title: Comparison between hereditary breast tumors and normal breast tissue samples.

status: Public on Dec 01 2013

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

institute: Spanish National Cancer Research Centre (CNIO)

summary:
Tumor associated miRNAs in hereditary breast cancer.
In this study we investigated the role of miRNAs in hereditary breast tumors comparing with normal breast tissue. Global miRNA expression profiling was performed on 22 hereditary breast tumors and 15 non-tumoral breast tissues. We identified 19 miRNAs differentially expressed, most of them down-regulated in tumors. An important proportion of deregulated miRNAs in hereditary tumors were previously identified commonly deregulated in sporadic breast tumors. Our results identify miRNAs associated to hereditary breast cancer, as well as miRNAs commonly miss-expressed in hereditary and sporadic tumors, suggesting common underlying mechanisms of tumor progression. In addition, we provide evidence that KRAS is a target of miR-30c, and that this miRNA suppresses breast cancer cell growth potentially through inhibition of KRAS signaling.

overall_design: Single color experiments in a pairwise comparison design.

first: Miljana

last: Tanic

first: Gonzalo

last: Gómez-López

first: Javier

last: Benítez

last: Martínez-Delgado


title: Exploring the larval transcriptome of the common sole (Solea solea L.)

status: Public on Sep 20 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: A microarray platform for Solea solea was developed to study gene expression profiles of common sole developmental stages.

overall_design:
Characterization of the transcriptome of S. solea, focusing on larval and juvenile stages. After transcriptome sequencing and annotation [TSA accession number GAAQ00000000], an oligo-DNA microarray for the detection of 12,836 unique transcripts was developed and applied to the study of gene expression profiles during larval-to-juvenile transition.
For microarray experiments, pooled samples of 10–5 individuals (depending on larval age) were sampled and RNA extracted at 1, 4, 6, 11, 13, 18, 24 and 33 days post-hatching (dph). The number of biological replicates was four for each sampling point.

first: Luca

last: Bargelloni


title: microRNA expression profiles in bone marrow fractions from gastric cancer patients

status: Public on Aug 23 2013

city: Tokyo

first: Ken

last: Okano

address: Toyo Ekimae bldg. 2-20, Toyo 2-Chome, Koto-Ku

country: Japan

institute: Cosmo Bio Co., LTD.

summary: Both disseminated tumor cells and noncancerous host cells contributed to cancer progression cooperatively in bone marrow. Bone marrow samples were obtained from 4 gastric cancer patients, and were separated into 3 fractions (CD45 positive, CD45 negative/EpCAM positive, and CD14 positive fractions) by the automagnetic-activated cell separation (AutoMACS) system using CD45, EpCAM, and CD14 microbeads (Miltenyi Biotec, Germany). microRNA expression profiles in each fractions were evaluated in order to identify candidate prognostic markers for gastric cancer patients.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In 4 patients with gastric cancer, bone marrow samples (40 mL) were obtained from iliac bones. Nucleated cells were collected by gradient centrifugation using Ficoll-Paque PREMIUM (GE Healthcare Life Science, USA) and Leucosep (Greiner Bio-One, Germany) according to the manufacturer’s instructions. Next, we separated bone marrow cells into 3 fractions using MACS: CD45 positive (CD45+), CD45 negative/EpCAM positive (CD45-/EpCAM+), and CD14 positive (CD14+). microRNA expression levels of whole bone marrow cells and each fractions were measured by the miRCURY™ LNA array microarray (6th gen-hsa, mmu & rno#208402, Exiqon, Vedbaek, Denmark). The miRCURY™ LNA array microarray slides were scanned using  the Agilent  G2505C Microarray Scanner System (Agilent Technologies, Inc., USA) and the data analysis was carried out using the Feature Extraction 10.7.3.1 (Agilent Technologies, Inc., USA).

first: Koshi

last: Mimori

first: Hisae

last: Iinuma

first: Masaki

last: Mori


title: H3K4me3 in mortal and immortal breast cells

status: Public on Jul 03 2013

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

country: USA

institute: University of Arizona

type: Genome binding/occupancy profiling by genome tiling array

summary: H3K4me3 changes during immortalization of breast cells. The aim of the study was to determine whether differential epigentic state of TERT gene is involved in immortalization of breast cells.

overall_design: comparison of Pre-Stasis, Post-Selection, and immortal cells

first: James

middle: C

last: Garbe

first: Martha

middle: R

last: Stampfer

first: Bernard

middle: W

last: Futscher


title: H3K27me3 in mortal and immortal breast cells

summary: H3K27me3 changes during immortalization of breast cells. The aim of the study was to determine whether differential epigentic state of TERT gene is involved in immortalization of breast cells.


title: DNA methylation of mortal and immortal breast cells

type: Methylation profiling by genome tiling array

summary: DNA methylation changes during immortalization of breast cells. The aim of the study was to determine whether differential epigentic state of TERT gene is involved in immortalization of breast cells.


title: Expression data from late-luteal bovine endometrium

status: Public on Aug 22 2013

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary:
In both beef and dairy cattle, the majority of embryo loss occurs in the first 14-16 days following insemination. During this period, the embryo is completely dependent on its maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to embryo survival.
We used microarrays to assess endometrial gene expression in high and low fertility heifers during the late-luteal phase of the estrous cycle.

overall_design:
Charlaois × Limousin heifers were artificially inseminated on 4 successive occasions and heifers were subsequently characterized as either high or low fertility (HF; LF) based on the presence of an embryo on day 28 of pregnancy on all four inseminations or on one occasion only, respectively. From this population of animals, HF and LF heifers were slaughtered on day 14 of a synchronized estrous cycle and global gene expression in uterine endometrial tissue was determined using the Affymetrix® 23K Bovine GeneChip.
Array Annotation link: http://mad-db.science.uva.nl/~wdeleeuw/HybridAnnot/

first: Aideen

middle: P

last: Killeen

first: David

middle: A

last: Kenny

first: Michael

last: Diskin

first: Sinead

middle: M

last: Waters


title: Expression data from canine B-cell lymphomas

status: Public on Jul 02 2013

city: Chapel Hill

first: Kristy

middle: L

last: Richards

state: NC

address: 1062 Genetic Medicine Bldg.

department: Medicine

institute: University of North Carolina

summary:
Pet dogs may provide a useful large-animal model of spontaneously occuring non-Hodgkin lymphoma, but complete molecular characterization is lacking.
We used gene expression microarrays to molecularly characterize canine lymphoma, and found similarities between canine B-cell lymphoma and human diffuse large B-cell lymphoma.

overall_design: We isolated RNA from pre-treatment biopsies from dogs with B-cell lymphoma and performed gene expression profiling.

first: Steven

middle: E

last: Suter


title: Efficient immortalization of normal human mammary epithelial cells using two pathologically relevant agents does not require gross genomic alterations

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

overall_design: Refer to individual Series


title: MicroRNAs differentially expressed in MUC1 overexpressing cells

status: Public on Aug 10 2013

city: Omaha

first: Ashley

last: Mohr

state: NE

address: 985950 Nebraska Medical Center

institute: University of Nebraska Medical Center

summary:
To determine if overexpression of MUC1 alters the microRNA profile of pancreatic cancer cells S2.013.
Comparison of miRNAs differentially regulated in pancreatic cancer cell line S2.013 with and without MUC1 overexpression.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: MiRCURY LNA microarray was used to determine differential microRNA expression in one replicate of S2.013.Neo (control) cells compared to S2.013.MUC1 (experimental) cells.  Confirmation with qRT-PCR was performed on a subset of microRNAs identified as differentially regulated between the two groups.

first: Jennifer

last: Bailey

first: Michelle

last: Lewallen

first: Xiang

last: Liu

first: Prakash

last: Radhakrishnan

first: Fang

last: Yu

first: William

last: Tapprich

last: Hollingsworth


title: MicroRNA profiling of bleomycin-induced pulmonary fibrosis in mice

status: Public on Sep 01 2013

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

country: Canada

institute: McGill University

summary: Pulmonary fibrosis is a disease characterized by inflammatory cell infiltration, scar formation, deposition of extracellular matrix, alveolar epithelial cell injury and hyperplasia. To determine if alterations in microRNA expression contribute to these phenotypes, microRNA expression profiling of the lungs from bleomycin treated C57Bl/6J mice, relative to that of untreated controls, was undertaken.  Mice were treated at 8 weeks old with 100 Units/kg of bleomycin delivered subcutaneously with osmotic minipumps. At 42 days post treatment mice were euthanized and lung microRNA isolated. We identified 11 microRNA's to be significantly differentially expressed (FDR threshold of 0.01) in the lungs of bleomycin treated mice and confirmed these data with real time PCR measurements. These included bleomycin upregulated miR-34a, 335-5p, 207, 21, 301a, 146b, 199a-5p, and 449a and bleomycin downregulated miR-151-3p, 26a and 676. We have previously shown that 1558 genes are differentially expressed in the lungs of bleomycin treated mice. Of the 1412 targets of upregulated microRNAs, 142 were confirmed to be downregulated in the gene expression profile (GEP). Of the 583 targets of downregulated microRNAs, 53 were confirmed to be upregulated in the gene expression profile.  Pathway analysis of the microRNA targets and GEP overlapping genes indicated that altered microRNA expression is associated with cellular development, cellular growth, cellular proliferation and changed tissue/cell morphology. Specific pathways include HGF signaling, Cholecystokinin/Gastrin-mediated signaling, Endothelin-1 signaling, RAR activation, Phospholipase C signaling and IGF1 signaling. We conclude that altered microRNA expression is a feature of pulmonary fibrosis which putatively influences components of the altered airway disease.

overall_design: Two condition study, C57Bl/6J mice treated with 100 Units/kg bleomycin and untreated controls. Biological replicated n =3 for each group. Left lung tissue.

