facility of the Institute of Molecular Genetics AS CR, Prague, Czech Rep.)

first: Tanmoy

last: Bhattacharyya

first: Jiri

last: Forejt


title: microRNA expression data from peripheral blood mononuclear cell in patients with type 1 diabetes  compared with normal controls.

status: Public on Aug 16 2014

city: shanghai

first: wei

middle: qiong

last: gu

address: 197#,second ruijin road

institute: ruijin hospital

summary:
Type 1 diabetes mellitus (T1D) is a common autoimmune disease mediated by autoimmune attack against pancreatic b cells. It has been reported that dys-regulation of microRNAs (miRNAs) may contribute to the pathogenesis of autoimmune diseases, including T1D.
This study sought to identify T1D associated miRNAs in the peripheral blood mononuclear cell (PBMC).

overall_design: Peripheral blood mononuclear of newly diagnosed type1 diabetes patients and normal controls were purified by LymphoprepTm gradient purification according to the manufacturer’s instructions (Axis-Shield PoC AS, Oslo, Norway) for futher microarray analysis.

first: M

last: Yang

first: L

last: Ye


title: Affymetrix SNP 250K array data for paediatric high grade gliomas

status: Public on Jul 24 2014

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

summary: Alkylating agents are a frontline therapy for the treatment of several cancers including pediatric glioblastoma, a devastating lethal tumor in children. Unfortunately, many tumors are resistant to this therapy. We sought to identify ways of sensitizing tumor cells to alkylating agents while leaving normal cells unharmed; increasing therapeutic response while minimizing toxicity. Here we report using a siRNA screen targeting over 240 DNA damage response genes identified novel sensitizers to alkylating agents. In particular the base excision repair (BER) pathway, including 3-methylpurine-DNA glycosylase (MPG), as well as ataxia telangiectasia mutated (ATM) were identified in our screen. Interestingly, we identified MPG as a direct novel substrate of ATM. ATM-mediated phosphorylation of MPG was required for enhanced MPG function. Importantly, combined inhibition or loss of MPG and ATM resulted in increased alkylating agent-induced cytotoxicity in vitro and prolonged survival in vivo. The discovery of the ATM-MPG axis will lead to improved treatment of alkylating agent-resistant tumors.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from snap frozen biopsy and surgical brain tissue from paediatric high grade gliomas
Copy number analysis on Affymetrix SNP 250K arrays was performed for 35 paediatric high grade glioma samples and HapMap samples.

first: Sameer

last: Agnihotri

first: Kelly

last: Burrell

first: Marc

last: Remke

first: Brain

last: Golbourn

first: Yevgen

last: Chornenkyy

first: Aaron

last: Gajadhar

first: Nestor

middle: A

last: Fernandez

first: Ian

last: Clarke

first: Mark

last: Barszczyk

first: Sanja

last: Pajovic

first: Christian

last: Ternamian

first: Renee

last: Head

first: Nesrin

last: Sabha

first: Robert

last: Sobol

last: Taylor

first: James

last: Rutka

first: Chris

last: Jones

first: Peter

middle: B

last: Dirks

first: Gelareh

last: Zadeh

first: Cynthia

last: Hawkins


title: miRNA expression profiling of isolated populations of prepachytene spermatocytes, pachytene spermatocytes and spermatids of PWD and B6 male mice

first: Petr

last: Simecek

summary: MiRNA expression profiling of isolated populations of prepachytene spermatocytes (LP), pachytene spermatocytes (RP) and spermatids (ST) from PWD and B6 was performed to study the genome wide variation in miRNA expression between two mouse subspecies.

overall_design: Populations of pre-pachytene spermatocytes, pachytene spermatocytes and spermatids were isolated from PWD and B6 mice. All populations were isolated in triplicates from two bilogical replicas Hence, RNA was prepared from 18 samples and was then subject to labeling and hybridization on microarray chips.

first: Tanmoy

last: Bhattacharyya

first: Jiri

last: Forejt


title: Effect of lymphotoxin beta receptor blockade on microRNA expression in the spleen

status: Public on Jun 20 2014

city: Midlothian

first: Neil

middle: A.

last: Mabbott

address: Easter Bush

department: The Roslin Institute & Royal (Dick) School of Veterinary Sciences

country: United Kingdom

institute: University of Edinburgh

platform_organism:
Mus musculus
synthetic construct


title: microRNA expression in Mestenteric lymph samples from rat models of acute pancreatitis

status: Public on Mar 31 2014

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

department: Surgery

institute: University of Auckland

summary:
MicroRNAs in body fluids are becoming interesting markers for disease state. Here we assessed their presence in Mesenteric Lymph to identify candidate biomarkers for pancreatitis using a rat model of the disease.
We used Affymetrix microRNA arrays to assess the differences in mesenteric lymph fluid miRNAs in a taurocholate induced rat model of pancreatitis

overall_design: Mesenteric lymph was collected from five biological replicates from control sham operated animals (SHAM), fluid resuscitated taurocholate induced acute pancreatitis (RAP) and non-resuscitated taurocholate induced pancreatitis animals (AP). The latter group represent a more severe form of the disease.

first: Kathryn

last: Askelund

first: Satya

last: Shanbag

first: John

last: Windsor

first: Anthony

last: Phillips


title: miRNA expression profiles of primary ER-positive breast tumors following Tamoxifen treatment

status: Public on Jul 01 2014

city: Stuttgart

first: Hiltrud

last: Brauch

address: Auerbachstr. 112

institute: Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology

summary:
Adjuvant tamoxifen is a valid treatment option for women with estrogen receptor (ER)-positive breast cancer. However, up to 40% of patients experience distant or local recurrence or die. MicroRNAs have been suggested to be important prognosticators in breast cancer. This study aims to identify microRNAs with the potential to predict tamoxifen response.
We performed a global microRNA screen in primary tumours of six matched pairs of postmenopausal, ER-positive breast cancer patients treated with tamoxifen, who were either recurrence free or had developed a recurrence. Patients were treated at the Robert Bosch Hospital, Stuttgart, Germany, between 1986 and 2005.

overall_design: Total RNA from FFPE tissue from 12 postmenopausal patients with ER-positive breast cancer (6 patients with and 6 patients without recurrence) was extracted. Hybridisation of biotin-labelled RNA was performed on Affymetrix GeneChip miRNA_2.0 Arrays.

first: Reiner

last: Hoppe

first: Joanna

last: Achinger-Kawecka

first: Stefan

last: Winter

first: Piter

last: Fritz

first: Wing-Yee

last: Lo

first: Werner

last: Schroth


title: Dynamics of Nitrogen-regulated Gene Expression Reveals a Reciprocal Relationship between Cell Growth Rate and Nitrogen Catabolism

status: Public on May 05 2014

city: New York

first: David

last: Gresham

state: NY

address: 12 Waverly Place, Rm 203

department: Biology

country: USA

institute: New York University

summary: Cell growth rate is regulated in response to resource availability including the abundance, and molecular form, of essential nutrients.  In the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen impacts both cell growth rate and mRNA expression.  Disentangling causal relationships between nitrogen availability, cell growth rate and differential gene expression poses a considerable challenge.  Using experimental control of cell growth rate using chemostats, we studied the effect of variation in environmental nitrogen on differential gene expression.  We find that the primary determinant of nitrogen-regulated gene expression is nitrogen abundance whereas variation in nitrogen source affects the expression of only a small number of transcripts with highly specialized functions.  To study the dynamics of nitrogen-responsive gene expression we perturbed steady-state nitrogen-limited chemostat cultures by addition of either proline or glutamine.  Addition of either proline or glutamine to cells growing in nitrogen-limited chemostats results in repression of the nitrogen catabolite repression (NCR) regulon consistent with nitrogen abundance, and not nitrogen source, being the primary determinant of nitrogen-regulated gene expression.  We find that a transition from nitrogen-limited to nitrogen-replete conditions is accompanied by rapid induction of transcripts required for protein translation. We identified a reciprocal relationship between specific regulons required for protein translation (RP and RiBi) and the NCR regulon.  Using mathematical modeling we find evidence that cells adopt a metabolically inefficient growth mode during this transition.  By means of high resolution time series analysis we find evidence that rapid, and potentially accelerated, mRNA degradation plays an important role in remodeling gene expression programs in response to change in environmental nitrogen.  We propose that the evolutionarily conserved TORC1 signaling pathway orchestrates the balance between protein translation and assimilation of nitrogen sources at the transcriptional level to optimize rates of cell proliferation.

overall_design: A total of of 102 samples were analyzed in different nitrogen-limited conditions using chemostats in both steady-state and dynamic conditions.  A common reference obtained from an ammonium-limited chemostat growing at a dilution rate of 0.12/hr was used for all two color hybridization experiments.


title: Effect of lymphotoxin beta receptor blockade on microRNA expression in the spleen [AffyMircoRNA]

summary: Follicular dendritic cells (FDC) are important stromal cells within the B cell follicles and germinal centres (GC) of secondary lymphoid tissues.  FDC trap and retain native antigens on their surfaces in the form of immune complexes which they display to B cells, in order to select those cells with the highest antigen affinity.  MicroRNAs are short, non-coding RNAs of approximately 18-25 nucleotides in length that regulate gene expression at the post-transcriptional level by repressing the translation of target genes.  In the current study in vivo and in vitro systems were used to identify microRNAs that are differentially expressed as a result of FDC depletion.   Constitutive lymphotoxin-β receptor (LTβR) stimulation is required to maintain FDC in their differentiated state.  We show that the rapid de-differentiation of spleen FDC that followed LTβR-blockade, coincided with a significant decrease in the expression of mmu-miR-100-5p, mmu-miR-138-5p and mmu-miR-2137.  These microRNAs were shown to be expressed in the FDC-like cell line, FL-YB, and specific inhibition of mmu-miR-100-5p significantly enhanced expression of Il6, Ptgs1/2 and Tlr4 in this cell line.  The expression of each of these genes by FDC plays an important role in regulating GC size and promoting high-affinity antibody responses, suggesting that mmu-miR-100-5p may help regulate their expression during GC reactions.