first: Lisa

last: Honeyman

first: Mark

last: Bazett

first: Tomasz

last: Tomko

middle: K


title: miRNA expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD) [Study2]

status: Public on Dec 04 2013

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: Using a PTSD mouse model, we investigated the longitudinal transcriptomic changes in heart tissues after the exposure to stress through intimidation

overall_design:
We designed our time-course study (Study II) with three experimental conditions where we varied the length of time that subservient mice were exposed to aggressor mice with the same length of rest time after the exposure (1day).  The conditions included were 1day-exposure (T1R1), 2day-exposure (T2R1) and 3day-exposure (T3R1).
We designed our initial study (Study I) with four experimental conditions where we varied the length of time that subservient mice were exposed to aggressor mice and the length of rest time after the exposure.  The conditions included were short exposure-short rest (T5R1-T indicates the number of days of trauma exposure; R indicates the number of days of rest after exposure), short exposure-long rest (T5R10), long exposure-short rest (T10R1) and long exposure-long rest (T10R42)

first: Kai

last: Wang

first: Inyoul

last: Lee

first: Rasha

last: Hammamieh

last: Baxter

first: Kelsey

last: Scherler

first: Alton

last: Etheridge

first: Yue

last: Yuan

first: Sara

last: McClarty

first: Alena

last: Kulchenko

first: Aarti

last: Gautam

first: Seid

last: Muhie

first: Nabarun

last: Chakraborty

first: Marti

last: Jett

middle: J

last: Galas

first: Leroy

last: Hood


title: All Differentially Expressed miRNA in burned murine skin tissue compared to normal skin tissue

status: Public on May 07 2013

city: shanghai

first: gan

last: wu

address: nm 928 wenxiang road

country: China

institute: yingbiotech

summary:
Interactions between stromal cell-derived factor-1α (SDF-1α) and its cognate receptor CXCR4 are crucial for the recruitment of mesenchymal stem cells (MSCs) from bone marrow (BM) reservoirs to damaged tissues for repair during alarm situations. MicroRNAs are differentially expressed in stem cell niches, suggesting a specialized role in stem cell regulation. Here, we gain insight into the molecular mechanisms involved in regulating SDF-1α.
Individualized outcome prediction classifiers were successfully constructed through expression profiling of microRNAs (in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk))in one burned murine skin tissue compared to normal skin tissue,which had 57 upregulated microRNAs and 28  down-regulated microRNAs

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 2  cases, was used to acquire expression profiles of microRNAs(in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk)), leading to the successful construction of supervised .

first: Mu

middle: H

last: Lv

first: Guang

last: Liang


title: miRNA profiling of celiac disease

status: Public on Apr 19 2013

city: milan

first: luca

last: elli

address: via f. sforza 35

institute: Fondazione IRCCS Ca' Granda

summary: microRNAs were profiled in healthy controls, classic celiac patients (CD), CD patients with anemia and GFD treated CD with normalization of duodenal mucosa

overall_design: all CD conditions were related to controls. For each group, five patients were pooled. One replicate per experiment

first: Luca

last: Elli


title: Differentially expressed miRNA in burned murine skin tissue compared to normal skin tissue

status: Public on May 02 2013

city: chongqing

first: li

middle: mu

last: han

address: gaotanyuan street

institute: Southwest Hospital, Third Military Medical University

summary:
Interactions between stromal cell-derived factor-1α (SDF-1α) and its cognate receptor CXCR4 are crucial for the recruitment of mesenchymal stem cells (MSCs) from bone marrow (BM) reservoirs to damaged tissues for repair during alarm situations. MicroRNAs are differentially expressed in stem cell niches, suggesting a specialized role in stem cell regulation. Here, we gain insight into the molecular mechanisms involved in regulating SDF-1α.
Individualized outcome prediction classifiers were successfully constructed through expression profiling of microRNAs (in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk))in one burned murine skin tissue compared to normal skin tissue,which had 57 upregulated microRNAs and 28  down-regulated microRNAs.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 2  cases, was used to acquire expression profiles of microRNAs (in all organisms as annotated in Sanger miRBase Release 11.0 (http://microrna.sanger.ac.uk)), leading to the successful construction of supervised. The most recent version of the array (v.11.0 - hsa, mmu & rno array) contains more than 1700 capture probes, covering all microRNAs annotated in miRBase 11.0, as well as all viral microRNAs, related to these species.

first: L

last: Chen


title: miRNA-720 controls stem cell phenotype, proliferation and differentiation of dental pulp cells

status: Public on May 17 2013

city: Okayama-shi

first: Emilio

middle: Satoshi

last: Hara

state: Okayama-ken

address: Shikata-cho 2-5-1

institute: Okayama University

summary: Dental pulp cells (DPCs) are known to be enriched in stem/progenitor cells but not well characterized yet. Small non-coding microRNAs (miRNAs) have been identified to control protein translation, mRNA stability and transcription, and have been reported to play important roles in stem cell biology, related to cell reprogramming, maintenance of stemness and regulation of cell differentiation. In order to characterize dental pulp stem/progenitor cells and its mechanism of differentiation, we herein sorted stem-cell-enriched side population (SP) cells from human DPCs and periodontal ligament cells (PDLCs), and performed a locked nucleic acid (LNA)-based miRNA array. As a result, miR-720 was highly expressed in the differentiated main population (MP) cells compared to that in SP cells. In silico analysis and a reporter assay showed that miR-720 targets the stem cell marker NANOG, indicating that miR-720 could promote differentiation of dental pulp stem/progenitor cells by repressing NANOG. Indeed, gain-and loss-of-function analyses showed that miR-720 controls NANOG transcript and protein levels. Moreover, transfection of miR-720 significantly decreased the number of cells positive for the early stem cell marker SSEA-4. Concomitantly, mRNA levels of DNA methyltransferases (DNMTs), which are known to play crucial factors during stem cell differentiation, were also increased by miR-720 through unknown mechanism. Finally, miR-720 decreased DPC proliferation as determined by immunocytochemical analysis against ki-67, and promoted odontogenic differentiation as demonstrated by alizarin red staining, as well as alkaline phosphatase and osteopontin mRNA levels. Our findings identify miR-720 as a novel miRNA regulating the differentiation of DPCs.

overall_design: Two cell types (dental pulp cells(DPCs), periodontal ligament cells(PDLCs)) were sorted by FACS to isolate side population (SP) and main population (MP) cells. Then a microRNA array was performed with the SP and MP cells of DPCs and PDLCs.

middle: S

first: Mitsuaki

last: Ono

first: Takanori

last: Eguchi

first: Satoshi

last: Kubota

first: Hai

middle: T

last: Pham

first: Wataru

last: Sonoyama

first: Shoji

last: Tajima

first: Masaharu

last: Takigawa

first: Stuart

last: Calderwood

first: Takuo

last: Kuboki


title: miRNA expression profile in PC12 cells under NGF treatment and deprivation

status: Public on May 11 2013

city: Roma

first: Sergio

last: Nasi

state: Italia

address: P.le A. Moro 5

department: IBPM - Sapienza Università di Roma

institute: CNR - Consiglio Nazionale delle Ricerche

summary: miRNA profiling of PC12 rat pheochromocytoma cells during NGF-induced differentiation and apoptosis of differentiated cells after 24h of NGF deprivation. miRNA expression in differentiating and deprivated cells was compared  to untreated and terminally differentiated PC12 cells respectivelly.

overall_design: Five-condition experiment, NGF-treated cells (1h, 3h, 6h, 24h, 240h) vs. untreated. One-condition experiment, NGF-deprivated vs. differentiated cells.

first: Enrica

last: Montalban

first: Marco

last: Scarnò

first: Mauro

last: Savino

first: Gianluca

last: Prosperini


title: 1,25-Dihydroxyvitamin D Promotes Negative Feedback Regulation of Toll-Like Receptor Signaling via Targeting MicroRNA-155-SOCS1 in Macrophages

status: Public on Jan 05 2013

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

summary: The negative feedback mechanism is essential to maintain effective immunity and tissue homeostasis. 1,25-dihydroxyvitamin D (1,25(OH)2D3) modulates innate immune response, but the mechanism remains poorly understood. Here we report that vitamin D receptor (VDR) signaling attenuates Toll-like receptor-mediated inflammation by enhancing the negative feedback inhibition. VDR inactivation leads to a hyperinflammatory response in mice and macrophage cultures when challenged with lipopolysaccharide (LPS) due to miR-155 overproduction that excessively suppresses SOCS1, a key regulator that enhances the negative feedback loop. Deletion of miR-155 attenuates vitamin D suppression of LPS-induced inflammation, confirming that 1,25(OH)2D3 stimulates SOCS1 by down-regulating miR-155. 1,25(OH)2D3 down-regulates bic transcription by inhibiting NF-kappaB activation, which is mediated by a kappaB cis-DNA element located within the first intron of the bic gene. Together these data identify a novel regulatory mechanism for vitamin D to control innate immunity.

overall_design: MicroRNA arrays. Total RNAs were extracted from RAW264.7 cells (mouse macrophage line) treated with LPS (100ng/ml) in the presence or absence of 1,25(OH)2D3 (20 nM) overnight. MicroRNA profiling was performed using the miRCURY LNA microRNA Arrays (Exiqon, Vedvaek,Denmark) according to the manufacture'¹s standard protocols. The arrays were scanned with the GenePix 4000B scanner using the manufacturer's recommended settings. The raw data was extracted using GenePix Pro and imported into GeneSpring GX10 for analyses.

first: Yunzi

first: Weicheng

last: Liu

first: Tao

last: Sun

first: Youli

last: Wang

first: Dilip

last: Deb

first: Dosuk

last: Yoon

first: Juan

last: Kong

first: Ravi

last: Thadhani

first: Yan

middle: C

last: Li


title: miRNA in mouse macrophages

status: Public on Apr 17 2013

city: Birmingham

first: Gang

state: Alabama

address: 901 19TH ST S

institute: University of Alabama at Birmingham

summary: By employing miRCURY LNA™ microRNA Array, we have identified a subset of 21 top miRNAs that are differentially expressed between GM-BMM and M-BMM cells

overall_design: To know the differential expression of miRNA in mouse GM-CSF-induced bone marrow-derived macrophages (GM-BMM) vs. M-CSF-induced BMM (M-BMM)


title: Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

status: Public on Mar 04 2013

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary:
******************************************************************