overall_design: C57BL/6 mice were given a single intravenous injection of 100 µg of LTβR to temporarily deplete their FDC.  At intervals after treatment 4 spleens from each group were harvested and RNA prepared.   For each group samples were pooled into 2 groups of 2 and microRNA expression levels compared.  Spleens from LTb-/- mice were also analysed.

first: Susan

last: Aungier

first: Hotshi

last: Ohmori

first: Michael

last: Clinton


title: Hormonal Regulation of MicroRNA Expression in Rat Adrenal Gland

status: Public on May 16 2014

city: Palo Alto

first: Wen-Jun

last: Shen

state: CA

address: 3801 Miranda Avenue

department: Medicine

institute: Stanford University

summary: To determine miRNA profiles in rat adrenals from animals treated with vehicle, ACTH, 17α-ethinyl estradiol (17α-E2) or dexamethasone (DEX).  miRNA expression profiling was performed using Affymetrix® GeneChip® miRNA 2.0 Arrays. Together with qRT-PCR, several adrenal miRNAs have been identified, whose expression is subject to regulation by one or more than one hormone.

overall_design: RNA was extracted from four group rat adrenal gland and miRNA profiles were established using microarray using Affymetrix® GeneChip® miRNA 2.0 Arrays and confirmed with qRT-PCR. The microarray data were analyzed using Partek® Genome Suite software, version 6.3 Copyright© 2008 (Partek Inc., St. Louis, MO, USA) to comprehensively evaluate the differential expression level of the various samples.

first: Zhigang

last: Hu

first: Yuan

last: Cortez

first: Xudong

last: Tang

first: Li-Fen

last: Liu

first: Fredric

last: Kraemer

first: Salman

last: Azhar


title: miRNA profiling of EV71 infected HT29 cells

status: Public on May 08 2014

city: Brisbane

first: Edmund

last: Lui

state: qld

address: 2 George Street, Brisbane QLD 4000

country: Australia

institute: Queensland University of Technology

summary:
HT29 cells was infected with EV71 at MOI 1 or nil respectively and harvested at 36hpi
We use miRNA microarray to profile and identify miRNA which are up or down regulated due to EV71 infection

overall_design: 3 biological replicate (6 samples)


title: The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

city: Athens

first: Xiaoyu

last: Zhang

state: GA

address: 4409 Miller Plant Sci. bldg

department: Department of Plant Biology

institute: University of Georgia

type: Genome binding/occupancy profiling by genome tiling array

summary: Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

overall_design: In total 9 samples; 3 H3K9ac ChIP-chip, 3 H3K14ac ChIP-chip, 3 H3 ChIP-chip


title: Axin2/Runx2 mouse calvaria microRNA expression

status: Public on Jul 04 2014

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Runx2 and Axin2 regulate skeletal development. We recently determined that Axin2 and Runx2 molecularly interact in differentiating osteoblasts to regulate intramembranous bone formation, but the relationship between these factors in endochondral bone formation was unresolved. To address this, we examined the effects of Axin2 deficiency on the cleidocranial dysplasia (CCD) phenotype of Runx2+/- mice, focusing on skeletal defects attributed to improper endochondral bone formation. Axin2 deficiency unexpectedly exacerbated calvarial components of the CCD phenotype in the Runx2+/- mice; the endocranial layer of the frontal suture, which develops by endochondral bone formation, failed to mineralize in the Axin2-/-:Runx2+/-mice, resulting in a cartilaginous, fibrotic and larger fontanel than observed in Runx2+/- mice. Transcripts associated with cartilage development (e.g., Acan, miR140) were expressed at higher levels, whereas blood vessel morphogenesis transcripts (e.g., Slit2) were suppressed in Axin2-/-:Runx2+/-calvaria. Cartilage maturation was impaired, as primary chondrocytes from double mutant mice demonstrated delayed differentiation and produced less calcified matrix in vitro. The genetic dominance of Runx2 was also reflected during endochondral fracture repair, as both Runx2+/- and double mutant Axin2-/-:Runx2+/- mice had enlarged fracture calluses at early stages of healing. However, by the end stages of fracture healing, double mutant animals diverged from the Runx2+/- mice, showing smaller calluses and increased torsional strength indicative of more rapid end stage bone formation as seen in the Axin2-/- mice. Taken together, our data demonstrate a dominant role for Runx2 in chondrocyte maturation, but implicate Axin2 as an important modulator of the terminal stages of endochondral bone formation.