450k ARRAY EXPANDED ANNOTATION PLATFORM:
SEARCH GPL16304

******************************************************************
Background: Measurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potentially functional changes in various pathological conditions. Illumina Infinium is a relatively inexpensive and user-friendly DNAm microarray platform used by many researchers to measure DNAm on a large scale. However it has been suggested that a subset of probes may give rise to misleading results due to issues related to probe design. To facilitate biologically significant data interpretation, we set out to enhance probe annotation of the newest HumanMethylation450 BeadChip array (with >485,000 probes covering 99% of RefSeq genes).
Results: Annotation that was added or expanded on includes 1) SNPs documented in the probe target, 2) probe binding specificity, 3) CpG classification of target sites and 4) gene feature classification of target sites. Probes with documented SNPs within 10bp of the target site and especially those with documented SNPs at the target CpG, were associated with increased within-tissue variation in DNAm. An example of a probe with a SNP at the target CpG was used to demonstrate how sample genotype can confound the measurement of DNAm. 8.6% of probes were identified as non-specific, in other words, these probes map to multiple locations in silico. DNAm measured from these non-specific probes likely represents a combination of DNAm from multiple genomic sites. The expanded biological annotation demonstrated that based on DNAm, grouping probes by alternative CpG classes rather than UCSC islands provides a more distinctive classification system of CpG sites. Finally variable enrichment for tissue-specific differentially methylated probes was noted across CpG classes and gene feature groups, depending on the tissues that were compared.
Conclusion: Probes containing SNPs and non-specific probes may affect the assessment of DNAm using the 450k array. Additionally CpG enrichment classes and to a lesser extent gene feature groups were associated with distinct patterns of DNAm. Thus, we recommend that confounded probes be removed from analyses and that genomic trends be considered in analyses of the Illumina HumanMethylation450 BeadChip. DNAm arrays offer a powerful approach for which thoughtful use of probe content can be utilized to better understand the biological processes affected.

overall_design: Bisulfite converted DNA from 4 buccal, 4 blood and 4 chorionic villus samples was hybridized to the Illumina Infinium HumanMethylation450 BeadChip array.

first: E

last: Price

first: Allison

last: Cotton

first: Lucia

last: Lam

first: Pau

last: Farré

first: Eldon

last: Emberly

first: Carolyn

last: Brown

first: Michael

last: Kobor


title: Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers [Affymetrix]

status: Public on Mar 07 2013

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin regulators have become highly attractive targets for cancer therapy, yet many of these regulators are expressed in a broad range of healthy cells and contribute generally to gene expression.  An important conundrum has thus emerged: how can inhibition of a general regulator of gene expression produce selective effects at specific oncogenes? Here we investigate how inhibition of the transcriptional coactivator BRD4 (Bromodomain containing 4) leads to selective inhibition of disease-critical oncogenes in a highly malignant blood cancer, multiple myeloma (MM).  We found that BRD4 generally occupies the promoter elements of active genes together with the Mediator coactivator, but remarkably high levels of these two coactivator proteins were associated with a small set of exceptionally large enhancers.  These super-enhancers are associated with genes that feature prominently in MM biology, including the MYC oncogene. Treatment of MM tumor cells with the BET-bromodomain inhibitor JQ1 led to preferential loss of BRD4 at super-enhancers and consequent transcription elongation defects that preferentially impact genes with super-enhancers, including the c-MYC oncogene.  Super-enhancers were found at key oncogenic drivers in many other tumor cells.  Thus, super-enhancers can regulate oncogenic drivers in tumor cells, which in some cells can be preferentially disrupted by BRD4 inhibition, which in turn contributes to the selective transcriptional effects observed at these oncogenes. These observations have implications for the discovery of novel cancer therapeutics directed at components of super-enhancers in diverse tumor types.

overall_design: Gene expression profiling in multiple myeloma cells after BET-Bromodomain inhibition with JQ1

first: Jakob

last: Loven

first: Heather

last: Hoke

first: Charles

middle: Y

last: Lin


title: Zinc-dependent regulation of the adh1 antisense transcript in fission yeast

status: Public on Dec 12 2012

city: Columbus

first: Amanda

middle: Jane

last: Bird

state: OH

address: 1787 Neil Avenue

department: Human Nutrition and Molecular Genetics

institute: The Ohio State University

type: Expression profiling by genome tiling array

summary: In yeast, alcohol dehydrogenase I (Adh1) is an abundant zinc binding protein that is required for the conversion of acetaldehyde to ethanol. Through transcriptome profiling of the Schizosaccharomyces pombe genome, we identified a natural antisense transcript at the adh1 locus that is induced in response to zinc-limitation. This antisense transcript (adh1AS) shows a reciprocal expression pattern to that the adh1 mRNA partner. In this study we show that increased expression of the adh1AS transcript in zinc-limited cells is necessary for the repression of adh1 gene expression and that the increased level of the adh1AS transcript in zinc-limited cells is a result of two mechanisms. At the transcriptional level, the adh1AS transcript is expressed at a high level in zinc-limited cells. In addition to this transcriptional control, adh1AS transcripts preferentially accumulate in zinc-limited cells when the adh1AS transcript is expressed from a constitutive promoter. This secondary mechanism requires the simultaneous expression of adh1. Our studies reveal how multiple mechanisms can synergistically control the ratio of sense to antisense transcripts, and highlight a novel mechanism by which adh1 gene expression can be controlled by cellular zinc availability

overall_design: Sense and antisense expression of the S. pombe transcriptome was measured under zinc-limiting and zinc-replete conditions, using 3 replicates of each condition and an anti-RNA/DNA antibody labeling technique.

first: Kate

last: Ehrensberger

first: Carter

last: Mason

first: Mark

last: Corkins

first: Cole

last: Anderson

first: Natalie

last: Dutrow

first: Bradley

middle: R

last: Cairns

first: Brian

last: Dalley

first: Brett

last: Milash


title: Revisiting Global Gene Expression Analysis (Microarray)

status: Public on Oct 25 2012

summary: Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease and for many other purposes.  Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data.  We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.

overall_design: RNA was extracted from cells expressing low, moderate or high levels of c-Myc. A panel of synthetic RNA's was added to these populations, based on cell number. Total RNA was then extracted and processed on Affymetrix microarrays in biological duplicate.

first: David

last: Orlando

first: Alla

last: Sigova


title: MicroRNA expression profiling of highly purified CD4+ human T cell subsets

status: Public on Oct 16 2012

city: Bellinzona

first: Silvia

last: Monticelli

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

summary: The development and propagation of an adaptive immune response to an invading pathogen is a highly orchestrated process that involves the precise regulation of cytokine expression. Naïve CD4+ T lymphocytes give rise to T helper (Th) cell subsets with functions that are tailored to their respective roles in host defense. MicroRNAs are important regulators of most cellular processes, including many responses in the immune system. To identify novel microRNAs that might be important in human T helper cell differentiation to different subsets we purified T cell subsets from peripheral blood and performed microRNA arratys at Exiqon.

overall_design: Naïve, Th1, Th2, Th17 and Tregs were FACS-sorted ex-vivo from peripheral blood of 6-11 donors. Due to the very low amount of starting material total RNA from at least 6 different donors was pooled and anlaysed on the arrays. All samples were analyzed against a common reference, which was made by pooling together a small amount of total CD4+ cells from all donors.

first: Christina

last: Zielinski


title: microRNA expression profile of dermal MSCs derived from psoriasis patients and normal control

status: Public on Nov 30 2012

city: Taiyuan

first: Ruixia

last: Hou

state: Shanxi

address: 1,Dong San Dao Xiang, Jiefang Road

department: Dermatology

institute: Taiyuan City Central Hospital

summary: Several studies have suggested that MSCs have pleiotropic immuno-modulatory effects,  including inhibition of T cell proliferation, suppression of NK cells proliferation, modulation of cytokine production, and inhibition of dendritic cell (DC) maturation etc. But the exactly mechanism are still largely unclear. We proposed to investigate the microRNA expression profile of psoriatic MSCs.

overall_design: 6 patients and 6 normal control were inrolled in the study, the microRNA expression profile of dermal MSCs were studied using the microarry.

first: Kaiming

last: Zhang


title: miRNA profile of rat vascular smooth muscle cell stimulated by 2.6 mM high-phosphate

status: Public on Jul 28 2012

city: Beijing

first: Wei

last: Kong

address: 38#, Xueyuan Street, Haidian district

department: Department of Physiology and Pathophysiology

institute: Peking University Health Science Center

summary: We compared time-series miRNA expression profile in high-phosphate–stimulated rat vascular smooth muscle cells at 0, 3, and 12 hr respectively.

overall_design: Total RNA of rat VSMCs stimulated with 2.6 mM inorganic phosphate for 0, 3 or 12 hr was harvested by the Trizol method (Invitrogen) or use of the miRNeasy mini kit (QIAGEN). The samples were labeled by use of the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.16.0) (Exiqon, Denmark). After washing slides were scanned by use of the Axon GenePix 4000B microarray scanner. Expressed data were normalized by the Median normalization method, and then relative fold change at each time was detected by level of fluorescence in the phosphate-treated group normalized to that in the control group. Finally, hierarchical clustering was performed for miRNA expression profiling. Student t test was used to compare differences between 2 groups, and a 1.5-fold change was considered significant.

first: Yaoyao

last: Du


title: miRNA profiling in HIV-1 latently infected cells

status: Public on Dec 01 2012

city: Hangzhou

first: Jin

last: Yang

address: Qingchun Road 79

institute: Zhejiang University

summary: Herein expression trends of host miRNA were measured in HIV-1 latently infected and persistent replication cells, as well as the control cells. HIV-1 latency infection was established by infecting CEM-SS lymphocytes with HIV-1 Bru strain. After selection and long-term culture, the chronically infected cell showed the characteristics of latency definition: 1. The provirus was intergrated in to the host genome.2. No viral expression could be detected during culture.3 .Cell stimulators, such as TNFa,PMA, etc, reactivate the viral expression. As expected, miRNA trend was different in HIV-1 latency when compared to the control or HIV-1 replication. A subset of miRNAs is enriched in HIV-1 latency model. The observation reinforces the concept of active HIV-1 interplay with host small RNAs that modulate HIV-1 infection mode.

overall_design: In this study, the in vitro steady cell culture was used to explore the miRNA transcription signatures in HIV-1 infection. miRNA profiles were performed and compared among normal control,HIV-1 latency and HIV-1 replication .

first: Juan

last: Wang

first: Zongxing

first: Linfang

last: Cheng

first: Nanping

last: Wu


title: Alteration of MicroRNA Expression Profile Linked to Microcystin-LR-Induced Tumorigenicity in Human WRL-68 Cell Line

status: Public on Jul 31 2012

city: Nanjing

first: Lizhi

last: Xu

state: Jiangsu

address: 22 Hankou Road

department: School of Medicine

institute: Nanjing University

summary: We report microcystin-LR, a cyclic heptapeptide that acts as a potent hepatotoxin and carcinogen, was used to induce the malignant transformation of the WRL-68 cell line and alterations in microRNA (miRNA) expression in the transformed cells.

overall_design: In this work, MC-LR was used to induce the malignant transformation of the WRL-68 cell line and alterations in microRNA (miRNA) expression in the transformed cells.

first: Yaping


title: A mutation in the Srrm4 gene causes pre-mRNA splicing defects and deafness in Bronx waltzer mice.

status: Public on Oct 21 2012

city: Coralville

first: Botond

last: Banfi

state: Iowa

address: 2501 Crosspark Road

department: Anatomy and Cell Biology

institute: University of Iowa

summary:
The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY).
In this dataset, we include probe-set level data obtained from cerebellar samples. The processed data represent probe-set intensities that have been normalized to gene expression levels.

overall_design: 8 total samples were analyzed in this series: cerebellums from 4 heterozygous (bv/+) and 4 homozygous (bv/bv) mice at P15.

first: Yoko

last: Nakano


title: MJAY analysis of vestibular macula RNA obtained from Bronx waltzer and control mice.

summary:
The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY).
In this dataset, we include probe-set level data obtained from vestibular macula samples. The processed data represent probe-set intensities that have been normalized to gene expression levels (Inorm). Inorm was calculated using batch-corrected data as well as data that were not corrected for a batch effect.

overall_design: 7 total samples were analyzed: vestibular maculas from 4 heterozygous (bv/+) and 3 homozygous (bv/bv) mouse embryos at E16.5.


title: A mutation in the Srrm4 gene causes alternative splicing defects and deafness in Bronx waltzer mice.

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

overall_design: Refer to individual Series


title: Murine small intestinal crypt cell line IEC-6: control vs. TGF-beta stimulated

status: Public on Jun 19 2012

city: Davis

first: Bo

last: Lonnerdal

state: CA

address: 1 Shields Ave.

department: Nutrition

institute: University of California, Davis

summary: microRNA profiling of rat small intestinal crypt cell IEC-6. Comparing control untreated with cells treated with transforming growth factor-beta (TGF-beta). TGF-beta stimulated cell differentiation, as observed in the stimulation of intestinal epithelial cell markers (alkaline phophotase, villin, aminopeptidase N, etc.).

overall_design: Two condition experiment. Control vs TGF-beta treatment. Biological replicates: 3 control, 3 treated. Independently grown and harvested. One replicate per array

first: Yalin

last: Liao

last: Lönnerdal


title: miRNA profiles in head and neck natural epithelial - mesenchymal phenotype cell line pair,  and in TGF-β induced EMT models

status: Public on Jun 05 2012

city: Shanghai

first: zhiyuan

last: zhang

address: 639 zhizaoju Road

institute: Shanghai Jiaotong University

summary: Sixth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to search and validate some unidentified miRNAs that regulate EMT in head and neck cancer carcinoma.

overall_design: MiRNA array screening was performed to identify the differential expression of miRNAs involved in EMT in natural epithelial - mesenchymal phenotype cell line pair（HN-4, HN-12) and in TGF-β induced EMT models (HN-4 TGF-β,HN-4). HN-4 parental cell was served as the control.One µg total RNA from sample and control was labeled with Hy5™ and Hy3™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.


title: wqq_MDSC_miRNA Array

status: Public on Mar 20 2012

first: Yang

last: Liu

state: Zhejiang

address: 388 Yu Hang Tang Road

department: Institute of Immunology

institute: Zhejiang University School of Medicine

summary: Myeloid-derived suppressor cells (MDSCs) potently suppress the anti-tumor immune responses and also orchestrate the tumor microenvironment that favors tumor angiogenesis and metastasis. The immunosuppressive activity of MDSCs has been extensively investigated, however the molecular networks regulating the non-immunological functions of tumor-expanded MDSCs, are largely unknown. In this study, we identified microRNA-494 (miR-494), whose expression was dramatically induced by tumor-derived factors (TDFs), as an essential player, in regulating the non-immunological activity of MDSCs by targeting PTEN and activating the Akt pathway. TGF-beta 1 was found to be a main tumor-derived factor responsible for the up-regulation of miR-494 in MDSCs. Expression of miR-494 not only enhanced CXCR4-mediated MDSC chemotaxis but also altered the intrinsic apoptotic/survival signal by targeting PTEN, thus contributing to the accumulation of MDSCs in tumor tissues. Consequently, down-regulation of PTEN resulted in increased activity of the Akt pathway and the subsequent up-regulation of matrix metalloproteinases (MMPs) for facilitating tumor cell invasion and metastasis. Knock down of miR-494 significantly reversed the activity of MDSCs and inhibited the tumor growth and metastasis of 4T1 murine breast cancer in vivo. Collectively, our findings reveal that TGF-beta 1-induced miR-494 expression in MDSCs plays a critical role in the molecular events governing the accumulation and non-immunological functions of tumor-expanded MDSCs, and might be identified as a potential target in cancer therapy.

overall_design: BALB/c mice (female, 6- to 8-wk-old) were injected subcutaneously in  the mammary fat pad with 100,000 4T1 tumor cells. Three weeks later, tumor-bearing animals were used for the indicated studies. Gr-1+ CD11b+ cells were isolated by immunomagnetic selection from the bone marrow of 4T1 tumor-bearing mice (n=3) and tumor-free BALB/c mice (n=3), then the miRNA expression profile were analyzed using miRCURY LNA™ microRNA Arrays.

first: QingQing


title: MicroRNA expression in neonatal and adult rat cardiomyocytes

status: Public on Oct 13 2012

city: Trieste

first: Miguel

last: Mano

address: Padriciano 99

institute: International Centre for Genetic Engineering and Biotechnology - ICGEB

summary: Expression profiles of microRNAs in neonatal (isolated from day0 newborn rats) and adult rat cardiomyocytes (isolated from 2month old rats)

overall_design: Two condition experiment; Biological replicates: 7 samples of cardiomyocytes from neonatal rats (from independent isolations); 6 samples of cardiomyocytes isolated from adult animals (from independent isolations)

first: Ana

last: Eulalio

first: Matteo

last: Dal Ferro

first: Lorena

last: Zentilin

first: Giafranco

last: Sinagra

first: Serena

last: Zacchigna

first: Mauro

last: Giacca


title: Chromosome interaction copy number analysis of mouse neonatal liver cells, and undifferentiated and differentiated embryonic stem cells using circular chromosome conformation capture (4C) assays

status: Public on Mar 28 2012

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

type: Genome variation profiling by genome tiling array

summary:
Using Circular chromosome conformation capture (4C) assay to uncovers epigenetically regulated intra- and inter-chromosomal interaction network
To examine restrictions imposed by the nuclear structure on such cis/trans-chromosomal networks, we developed a high-throughput screening assay 4C and identified 114 different sequences from all autosomes in mouse liver cells. To check the relative frequencies of interactions, the 114 sequences were PCR amplified and spotted on glass to make dedicated microarray. The microarray and 3C validation showed that most of the sequences interact with primarily the maternally inherited H19 imprinting control region (ICR). The epigenetic feature of these interactions was highlighted by the observation that 19% of 4C library sequences are derived from 11 different imprinted domains. In some of these instances, differentially methylated regions (DMRs) interact both in cis and in trans. Moreover, the patterns of chromosomal interactions undergo reprogramming during in vitro maturation of embryonic stem cells. We propose that the nuclear organization of mammalian cells displays considerable plasticity to potentially throw new light on development, cancer epigenetics and evolution of imprinting.  Keywords: Chromosome conformation capture, CTCF, ICR(Imprinting Control Region)

overall_design: 4C Assay on MBoI, MSeI, PM-Liv and MM-Liv

first: Zhihu

last: Zhao

first: Alejandro

middle: F

last: Woodbridge


title: Effect of costimulation on microRNAs levels in human naïve CD4 T cells

status: Public on Feb 25 2012

city: San Francisco

first: Dimitri

last: de Kouchkovsky

address: 513 Parnassus Ave HSW 1102 Box 0540

department: Diabetes Center

institute: UCSF

summary: microRNA transcriptional profiling of human naïve CD4 T cells comparing cells that saw no activation, only anti-CD3 or anti-CD3 and anti-CD28 to identify microRNAs specifically upregulated by CD28-mediated costimulation.

overall_design: Three conditions experiment. PBS, anti-CD3, anti-CD3 + anti-CD28 all compared to a reference sample. Biological triplicates, independently extracted and activated.

first: Jonathan

last: Esensten

first: Lukas

last: Jeker

first: Jeffrey

last: Bluestone


title: Notch regulated miRNAs in human T-ALL cell line

status: Public on May 23 2012

first: Andrew

middle: P

last: Weng

address: 675 West 10th Ave

department: Pathology

institute: BC Cancer Agency

summary: In an attempt to identify miRNAs regulated by oncogenic Notch signaling, we performed miRNA profiling of human T-cell acute lymphoblastic leukemia (T-ALL) cells with or without the treatment of γ-secretase inhibitor (GSI) to block Notch signaling. We found miR-223 levels to increase after GSI treatment suggesting that active Notch signaling represses miR-223 expression. We confirmed insulin-like growth factor-1 receptor (IGF1R) to be regulated by miR-223, but were unable to demonstrate functional effects on T-ALL cell growth by overexpression or knock-down of miR-223 alone.