overall_design: 4 mice per genotype X 4 genotypes: wildtype (WT), Runx2+/- (R-Het), Axin2-/- (A-KO), Axin2-/-:Runx2+/- (A-KO:R-Het).   Total = 16 samples

first: Jennifer

last: Westendorf

first: Meghan

middle: E

last: McGee-Lawrence


title: 250K SNP array data for 40 high-grade myogenic cancers

status: Public on May 02 2014

city: Boston

first: Jonathan

last: Fletcher

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital and Harvard Medical School

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

summary: Many common human mesenchymal tumors, including gastrointestinal stromal tumor (GIST), rhabdomyosarcoma (RMS), and leiomyosarcoma (LMS), feature myogenic differentiation. Here we report that intragenic deletion of the dystrophin-encoding and muscular dystrophy-associated DMD gene is a frequent mechanism by which myogenic tumors progress to high-grade, lethal sarcomas. Dystrophin is expressed in nonneoplastic and benign counterparts for GIST, RMS and LMS, and the DMD deletions inactivate larger dystrophin isoforms, including 427kDa dystrophin, while preserving expression of an essential 71kDa isoform. Dystrophin inhibits myogenic sarcoma cell migration, invasion, anchorage independence, and invadopodia formation, and dystrophin inactivation was found in 96%, 100%, and 62% of metastatic GIST, embryonal RMS, and LMS, respectively. These findings validate dystrophin as a tumor suppressor and likely anti-metastatic factor, suggesting that therapies in development for muscular dystrophies may also have relevance in treatment of cancer.

overall_design: High molecular weight genomic DNA was isolated from 40 high-grade myogenic cancers (including 7 normal tissue/tumor pairs and 33 additional tumors) using QIAamp DNA Mini Kit (QIAGEN) and analyzed by Affymetrix 250K SNP array.

first: Yuexiang

last: Wang

first: Adrian

last: Marino-Enriquez


title: Affymetrix SNP array data for nasopharyngeal carcinoma samples

status: Public on May 01 2014

city: Singapore

first: Lizhen

address: 14 Medical Drive

institute: Cancer Science Institute

summary: Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. We determined the genomic landscape of 52 NPC cases with SNP-array analysis. This approach identified multiple recurrent SCNVs, with the most frequent deletion peak spanning the CDKN2A gene on 9p21. Additional SCNVs involving established cancer genes including CCND1, AKT2, MYC and TP53 were observed. Notably, we identified that one component of the SWI/SNF complex, ARID1A, was frequently deleted in NPC.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen nasopharyngeal carcinoma biopsy tissues
Copy number analysis of Affymetrix 250K SNP arrays was performed for 52 nasopharyngeal carcinoma samples.

Please note that the sample characteristics 'primary tumor size, metastasis, and regional lymph node' represents T, M and N in WHO TNM staging of nasopharyngeal cancer (according to American Joint Committee on Cancer (AJCC)), respectively.

first: De-Chen

last: Lin

first: H

last: Koeffler


title: ChIP-chip analysis of GBF1 in the presence and absence of its heterodimerizing partners, HY5 and HYH

status: Public on Mar 24 2014

city: New Delhi

first: Sudip

last: Chattopadhyay

state: Delhi

address: Aruna Asaf Ali Marg, JNU Campus

department: Development Biology

country: India

institute: National Institute of Plant Genome Research

summary: Transcription factors are key components of light signalling as they amplify the signal, which results in massive changes in genome-wide expression during photomorphogenesis. Three bZIP transcription factors (TFs), namely GBF1, HY5, and HYH, form heterodimers with each other and regulate photomorphogenesis in an interdependent manner. GBF1 acts as both a positive and negative regulator of photomorphogenesis, whereas HY5 and HYH mainly act as positive regulators of photomorphogenesis. In this study, the impact of heterodimerization of GBF1 with HY5 and HYH was analyzed for genome-wide binding of GBF1 through ChIP-chip in GBF1. We identified more than 2000 direct targets of GBF1 in the presence of HY5 and HYH. However, in the absence of HY5, very few binding sites were found, and in the absence of functional HYH protein, the number of GBF1 direct targets reduced to only half compared to when functional HYH was present.

overall_design: ChIPed DNA with GBF1 antibody from GBF1OE, hy5 GBF1OE, and hyh GBF1OE lines vs. ChIPed DNA with GBF1 antibody from wild-type.

first: Hathi

last: Ram

first: Mukesh

last: Jain


title: miRNA Profile in Normal and Preeclamptic Placenta

status: Public on Apr 25 2014

city: Shreveport

first: Yuping

state: LA

address: 1501 Kings Hwy

department: OB/GYN

institute: LSUHSC-Shreveport

summary: The purpose of this study was to determine the difference of the miRNA profiles between normal and preeclamptic placenta.

overall_design: Ten placental samples were analyzed.  Six were from preeclamptic patients and four were from normal pregnancies.