overall_design: 4 samples analyzed, 2 cell lines each treated (GSI) and mock treated

first: Sam

middle: D

last: Gusscott


title: Aberrant DNA methylation of miRNA genes in breast cancer

status: Public on May 26 2012

city: Tucson

last: Vrba

state: AZ

address: 1515 N Campbell Ave

institute: University of Arizona

summary: Aberrant DNA methylation is frequently observed in cancer. The aim of the study was to determine how is DNA methylation of miRNA genes changed in breast cancer cell lines an breast tumor specimens.

overall_design: Breast cancer cell lines vs. HMEC.  Breast tumor tissue specimens vs. non-tumor tissue specimens. Biological replicates: 12 breast tumor specimens, 5 breast non-tumor specimens, 7 breast cancer cell lines, 3 HMEC genotypes, 3 HMF genotypes. Immunoprecipitation using anti-Methylcytosine (5MeC) antibody.

first: Jose

middle: L

last: Munoz-Rodriguez

first: Martha

last: Stampfer

first: Bernard

middle: W

last: Futscher


title: Epstein-Barr Virus (EBV)-positive B-cell strain, 28-2: Low v. High latent membrane protein 1 (LMP1)-mRFP expression (miRNA)

status: Public on Feb 01 2012

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

summary: Expression of miRNAs in an EBV-positive B-cell strain, 28-2.  28-2 are infected with a derivative of the B-958 strain of EBV, which expresses eGFP constitutively and LMP1 fused to mRFP from its native promoter.  Single cells were sorted by flow cytometry for their levels of LMP1-mRFP (5% expressing the lowest levels of LMP1-mRFP or 5% expressing the highest levels of LMP1-mRFP)

overall_design: Two-condition experiment: Low v. High LMP1-mRFP expression.  Biological replicates: 3 Low LMP1-mRFP, 3 High LMP1-mRFP.  Samples were normalized to the expression of miRNAs in a pool of unsorted 28-2 cells.

first: Bill

last: Sugden


title: Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka)

status: Public on May 31 2012

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

summary: We collected sockeye salmon from the Fraser River, British Columbia, and held them at ecologically relevant temperatures (14C and 19C) determine the effect of elevated water temperature on cellular processes in non-lethally sampled gill tissue and blood plasma over a period of seven days that represents a significant portion of their upstream migration. Time-matched fish that died prematurely over the course of the holding study were also sampled for gill tissue and the transcriptomic responses in moribund fish were compared with surviving fish. This is the first study to experimentally examine transcriptomic responses to high water temperature and premature mortality in wild-caught Pacific salmon and the results will help in understanding some of the cellular mechanisms involved in large-scale migration mortality in Pacific salmon during warm water periods and for predicting or understanding causes of mortality in naturally senescing adult Pacific salmon.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Forty samples were analyzed on forty two-channel microarrays, using a common reference design, with multiple biological replicates for each temperature condition. Fish were further classified into survivor and moribund based on their status after 7 days in captivity.


title: Murine colon: IL-10-/- versus BALB/c

status: Public on Jan 01 2012

city: Houston

first: Jeremy

last: Schaefer

state: TX

address: 1941 East Rd

department: Diagnostic Sciences

institute: The University of Texas Health Science Center at Houston School of Dentistry

summary: MicroRNA profiling of mouse colonic tissue comparing severe colon pathology with mild and no pathology.

overall_design: Three condition experiment: BALB/c (No Pathology Control), IL-10-/- with Pathology = 1, IL-10-/- with Pathology > 3.  Biological replicates were pooled RNA samples of 3 separate mice per condition.

first: John

last: Klein


title: Regulation of miRNA biogenesis by MCPIP1

status: Public on Nov 05 2011

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: Effect of MCPIP1 knockdown on miRNA expression profile.

overall_design: HepG2 cells were transfected with control siRNA or siRNA against MCPIP1, and subjected to miRNA microarray analysis.

middle: I


title: CD36-DEFICIENT CONGENIC STRAINS SHOW IMPROVED GLUCOSE TOLERANCE AND DISTINCT SHIFTS IN METABOLIC AND TRANSCRIPTOMIC PROFILES

city: Prague

first: Ondrej

last: Seda

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University in Prague

summary: Deficiency of fatty acid translocase Cd36 has been shown to play major role in pathogenesis of metabolic syndrome components in the spontaneously hypertensive rat (SHR). We have tested the hypothesis that effects of Cd36 mutation on features of metabolic syndrome are contextually-dependent on genomic background. We have derived two new congenic strains by introgression of limited chromosome 4 regions of SHR origin, both including defective Cd36 gene, into genetic background of highly inbred model of insulin resistance and dyslipidemia, polydactylous (PD) rat strain. We have subjected standard diet-fed adult males of PD and the 2 congenic PD.SHR4 strains to metabolic, morphometric and transcriptomic (Affymetrix Rat 1.0 ST Exon array) profiling. We observed significantly improved glucose tolerance and lower fasting insulin in PD.SHR4 congenics than in PD. One of the PD.SHR4 strains also showed lower triglyceride concentrations across major lipoprotein fractions combined with higher concentrations of LDL cholesterol compared to PD progenitor. The other PD.SHR4 strain had lower total and HDL cholesterol as well as lower LDL and HDL triacylglycerol content compared to PD. The hepatic transcriptome assessment revealed network of genes differentially expressed between PD and PD.SHR4 with significant enrichment by members of circadian rhythmicity pathway (Arntl (Bmal1), Clock, Nfil3, Per2 and Per3). In summary, the introduction of chromosome .4 region of SHR origin including defective Cd36 into PD genetic background resulted in disconnected shifts of metabolic profile along with distinct changes in hepatic transcriptome. The synthesis of the current results with those obtained in other Cd36-deficient strains indicate that the eventual metabolic effect of deleterious mutation such as that of SHR-derived Cd36 is not absolute, but rather a function of complex interactions between environment and genomic background, upon which it operates.

overall_design: Affymetrix GeneChip® Rat Exon 1.0 ST Array was used to determine the transcriptomic characteristics of the PD.SHR4a and the progenitor PD strain. We extracted total RNA from the liver of 4-month-old males of both strains (n=8/per strain) using phenol-chloroform and purified with the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol. The quality of the total RNA was verified by the Agilent 2100 Bioanalyzer system. Double-stranded complementary DNA (cDNA) was synthesized from total RNA. The labeled and fragmented cDNA was pooled for each strain and hybridized to Affymetrix GeneChip® Rat Exon 1.0 ST Arrays (PD.SHR4a - 2 chips; PD - 3 chips). The whole hybridization procedure including DNA adjustment was performed according to the protocol recommended by Affymetrix.

first: Lucie

last: Sedova

first: Frantisek

last: Liska

first: Drahomira

last: Krenova

first: Ludmila

last: Kazdova

first: Johanne

last: Tremblay

first: Michaela

last: Krupkova

first: Gilles

last: Corbeil

first: Pavel

last: Hamet

first: Vladimir

last: Kren


title: Integration of BRCA1-mediated miRNA and mRNA signatures reveal miR-146a, miR-99b and miR-205 regulation of the TRAF2 and NFkB pathways (miRNA dataset)

status: Public on Dec 24 2011

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Microarray‐based techniques are being used to obtain miRNA and gene expression signatures associated with different samples. In order to deepen our understanding of BRCA1-associated tumorigenesis, we integrated data from microarray experiments to obtain significant miRNA-mRNA relationships associated with the presence of the BRCA1 gene. We obtained significant miRNA-gene-pathway relationships underlying the array signatures. Furthermore, we have demonstrated that miR-146a, miR-99b and miR-205, induced in HCC1937 BRCA1-expressing cells, commonly regulate the TRAF2 gene, a key regulator of NF-κB and MAPK pathways. In addition, re-expression of miR-146a, miR-99b or miR-205 in HCC1937 BRCA1-null cells was sufficient to modulate NF-κB activity. Thus, integration between miRNA-mRNA expression data allowed us to define genes and pathways controlled by miRNAs induced in the context of BRCA1 expression.

overall_design: Comparison of miRNA expression profiles between two isogenic cell lines differing in BRCA1 gene expression status. Single-color experiments in a pairwise comparison design with three technical replicates per cell line.

first: Miljana

last: Tanic

first: Magdalena

last: Zajac

first: Gonzalo

last: Gomez-Lopez

first: Javier

last: Benitez


title: MicroRNA signatures in human cervical cancer

status: Public on Oct 11 2011

city: guangzhou

first: yao

middle: ting

last: ting

address: 107 Riverside Road

institute: SUN YAT-SEN  MEMORIAL,HOSPITAL,SUN YAT-SEN UNIVERSITY

summary: Our study investigates miRNAs might play a role in the pathogenesis of cervical cancer and identify altered miRNA gene methylation as a possible epigenetic mechanism involved in their aberrant expression.

overall_design: Cervical cancer cells were seeded at low density and cultured for 48 h. Experimental groups were treatment with 10 Amol/L 5-aza-2'-deoxycytidine (5-AZA;Sigma). After 24 hours, cells were collected and total RNA was isolated using Trizol reagent. The miRNA expression was then evaluated by microarray profiling and differentially expressed miRNAs were identified by univariate two-class t test with random variance mode.

first: Tingting

last: Yao

first: Qing

last: Chen

first: Longyang

last: Liu

first: Zhongqiu

last: Lin


title: Genome wide transcriptional profiling of BEAF-32 in wing imaginal tissues of wildtype and mutants [expresion array]

status: Public on Jul 06 2012

city: Atlanta

first: Gurudatta

last: Baraka Vishwanathan

state: GA

address: 1510 clifton road ne

department: Biology Department

institute: Emory University

summary:
The mutants in BEAF-32 gene in Drosophila caused the Neoplastic growth.
In order to understand the rold of BEAF-32 insulator function in  regualtion of gene expression we used the imagial tissue as a model to assay the transcriptional changes. The Imagianl tissues were disected in the icecold PBS and Total RNA was prepared using RNaeasy ( qiagen ) kit. This is followed by cDNA synthesis using Oligo dT.
Transcriptional changes assayed with two biological replicates and two experimental replicates

overall_design: Two biologial replicates and two experimental replicates were prepared in an independent experiments. Each cDNA samples were labeled with Cy3 due and hybridised and scaned as per manufactures instructions at Florida state university Nimblegen fecility.

first: Victor

last: Corces

middle: B

last: Vishwanathan

first: Edward

last: Ramos


title: Platelet microRNA-mRNA Co-Expression Profiles Correlate with Platelet Reactivity

status: Public on Sep 27 2011

city: Philadelphia

first: Leonard

middle: C.

last: Edelstein

state: PA

address: 1015 Walnut St.

department: Medicine/Hematology

institute: Thomas Jefferson University

summary: MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored.  We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects.  We found that human platelets express 284 miRNAs.  Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes.  Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response.  Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated.  Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA.  Reduced activation from platelets lacking PRKAR2B supported these findings.  In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.

overall_design:
Total RNA from the platelets of 19 donors was harvested and labeled with Hy3. Reference RNA (a pool of all samples) was labeled with Hy5.

This submission represents the miRNA expression component of the study.

first: Srikanth

last: Nagalla

first: Chad

last: Shaw

first: Altaf

middle: A

last: Kondkar

first: Xianguo

last: Kong

first: M

first: Junmei

first: Stanley

last: McKnight

first: Jose

last: Lopez

first: Linghai

last: Yang

first: Ying

last: Jin

first: Molly

last: Bray

first: Suzanne

middle: M

last: Leal

first: Jing-fei

last: Dong

first: Paul


title: MicroRNAs differentially expressed in liposarcoma

status: Public on Mar 22 2012

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We performed expression profiling of microRNAs comparing liposarcomas (n=17) with normal fat pad (n=8). We found 35 miRNAs differentially expression (P<0.0001, fold>1.5), including mir-155.

overall_design: We performed expression profiling of microRNAs comparing liposarcomas with normal fat pad.

first: Dina

last: Lev

first: Pingyu

last: Zhang


title: MicroRNA implication in murine liver regeneration

status: Public on Jan 18 2012

city: Nicosia

first: Apostolos

last: Zaravinos

state: Nicosia

address: Kallipoleos 75

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

summary: Liver is uniquely capable to repair itself after injury. Multiple molecular and biochemical processes initiated after partial hepatectomy, lead to proliferation of all cells within the liver. MicroRNAs (miRNAs) are a class of highly abundant non-coding RNA molecules that cause post-transcriptional gene repression and are involved in several biological processes including cell cycle regulation and differentiation. We examined the expression levels of miRNAs in liver tissue received from control mice (L0) and compared them with the corresponding levels in liver tissue 12 hours after liver regeneration induced by 2/3 partial hepatectomy (L12). MicroRNA expression was investigated using microRNA profiling. Further qPCR analysis was used for validation of the differentially expressed microRNAs at an early stage of liver regeneration, induced by 2/3 partial hepatectomy. TargetScan and Gene Ontology (GO) analysis was performed in order to identify the possible miRNA target genes and their ontology, respectively. A subset of miRNAs were found to be differentially expressed during liver regeneration. Mmu-miR-21 and mmu-miR-30b* showed the higher levels of up-regulation in liver tissue from the hepatectomized mice at the end of the experiment (L12) compared to the sham operated mice (L0). Mmu-miR-21 up-regulation was further confirmed by qPCR. In situ hybridization (ISH) revealed that mmu-miR-21 exhibited the higher levels of expression at 12 hours post hepatectomy. On the contrary, mmu-miR-34c*, mmu-miR-144, mmu-miR-207, mmu-miR-207, mmu-miR-451, mmu-miR-582-3p and mmu-miR-290-5p exhibited <0.5 down-regulation in liver tissue after partial hepatectomy in L12 vs. L0 mice. Microarrays and qPCR results were in good agreement (Pearson correlation = 0.881). Our results provide important information regarding how microRNAs are deferentially expressed in murine liver tissue before and after partial hepatectomy. The early up-regulation of mmu-miR-21 during the process of liver regeneration suggests a regulatory role in liver regeneration in vivo.

overall_design: Twenty male wild type mice C57BL6J (8 weeks old) fed a standard diet were used for the liver regeneration experiment. Mice were housed in the animal facility of the University of Patras Medical School in temperature-, light- and humidity-controlled rooms with a 12-h light/dark cycle. All animal procedures were approved by the institutional review board of the University of Patras Medical School and were in accordance with EC Directive 86/609/EEC. A 2/3 partial hepatectomy (PH) was performed on 10 mice according to a recently published standardized protocol whereby the median and left lobes of the liver were removed and another 10 sham operated mice were used as the control group. The liver was allowed to regenerate and mice were sacrificed 12 hours after operation. Liver samples were collected from the sham operated mice (L0) and the hepatectomized mice at the end of the experiment (L12).

first: Ioannis

middle: G

last: Habeos


title: The effects of YB1 knockdown on global gene expression in tumour cell lines.

status: Public on Nov 30 2011

city: Sydney

first: Hamish

last: Campbell

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

summary: Y-box binding factor 1 (YB1) has been associated with prognosis in many tumor types. Reduction of YB-1 inhibits tumor cell growth in vitro and in vivo

overall_design: Total RNA was isolated from A549, MCF7 and HCT116 tumor cell lines following 48hr treatment with 5nM Yb1 siRNA

first: H

first: Annette

last: Lasham

first: Weini

last: Samuel

first: Helen

last: Cao

first: Rachna

last: Patel

first: Reena

last: Mehta

first: J

last: Stern

first: Glen

last: Reid

first: Adele

last: Woolley

first: Lance

last: Miller

first: Michael

last: Black

first: Andrew

middle: N

last: Shelling

first: Cristin

last: Print

first: Antony

last: Braithwaite


title: Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections

status: Public on Sep 08 2011

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: Sixth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to profile in duplicate the expression of microRNAs in 250 or 400 ng of RNA isolated from a laser microdissectate of a formalin-fixed and paraffin-embedded human non-small cell lung cancer tumor.

overall_design:
Laser microdissection was performed on a hematoxylin-eosin-stained, 8 um-thick section of formalin-fixed and paraffin-embedded tissue. The microdissectate was treated with proteinase K overnight at 55 ºC. Total RNA from the lysate was then extracted using FFPE RNA Isolation Kit from Norgen Biotek® (Thorold, Canada). RiboGreen assay was used to quantify RNA in the preparation. Two-hundred-fifty or 400 ng of RNA was used in duplicate for dual-channel microarray-based microRNA expression profiling.
Sample RNA was labeled with the Cy3-like Hy3™ dye, mixed with a human universal reference RNA (product number AM6000, Ambion®, Austin, TX) labeled with the Cy5-like Hy5™ dye, and hybridized to the two-color miRCURY™ arrays.

middle: K

first: Eric

last: Kannisto

first: Sai

last: Yendamuri


title: Pancreatic cancer vs. paired normal control

status: Public on Apr 27 2011

first: Wenzhang

last: Wang

address: Handan Road 220#

institute: Fudan University

summary: The miRNA expression between normal and cancerous pancreatic tissues and identified preferentially expressed miRNAs.

overall_design: Two-condition experiment, pancreatic cancer vs. paired normal control. Biological replicates: 3 paired patients tissues.

first: Shuyu

last: Zhang

first: Chenghao

last: Shao


title: Differential expression of microRNA expression in tamoxifen-sensitive MCF-7 versus tamoxifen-resistant LY2 human breast cancer cells

status: Public on Mar 30 2011

city: Louisville

first: Carolyn

last: Klinge

state: KY

address: 580 S Preston St

department: Biochemistry & Molecular Biology

institute: University of Louisville School of Medicine

summary:
Introduction: Although changes in microRNA (miRNA) expression correlate with breast cancer diagnostic markers, comparatively little is known about miRNA regulation by selective estrogen receptor modulators (SERMs), e.g., tamoxifen (TAM), or their role in endocrine-resistance.
Methods: A microarray approach was used to identify miRNAs differentially expressed and regulated by 4-hydroxyTAM (4-OHT) in MCF-7/TAM-sensitive versus LY2 TAM/endocrine-resistant human breast cancer cells after 6 h treatment.  The expression of specific miRNAs was validated by quantitative, real-time PCR.  Control miRNAs and time-course studies showed important gene-, time-, and cell- specific differences in miRNA expression.
Results: 97 miRNAs were differentially expressed in MCF-7 versus LY2 cells.  Bioinformatic analyses to impute the biological significance of these miRNAs by identifying 36 predicted gene targets of these miRNAs from amongst those reported to be regulated by MCF-7 cells was performed and agreement was found in direction of anticipated regulation for 12 of those putative targets.  Among the miRNAs differentially expressed in MCF-7 versus LY2 cells, and that putatively target mRNAs regulated by 4-OHT in MCF-7 cells, are: miRs- 10a, 21, 22, 29a, 93, 125b, 181, 200a, 200b, 200c; 205, 221, and 222.  Q-PCR assessment showed agreement with microarray data: miR- 10a, 22, 125b, 181, and 222 are higher in LY2 whereas miR-21 and miR-200a are lower in LY2 than MCF-7.  4-OHT increased miR-10a, miR-21, miR-22, miR-125b, miR-181a, miR-200a, and miR-222 in MCF-7 cells and reduced miR-10a in LY2 cells.  E2 reduced the miR-21expression in MCF-7 cells.  Treatment with ICI 182,780 revealed that ER suppresses miR-10a, miR-21, miR-22, miR-200a, miR-221, and miR-222 expression in MCF-7 cells.  Time-dependent changes in select miRNA expression were observed in control, E2, and 4-OHT-treated MCF-7 cells.  ESR1/ERα was significantly lower in LY2 than MCF-7, commensurate with higher let-7 family member, miR-221, and miR-222 expression in LY2.   Reflecting inverse association with miR-200 family expression, the expression of ZEB1 was higher in LY2 than MCF-7 cells and concomitantly, E-cadherin expression was absent in LY2 cells indicating that LY2 have undergone epithelial to mesenchymal transition.
Conclusions: Our studies identifying miRNAs with opposite expression between the two cell lines, indicate the involvement of these miRNAs in endocrine resistance.