title: Epigenetic regulation of MYC modulates glioblastoma tumorigenicity

status: Public on Mar 28 2014

city: La Jolla

first: Olivier

last: Harismendy

state: California

address: 3855 Health Sciences Drive #0820

department: Medicine / Moores Cancer Center

institute: UC San Diego

summary: One aspect of intra-tumoral heterogeneity in glioblastoma involves subpopulations of cells capable of self-renewal and indefinite propagation. Conceptually, this capacity is frequently treated as a static property. Here we provide data suggesting that tumorigenicity in glioblastomais a dynamic property that can be acquired or lost. Integrated expression analyses suggest that tumorigenicity is determined by the level of MYC expression relative to a threshold. Transitions between tumorigenic and non-tumorigenic cell states are associated with changes in histone modifications at the MYC locus, suggesting tumorigenicity is epigenetically regulated.

overall_design: To verify genomic stability at the nucleotide level, we tested whether subclones derived from single cells shared common Single-Nucleotide Polymorphisms (SNPs). Ten single cell-derived subclones of U87MG underwent SNP profiling by Affymetrix Human Mapping 250K Nsp arrays.

first: Clark

last: C. Chen

first: Hiroko

last: Matsui

first: Kie

last: Li


title: Regulation of S-phase transcription factors by Cdk1

status: Public on Apr 10 2014

city: Worcester

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Analysis of gene expression across the cell cycle from wild type cells, and cells expressing alleles of Yox1, Yhp1, Hcm1, and Tos4 that cannot be phosphorylated by Cdk1. Expression of S-phase and M/G1 transcripts are downregulated when phosphorylation of these factors is blocked, demonstrating that Cdk1 promotes expression of late cell cycle genes.

overall_design: These experiments are two-color hybridizations of RNA isolated from synchronized wild type (WT) or phosphomutant (4P) cells, compared to RNA from asyncrhonous wild type cells in mid-log phase. Wild type and mutant cells were synchronized in G1 phase, released into the cell cycle and samples collected at 15 minute intervals. Each time course was carried out in duplicate, the replicate experiment was performed as a dye swap.

first: Benjamin

middle: D

last: Landry


title: Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia

status: Public on Mar 13 2014

first: Tsuneya

last: Ikezu

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

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

overall_design: Refer to individual Series


title: Global Profiling in Vestibular Schwannomas Shows Critical Deregulation of MicroRNAs and Upregulation in those included in Chromosomal Region 14q32

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

institute: Hospital Universitari Germans Trias i Pujol

summary:
Background: Vestibular Schwannomas are benign tumors that arise from Schwann cells in the VIII cranial pair and usually present NF2 gene mutations and/or loss of heterozygosity on chromosome 22q. Deregulation has also been found in several genes, such as ERBB2 and NRG1. MicroRNAs are non-coding RNAs approximately 21 to 23 nucleotides in length that regulate mRNAs, usually by degradation at the post-transcriptional level.
Methods: We used microarray technology to test the deregulation of miRNAs and other non-coding RNAs present in GeneChip miRNA 1.0 (Affymetrix) over 16 vestibular Schwannomas and 3 control-nerves, validating 10 of them by qRT-PCR.
Findings: Our results showed the deregulation of 174 miRNAs, including miR-10b, miR-206, miR-183 and miR-204, and the upregulation of miR-431, miR-221, miR-21 and miR-720, among others. The results also showed an aberrant expression of other non-coding RNAs. We also found a general upregulation of the miRNA cluster located at chromosome 14q32.
Conclusion: Our results suggest that several miRNAs are involved in tumor formation and/or maintenance and that global upregulation of the 14q32 chromosomal site may represent a therapeutic target for this neoplasm.

overall_design: 16 Vestibular Schwannomas and 3 control-nerves were analysed

first: Luis

last: Lassaletta

first: Juan

last: Rey


title: miRNA expression in fast and slow skeletal muscle of wild type and SOD1-G93A mice

status: Public on Mar 04 2014

city: Zaragoza

first: Janne

middle: M

last: Toivonen

address: Miguel servet 177

department: Departamento de Anatomía, Embriología y Genética Animal

institute: Universidad de Zaragoza

summary:
Amyotrophic lateral sclerosis (ALS) is a lethal motor neuron disease that progressively debilitates neuronal cells that control voluntary muscle activity. In a mouse model of ALS that expresses mutated human superoxide dismutase 1 (SOD1-G93A) skeletal muscle is one of the tissues affected early by mutant SOD1 toxicity. Fast-twitch and slow-twitch muscles are differentially affected in ALS patients and in the SOD1-G93A model, fast-twitch muscles being more vulnerable.
We used miRNA microarrays to investigate miRNA alterations in fast-twitch (EDL) and slow-twitch (soleus) skeletal muscles of symptomatic  SOD1-G93A animals and their age-matched wild type littermates.

overall_design: At age of 90 days RNA was extracted from extensor digitorum longus (EDL) and soleus (SOL) muscles of male SOD1-G93A animals and their age-matched wild type male littermates. RNA was hybridized on Affymetrix Multispecies miRNA-2_0 Array.

first: Raquel

last: Manzano

first: Sara

last: Olivan

first: Pilar

last: Zaragoza

first: Alberto

last: Garcia-Redondo

first: Rosario

last: Osta


title: Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia (miRNA)

summary:
The aim of this study was to determine the role that miRNAs have on influencing murine microgial phenotypes under M1(LPS) and M2a (IL-4) stimulating conditions.
This Series includes expression data obtained from miRNA gene expression microarrays; mRNA expression profiles obtained from the same RNA samples were deposited as a separate Series.

overall_design: 9 total samples were analyzed, n=3 for the three stimulating conditions (resting state, LPS and IL-4) for murine primary microglia. This allowed us to perform the following pairwise comparisons: PBS vs. LPS, and PBS vs. IL-4. This was performed for both mRNA and miRNA gene expression profiles.

first: Robert

last: Freilich


title: Disomes and Disomes ubp6∆ vs. wild-type

status: Public on Feb 20 2014

city: worcester

first: Eduardo

last: Torres

address: 364 Plantation Street, LRB-523

department: Department of Molecular, Cell and Cancer Biology

summary: Transcriptional profiling of anreuploid yeast strains grown in rich medium YEPD

overall_design: Cells were grown in YEPD at 30 degrees


title: Expression data from ccRCC specimens

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: To identify a  therapeutic candidate target molecule for ccRCC, we analyzed the microRNA (miRNA) expression signatures in ccRCC clinical specimens.

overall_design: 9 matched pair (normal tissue and ccRCC tissue) plus 7 ccRCC tissue were analyzed for miRNA-microarray

first: Yuko

last: Ueda

first: Kaori

last: Kitae


title: Yeast gene expression profiles of pressure-sensitive mutant strain

status: Public on Feb 19 2014

city: Gifu

first: Kazuki

last: Nomura

address: 1-1, Yanagido

institute: Gufu university

summary:
High hydrostatic pressure causes physical stress to organisms, and it induces growth inhibition and cellular death.
For Saccharomyces cerevisiae, more than 150 MPa at room temperature is lethal conditions. To understand the mechanism of pressure inactivation, we isolated pressure-sensitive mutant strain of S. cerevisiae and analyzed genome-wide mRNA expression profiles using DNA microarray. Mutant strain and parent strain were grown in YPD medium at 30°C for 48 h.

overall_design: Series contains four hybridization results from independent biological samples respectively in both strains of pressure-sensitive mutant strain and that parent strain.

first: Hitoshi

last: Iwahashi

first: Akinori

last: Iguchi

first: Toru

last: Shigematsu


title: Over-expression of CTR1 delta-300 alters element and transcription profiles in yeast

status: Public on Jan 28 2014

city: Dresden

first: Astrid

last: Schuller

address: Zellescher Weg 20B

country: Germany

institute: TU-Dresden

summary: In an approach to generate Saccharomyces cerevisiae strains with increased intracellular copper amounts for technical applications we over-expressed the copper transporter CTR1 and a variant of CTR1 with a truncation in the C-terminus after the 300 amino acids (CTR1 delta-300). We determined the copper sensitivity of the generated strains and used inductively coupled plasma spectrometry (ICP-OES and ICP-MS) analysis to investigate the effects of over-expression of both constructs under excess copper on the cellular content of different elements in S. cerevisiae. In addition, we ran DNA microarray analysis to obtain the gene expression profile under the changed element contents. Over-expression of CTR1 increased the copper content in the cells up to 160% and 78 genes were differentially regulated. Over-expression of the truncated CTR1 delta-300 resulted in an increased copper, iron and zinc content of more than 200% and 980 genes showed differential expression. We found that transition metal ion homeostasis was disrupted in CTR1 delta-300 over-expressing strains under excess copper and that this was combined with a transcriptional remodelling of cellular processes

overall_design: Transcription profiling was performed in Saccharomyces cerevisiae BY4741 (referred to as wild type) over-expressing CTR1 and in the ctr1- deletion strain BY4741 delta-ctr1 overexpressing CTR1 delta-300 after 7 hours of culture under excess copper (0.02 mM CuCl2). Control strains contained the corresponding empty vector. Three independent experiments were performed and 12 samples were analyzed.

first: Gudrun

last: Auffermann

first: Katja

last: Zoschke

first: Ulrike

last: Schmidt

first: Kai

last: Ostermann

first: Gerhard

last: Rödel


title: Expression data from high-grade serous ovarian carcinomas (HGSC), clear cell ovarian carcinomas (CCC) and ovarian surface epithelium (OSE)