overall_design:
The purpose of this experiment is:
1. To identify miRNAs that are regulated (up or down) by 4-OHT in MCF-7 and LY2 cell lines (comparison of values from EtOH versus 4-OHT treated cells).
2. To identify miRNAs that are differentially regulated under basal (EtOH) conditions between MCF-7 and LY2 cell lines.
3. To identify miRNAs that are differentially regulated by 4-OHT in MCF-7 versus LY2 cells.

first: Tissa

middle: T

last: Manavalan

first: Yun

last: Teng

first: Savitri

last: Appana

first: Susmita

last: Datta

first: Theodore

middle: S

last: Kalbfleisch

first: Yong

last: Li


title: microRNA profiling in Mouse Eye: Retina, Lens, Cornea, Retinal Pigment Epithelium

status: Public on Nov 22 2010

city: Naples

first: Marianthi

last: Karali

address: Via Pietro Castellino, 111

institute: Telethon Institute for Genetics & Medicine (TIGEM)

summary: MicroRNA expression in the mouse eye.MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.  In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina .  This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.

overall_design: microRNA profiling of ocular tissues from mouse. In particular we analysed the cornea, lens, Retina Pigment Epithelium (RPE) and retina and compared them against RNA extracted from the entire eye. The purpose of this experiment was to understand which microRNAs are present nd/or show differential expression in the various structures of the eye (cornea, lens, RPE, retina). The samples numbered 1 & 2 (i.e. CORNEA1, CORNEA2 etc ) are biological replicates, prepared from tissues dissecyed from different groups of wild-type animals. RNA extracted from the entire eye (EYE) served as the unique reference sample. For each tissue to be analysed we performed the following hybridizations:  - 2 slides for lens (LENS1, LENS2) vs entire eye (EYE)  - 2 slides for RPE (RPE1, RPE2) vs entire eye (EYE)  - 2 slides for retina (RETINA1, RETINA2) vs entire eye (EYE)  - 2 slides for cornea (CORNEA1, CORNEA2) vs entire eye (EYE)  - 1 slide for entire eye (EYE) vs entire eye (EYE)

first: Sandro

last: Banfi


title: MicroRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Exiqon miRNA array]

status: Public on Oct 18 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary:
Lack of change in microRNA expression in adult mouse liver following treatment with benzo(a)pyrene (BaP), as detected using Exiqon miRNA arrays.
Adult male mice were exposed to 150 mg/kg benzo(a)pyrene (BaP) or solvent for 3 days and sampled 4 hours after the last dose. MicroRNA expression levels in adult mouse liver were measured using Exiqon miRNA arrays. Our results indicate a distinct lack of effect of BaP of miRNA expression, despite widespread changes in mRNA levels (measured using Agilent arrays). Lack of miRNA changes was confirmed with Agilent miRNA arrays.

Keywords: Toxicology, miRNA

overall_design: Adult male B6C3F1 mice were exposed to a daily dose of corn oil (vehicle control group) or 150 mg/kg BaP (treatment group) for 3 d (n=6 per group). Mice were sacrificed at 4 h or 24 h following the last dose and liver lobes were extracted and flash frozen. Exiqon miRNA arrays were used to examine changes in miRNA transcript levels in random liver lobe sections.

first: Carole

last: Yauk

first: Kelly

last: Jackson


title: Murine small intestinal crypt cells: IGF-1 stimulated vs. control

status: Public on Nov 01 2010

city: Davis

first: Bo

last: Lonnerdal

address: 1 Shields Ave.

department: Nutrition

institute: University of California, Davis

summary: microRNA profiling of mouse small intestinal crypt cells comparing control untreated with cells treated with insulin growth factor-1 (IGF-1). IGF-1 stimulated cell proliferation, as observed in Brdu incoporation assay.

overall_design: Two condition experiment. Control vs IGF-1 treatment. Biological replicates: 3 control, 3 treated. Independently grown and harvested. One replicate per array

first: Yalin

last: Liao

last: Lönnerdal


title: miRNA profiles of tonsillar B cell subsets

status: Public on Feb 25 2011

city: Los Angeles

first: Dharma

middle: Raj

last: Thapa

address: 615 Charles E Young Dr S, BSRB 157-02

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

summary: In order to assess the miRNA signature of B cells undergoing the germinal center reaction, we isolated three subsets of B cells from tonsils--naive (N), germinal center (GC), and memory (M) and looked at their miRNA profile.

overall_design: We looked at three subsets of B cells, isolated from tonsils obtained from four different donors. Thus, we profiled a total of 12 samples, and each tonsillar subset--N, GC, and M, had four biological replicates.

middle: R

first: Otoniel

last: Martinez-Maza


title: miRNA Expression data of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates

status: Public on Jan 04 2011

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

summary:
Increasing evidence suggests that microRNAs may play important roles in regulating self-renewal and differentiation in mammalian stem cells (SCs). Here, we explore this issue in skin. We first characterize microRNA expression profiles of skin SCs versus their committed proliferative progenies and identify a microRNA subset associating with “stemness”. Of these, miR-125b is dramatically downregulated in early SC-progeny. We engineer an inducible mice system and show that when miR-125b is sustained in SC-progenies, tissue balance is reversibly skewed towards stemness at the expense of epidermal, oil-gland and HF differentiation. Using gain-and-loss of function in vitro, we further implicate miR-125b as a repressor of SC differentiation. In vivo, transcripts repressed upon miR-125b induction are enriched >700% for predicted miR-125b targets normally downregulated upon SC-lineage commitment. We verify some of these miR-125b targets, and show that Blimp1 and VDR in particular can account for many tissue imbalances we see when miR-125b is deregulated.

We used microarrays to compare the global miRNA expression profile of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates.

overall_design: Hair follicle cells were isolated from P4 Backskin (Dox since P3 for 24hrs) of DTG (K14-rtTA/TRE-miR-125b/K14-H2BGFP), TRE (TRE-miR-125b/K14-H2BGFP), KrtA (K14-rtTA/K14-H2BGFP) as following: interfollicular epidermis sheet was pealed from hair follicle & dermis after dispase treatment.The hair follicle & dermis were first digested by collagenase (Sigma). Intact hair follicles were separated from dermal cells by low speed spinning (20g). The hair follicles were then digested by Trypsin and filtered by 40 µm cell strainers. The isolated hair follicle cells were FACS sorted. During FACS, cells were first gated against CD34 (endothelial cells), CD45 (immune cells), CD114 (melanocytes) and DAPI (dead cells). ORS cells were sorted from the remaining cells as α6HiGFPHi.

first: Zhang

last: Liang

first: Stokes

last: Nicole

first: Polak

last: Lisa

first: Rose

last: Jason

first: Nowak

last: Jonathan

first: Fuchs

last: Elaine


title: Sirt1-microRNA profile

status: Public on Jun 24 2010

city: cambridge

first: wenyuan

last: wang

state: MA

address: 43 vassar st

department: BCS

institute: MIT

summary: Sirt1, a NAD-dependent deacetylase, has been shown involved in many complex biological functions. We previously demonstrated that Sirt-1 gain of function is neuroprotective in a model of neurodegenenration. We recently found that Sirt1 loss of function (Sirt1Δ mouse) impairs learning, memory, and synaptic plasticity. We used microarray screening to identify potential miRNAs that may be regulated by Sirt1 and ivolved in learning and memory. Total RNA from the hippocampus of SIRT1Δ and control mice was extracted and used for microRNA expression level evaluation.

overall_design: Two group experiment, in duplicates. Each sample is compared to a common reference sample, comprised of an equal mixture of all 4 experimental samples.

first: Wenyuan

last: Wang


title: The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping

status: Public on Jun 30 2008

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

summary:
We determined the strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA/DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA/DNA hybrid to detect RNA molecules hybridized to a high density DNA oligonucleotide tiling microarray.  HybMap exhibited exceptional dynamic range and reproducibility, and clearly revealed coding, non-coding and structural RNAs, as well as new RNAs conserved in distant yeast species. Virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription.  Transcriptomes of alternative growth conditions reveal changes in both coding and non-coding RNAs.  Interestingly, our analysis reveals large numbers of non-coding RNAs, extensive antisense transcription, new properties of antisense transcripts, and induced divergent transcription. Furthermore, HybMap informed the efficiency and locations of RNA splicing genome-wide. Finally, a remarkable feature is observed at heterochromatin boundaries inside centromeres; strand-specific transcription islands around tRNAs.  These new features are discussed in terms of organism fitness and transcriptome evolution.

Keywords: yeast, gene expression, bioinformatics

overall_design:
The dynamic transcriptome of S.pombe was determined using a whole genome tiling array hybridized to total RNA.  Transcripts were detected using an antibody specific to RNA/DNA hybrids.  This technique, called HybMap, was used across three different growth conditions (Heat shock, MMS treatment, and minimal media) in addtion to standard conditions.  To further  understand the transcriptome, we isolated PolyA RNA from S.pombe grown in standard conditions and used the HybMap method. Finally, the transcriptome was compared to Pol II, histone, and H3K36me3 ChIP occupancy.
NOTE: Processed microarray data values listed in this repository represent only those probes that align to unique genomic positions. Probes that align to multiple genomic locations (reported in the Platform description) may not have values. Please refer to the web link above for a complete genomic data set.

first: Natalie

last: Dutrow

first: David

last: Nix

first: Derick

last: Holt

first: Brett

last: Milash

first: Brian

last: Dalley

first: Erick

last: Westbroek

first: Bradley

last: Cairns


title: Vitamin D and microRNA Expression

status: Public on Feb 02 2010

city: Oxford

first: Adam

last: Handel

address: Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: Background: Vitamin D has been observed to affect the expression of a number of genes, however its mechanism of action has not been completely elucidated. MicroRNA molecules have recently been shown to be key mediators of gene regulation. We hypothesised therefore that vitamin D might modulate gene expression by influencing the expression of microRNAs.  Methodology/Principal findings: A microRNA array was used to investigate the expression of microRNAs in RNA extracted from cells exposed to calcitriol for 0, 8 or 36 hours.  A diverse panel of human cell lines were analysed including Hep-G2, HL60, K562, two fibroblast cell lines (AG09309 and AG09319), and four lymphoblastoid cell lines (GM15084, GM12878, GM07348 and GM07019).  When compared between 0, 8 and 36 hours of calcitriol treatment, there were several microRNAs that were differentially regulated but the significance of these was lost after correction for multiple hypothesis testing.  Conclusions/Significance: No microRNA showed significantly altered expression after exposure to vitamin D.  However, some nominally significant miRNA molecules may warrant further investigation for a potential vitamin D-related role in immune function.