status: Public on Feb 13 2014

city: Oslo

first: Bente

middle: Vilming

last: Elgaaen

address: Ullernchausseen 70

department: Department of Gynecological Oncology

country: Norway

institute: Oslo University Hospital

summary:
Background: The aim of this study was to identify differentially expressed miRNAs in high-grade serous ovarian carcinoma (HGSC), clear cell ovarian carcinoma (CCC) and ovarian surface epithelium (OSE). Selected miRNAs were evaluated for association with clinical parameters including survival, and miRNA/mRNA interactions were mapped.
Results: Differentially expressed miRNAs between HGSC, CCC and OSE were identified, of which 18 were validated (p<0.01) using RT-qPCR in an extended cohort. Compared with OSE, miR-205-5p was the most overexpressed miRNA in HGSC. miR-200 family members and miR-182-5p were the most overexpressed in HGSC and CCC compared with OSE, whereas miR-383 was the most underexpressed. miR-509-3-5p, miR-509-5p, miR-509-3p and miR-510 were among the strongest differentiators between HGSC and CCC, all being significantly overexpressed in CCC compared with HGSC. High miR-200c-3p expression was associated with poor progression-free (p=0.031) and overall (p=0.026) survival in HGSC. Interacting miRNAs and mRNA targets, including those of a TP53-related pathway presented previously, were identified in HGSC.
Conclusions: Several miRNAs are overexpressed in HGSC and CCC compared with OSE, including the miR-200 family, among which miR-200c-3p is associated with survival in HGSC. A set of miRNAs differentiates CCC from HGSC, of which miR-509-3-5p and miR-509-5p are the strongest classifiers. Several interactions between miRNAs and mRNAs in HGSC were mapped.

overall_design: Methods: Differences in miRNA expression between HGSC, CCC and OSE scrapings were analyzed by global miRNA expression profiling (Affymetrix GeneChip miRNA 2.0 Arrays, n=30), validated by RT-qPCR (n=63), and evaluated for associations with clinical parameters. For HGSC, differentially expressed miRNAs were linked to differentially expressed mRNAs identified previously (GSE36668).

middle: V

first: Ole

last: Olstad

first: Kari

last: Haug

first: Berit

last: Brusletto

first: Leiv

last: Sandvik

first: Anne

middle: C

last: Staff

first: Kaare

last: Gautvik

first: Ben

last: Davidson


title: Effects of YB-1 protein reduction on microRNA abundance in breast cancer cell-lines

status: Public on Jan 23 2014

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

institute: University of Auckland

summary:
To assess the association of the nucleic acid binding protein yb-1 with mature microRNAs levels in breast cancer. To do this we performed YB-1 siRNA treatement in triplicates alongside an siRNA control
Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S.

overall_design: Two cell-lines, treated with either siYB-1 or si-Ctrl in triplicate samples.

first: Annette

last: Lasham

first: Cristin

last: Print

first: Daniel

last: Hurley

first: Sandra

last: Fitzgerald


title: Identification of miRNAs which bind to YB-1 protein

summary:
To assess the direct association of the nucleic acid binding protein yb-1 with mature microRNAs in breast cancer. To do this we performed immunoprecipitation (IP) of YB-1 protein to pull-down linked RNAs
Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. An input control represents the RNA present in the lysate used for the IP, prior to treatment.

overall_design: IPs were performed in triplicates on different cell-lysates with one input control used as a representative of the RNA added to the IP reaction.


title: miRNA expression profiles in YT and NK92 cells

status: Public on Jan 21 2014

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

country: Taiwan

institute: National Taiwan University

summary: The miRNA expression profiles of of EBV-infected YT and NK92 cells are compared. YT cells have weaker expression of T-bet and IFNg than NK92 cells.  It was found that the EBV-encoded miR-BART20-5p inhibits the expression of T-bet and IFNg in YT cells.

overall_design: Approximately 100 ng total RNAs from YT and NK92 cells  were used as the input. The GeneChip miRNA 2.0 array from Affymetrix, including probes for 44 EBV-encoded miRNAs and 1105 human miRNAs, was used. The experiments were performed in the microarray core laboratory of National Health Research Institute, Taiwan.


title: Links between the Oncoprotein YB-1 and Small Non-Coding RNAs in Breast Cancer


title: MicroRNA expression profiles in WT and APP/PS1 mouse hippocampus

status: Public on Jan 08 2014

city: Beijing

first: Yan

last: Zhang

address: College of Lfe Sciences, Peking University

department: College of Life Sciences

country: China

institute: Peking Unversity

summary: With the criterion of 2-fold cutoff, 7 miRNAs were upregulated and 7 miRNAs were downregulated in APP/PS1 hippocampal tissues compared with WT hippocampal tissues

overall_design: Microarray analysis of miRNAs was performed on pooled hippocampal tissues from WT (n=16) and APP/PS1 mice (n=16) at E14

first: Xiaqin

last: Sun

first: Yu

last: Wu


title: microRNA expression profile in HEK293T cells infected with Chikungunya virus

status: Public on Jan 01 2014

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

institute: Indian Institute of Technology

summary:
HEK293T grown in 6 well plates were infected with CHIKV and total RNA was isolated from cells at 0, 12 and 24 hrs post infection.
CHIKV microRNA expression signature was generated.

overall_design: Cells grown on 6-well plates. Three biological replicates of uninfected and two biological replicates of infected samples

first: Tanvi

last: Saxena

first: Bhavna

last: Tandon

first: Shivani

last: Sharma

first: Pratima

last: Ray

first: Alok

middle: R

first: Ritu


title: miRNA expression in aging skin

status: Public on Feb 25 2014

city: Neuherberg

first: Steffen

last: Sass

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: Fibroblasts were isolated from healthy skin, donors were young, middlege and old. We used Affymetrix miRNA microarrays to detail the global expression of miRNAs.

overall_design: Primary fibroblasts were isolated from healthy skin, donnors were young, middlege and old and kept in culture for a short time in order to avoid scenescence.

first: A

last: Reifenberger

last: Florea


title: Tissue and blood microRNA array profiles of colorectal cancer patients

status: Public on Dec 30 2013

city: Kuala Lumpur

first: Yong

middle: Fung

address: Faculty of Medicine, University of Malaya

department: Surgery

country: Malaysia

institute: University of Malaya

summary: microRNAs (miRNAs) are short, non-coding RNA molecules that act as regulators of gene expression. Circulating blood miRNAs offer great potential as cancer biomarkers. The objective of the study was to correlate the differential expression of miRNAs in tissue and blood in the identification of biomarkers for early detection of colorectal cancer (CRC).

overall_design: miRNA biomarker discovery via miRNA array profiling using paired cancer tissues (n = 30) and blood samples (CRC, n = 42; control, n = 18).

first: Fung

middle: L

last: Yong

first: Chee

middle: W

last: Law

last: Wang


title: microRNA (miRNA) expression data from induced pluripotent stem cell  (iPSC)-derived neurons exposed to soman/GD

status: Public on Dec 31 2013

city: Aberdeen Proving Ground

first: E Chepchumba

middle: K

last: Yego

state: MD

address: 3100 Ricketts Point Road

department: Research

institute: US Army Medical Research Institute of Chemical Defense

summary:
Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart.
Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures.
This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent GD/soman (O-Pinacolyl methylphosphonofluoridate) on human-induced pluripotent stem cell (iPSC)-derived neurons

overall_design: iPSC-derived neurons were treated with GD  at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips

first: E

first: James

middle: F

last: Dillman

first: Heidi

last: Hoard-Fruchey


title: microRNA (miRNA) expression data from induced pluripotent stem cell (iPSC)-derived neurons exposed to VX

summary:
Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart.
Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures.
This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent VX (o-ethyl-s-[2 (diisopropylamino) ethyl] methylphosphonothiolate) on human-induced pluripotent stem cell (iPSC)-derived neurons

overall_design: iPSC-derived neurons were treated with VX  at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips


title: microRNA (miRNA) expression data from induced pluripotent stem cell derived (iPSC) derived cardiomyocytes exposed to VX

summary:
Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart.
Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures.
This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent VX (o-ethyl-s-[2 (diisopropylamino) ethyl]) on human (iPSC)-derived neurons and iPSC-derived cardiomyocytes.

overall_design: iPSC-derived cardiomyocytes were treated with VX  at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips


title: microRNA (miRNA) expression data from induced pluripotent stem cell derived (iPSC) derived cardiomyocytes exposed to soman/GD

summary:
Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart.
Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures.
This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent GD/soman (O-Pinacolyl methylphosphonofluoridate) on human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes

overall_design: iPSC-derived cardiomyocytes were treated with GD  at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips


title: Analysis of differential miRNA expression profiling in Namalwa cells

status: Public on Dec 27 2013

city: Bengbu

first: yiwen

last: zhang

state: Anhui

address: 287 Chang Huai Road

department: Hematology

institute: The First Affiliated Hospital of Bengbu Medical College

summary: To analyze the differential miRNA expression profiling in human lymphoma cells (Namalwa cell line) before and after treatment by DNA methylation inhibitor 5-aza-2'-deoxycytidine (Decitabine; 5-aza).

overall_design: Six total samples were analyzed, two groups, and triplicate for each group. The abbreviation of Con represents Namalwa cells without the treatment of 5-aza, and Add represents Namalwa cells after treatment by 5-aza for 3 days.

first: Yiwen

last: Zhang

first: Lin

last: Liu


title: Genomic analysis of relapsed Acute Lymphoblastic Leukaemia in children

status: Public on Dec 21 2013

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

institute: Newcastle University

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

summary: Identification of de novo copy number abnormalities arising in relapsed paediatric ALL in matched presentation and relapse samples. We identified deletions of BACH2, (BTB and CNC homology 1, basic leucine zipper transcription factor 2) at relapse. To study the role of Bach2 in pre-B ALL in a genetic experiment, we transformed pre-B cells from Bach2–/– mice with BCR-ABL1. Our findings identify Bach2 as a novel tumor suppressor upstream of p53 in pre-B ALL.

overall_design: 64 arrays (32 250K Nsp and 32 250K Sty) are included in this study. DNA was extracted from the presentation and relapse samples from 11 paediatric patients and DNA was extarcted from the remission samples from 10 patient and hybridised to the Affymetrix Human Mapping 500K Array Set.