overall_design: We used nine cell lines (Hep-G2, HL60, K562, AG09309, AG09319, GM15084, GM12878, GM07348 and GM07019).  These were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, 0.2 mM L-glutamine at 37 oC in 5% humidified CO2.  We stimulated cells with 0.1 microM calcitriol for 0 hours, 8 hours or 36 hours.  We performed 2 replicates of each condition with each cell line.  After harvesting, cells were lysed in 500 uL of lysis buffer (Promega).  Homogenised samples were immediately stored at -80 oC.  The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 400 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 [21]) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

middle: E

first: Narelle

last: Maugeri

first: Antonio

last: Berlanga

first: Corey

last: Watson

first: Lahiru

last: Handunnetthi

first: Julia

last: Morahan

first: A

middle: D

last: Sadovnick

first: Gavin

last: Giovannoni

first: Julian

last: Knight

first: George

middle: C

last: Ebers

first: Sreeram

middle: V

last: Ramagopalan


title: Murine retina: Control vs. experimental autoimmune uveoretinitis

status: Public on Jul 01 2010

city: Nankoku

first: Atsuki

last: Fukushima

state: Kochi

address: Kohasu,Oko-cho

department: Ophthalmology

institute: Kochi Medical School

summary: Transcriptional profiling of mouse retina comparing naïve mouse and experimental autoimmune uveoretinitis (EAU)-developing mouse. EAU was induced by immunization of retinal autoantigens in adjuvants. Retinas were harvested 14 days after immunization.

overall_design: Two-condition experiment, Naïve retinal cells vs. EAU-developing mouse retinal cells on day 14. 3 control, 3 EAU-developing, independently harvested.

first: Waka

last: Ishida


title: microRNA expression of Ink4a/Arf-/- Pten-/- mouse astrocytes

status: Public on Dec 30 2009

city: Boston

first: Hailei

last: Zhang

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary: To identify QK-modulated microRNAs exhibiting a >1.5-fold change across all three cell model systems: human GBM cell lines, U87 and Hs683, and Ink4a/Arf-/- Pten-/- mouse astrocytes

overall_design: Ink4a/Arf-/- Pten-/- mouse astrocytes

first: An-Jou

last: Chen


title: Mature thymic NKT and T cells

status: Public on Jul 01 2009

city: Milan

first: Maya

last: Fedeli

state: MI

address: via Olgettina 58

department: DIBIT

institute: San Raffaele Scientific Institute

summary: Invariant Natural killer T (iNKT) cells are a separate lineage of T lymphocytes with innate effector functions. They express an invariant TCR specific for lipids presented by CD1d and their development and effector differentiation rely on a unique gene expression program. We asked whether this program includes microRNAs, small non-coding RNAs that regulate gene expression posttranscriptionally and play key role in the control of cellular differentiation programs. We identified a miRNA profile specific for iNKT cells, which exhibits features of activated/effector T lymphocytes.

overall_design:
In this experiment we compared microRNAs of NKT cells versus those of conventional T lymphocytes, both extracted from wild type mouse thymus.
To produce the populations we enriched mature thymocytes and then sorted NKT cells and conventional T cells (from one sorting we obtain one “NKT” sample and one “T” sample). We performed the experiment in triplicate; the sample NKT 1 was sorted the same day of the sample T 1, NKT 2 with T 2, NKT 3 with T 3.
We used a common reference approach for the 6 samples; as a common reference we produced RNA from total thymocytes, without the enrichment for mature cells and without the sorting; we pooled thymocytes derived from all the thymi used in the study.
The aim of the experiment was to demonstrate that NKT cells have a microRNA profile different from that of conventional T cells.

first: Paolo

last: Dellabona

first: Giulia

last: Casorati


title: microRNA expression of Hs683 and U87


title: Temporal effects of intermittent- and sustained hypoxia on gene expression patterns in rat lungs

status: Public on Dec 18 2008

city: Pittsburgh

first: Wei

last: Wu

address: MUH 628 NW, 3459 Fifth Ave

department: Medicine/PACCM

institute: University of Pittsburgh

summary:
Time-course gene expression profiles were obtained from lung tissues of the rats treated with room air, intermittent- (IH) or sustained hypoxia (SH) for 1, 3, 7, 14 and 30 days using CodeLink microarrays. Using a systems biology approach, we observed that two different mechanisms are involved in the lung responses to IH and SH: IH leads to increased G-protein coupled signaling-, ion transport-, neuronal- and steroid hormone receptor activities; whereas SH causes increased blood vessel morphogenesis and immune responses. Our results provide insight into molecular mechanisms underlying IH and SH.
Keywords: gene expression array-based, count

overall_design: rats were treated with intermittent- (IH) or sustained hypoxia (SH) for 1, 3, 7, 14 and 30 days; rats treated with room air were used as controls; gene expression profiles were obtained from these rats


title: miRNA profile in esophageal squamous cell carcinoma (ESCC)

status: Public on Aug 12 2010

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

institute: Shantou university, medical college

summary: MicroRNAs (miRNAs) are an endogenous conserved class of non-coding 20–22 nt small RNAs that regulate gene expression at post-transcriptional level by mostly binding to 3′-UTR of target mRNAs, leading to mRNA degradation or translation inhibition. Recent reports demonstrate a role for miRNA expression in the disease progression and outcome. By now, many researcher focusing on miRNA expression profiles in Barrett's esophagus and esophageal adenocarcinoma have been reported. Nevertheless, there is still a little information available about specific miRNA expression pattern and their roles in ESCC. To develop novel diagnostic and therapeutic targets for esophageal squamous cancer, we first investigated the expression profile of miRNA in three pairs of ESCC clinical samples.

overall_design: Tissues of ESCC and the matched normal counterparts were obtained from surgical specimens immediately after resection from patients undergoing primary surgical treatment of esophageal carcinoma from the Department of Tumor Surgery of Shantou Central Hospital, China. RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly, total RNA from three pairs of esophageal carcinoma and matched normal tissues were isolated by Trizol (Invitrogen, USA) and purified by RNeasy mini kit (QIAGEN, German). The concentration and quality of total RNA were measured by NanoDrop ND-1000 at 260 and 280 nm (A260/280) and checked by gel electrophoresis. Each RNA sample from three pairs of ESCC was separately labeled either using the miRCURY Hy3/Hy5 labeling kit and hybridized on the six miRCURYTM locked nucleic acid (LNA) array version 11.0 (Exiqon, Denmark), which contains probes for 1700 mature miRNA. Scans were quantified by using GenePix software (Molecular Devices). The data were exported to Microsoft Excel worksheets, log2 transformed, normalized using global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System).

first: Wu

last: Bingli

first: Xu

last: Liyan

first: Li

last: Enmin


title: MicroRNA profiling of cystic fibrosis intestinal disease in mice

status: Public on Jun 01 2011

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

institute: McGill University

summary: Cystic fibrosis (CF) intestinal disease is characterized by alterations in processes such as proliferation and apoptosis which are known to be regulated in part by microRNA’s. Herein, we completed microRNA expression profiling of the intestinal tissue from the cystic fibrosis mouse model of cystic fibrosis transmembrane conductance regulator (Cftr) deficient mice (BALBc/J Cftrtm1UNC), relative to that of wildtype littermates, to determine whether changes in microRNA expression level are part of this phenotype.  We identified 24 microRNA's to be significantly differentially expressed in tissue from CF mice compared to wildtype, with the higher expression in tissue from CF mice. These data were confirmed with real time PCR measurements. A comparison of the list of genes previously reported to have decreased expression in the BALB x C57BL/6J F2 CF intestine to that of genes putatively targeted by the 24 microRNA’s, determined from target prediction software, revealed 20% of the gene expression profile to overlap with predicted targets. Pathway analysis identified these common genes to function in phosphatase and tensin homolog-, protein kinase A-, phosphoinositide-3 kinase/Akt- and peroxisome proliferator-activated receptor alpha/retinoid X receptor alpha signaling pathways, among others, and through real time PCR experiments genes of these pathways were demonstrated to have lower expression in the BALB CF intestine. We conclude that altered microRNA expression is a feature which putatively influences both metabolic abnormalities and the altered tissue homeostasis component of CF intestinal disease.

overall_design: Two condition experiment, Balbc/J Cftrtm1UNC -/- (Cystic Fibrosis (CF) Mice) and Balbc/J Cftrtm1UNC +/+ (Wild Type (WT) Mice).  Biological Replicates: 7 WT, 8CF.  Ileum Tissue.

first: Mark

last: Bazett


title: Differential regulation of microRNA in ocular wound healing

status: Public on Apr 15 2010

city: Singapore

first: Silin

address: 11 Third Hospital Avenue

country: Singapore

institute: Singapore Eye Research Institute

summary: Pterygium is a relatively common human ocular surface fibroproliferative disease that affects vision. Endogenously produced microRNA (miRNA) regulates gene expression in various ocular surface diseases and possibly  pterygium. We aimed to investigate the role of miRNA in pterygium. Paired human pterygium and conjunctival tissues were obtained from patients diagnosed with primary pterygium. miRNA microarray profiling identified statistically significant miRNA changes which were matched to reciprocal significant changes in their target transcripts. We employed quantitative real-time polymerase chain reaction and found that hsa-miR-766 was up-regulated (2.57-fold) whilst hsa-miR-215 was down-regulated (0.49-fold) in pterygium compared to conjunctival control. Localization of miRNA was performed using in-situ hybridization. Transcript levels of predicted hsa-miR-766 targets, nuclear receptor subfamily 4, group A, member 1 and epidermal growth factor-containing fibulin-like extracellular matrix protein 1, were down-regulated in pterygium compared to conjunctiva by 0.53- and 0.64-fold, respectively. Collagens type 3, alpha 1 and type 4, alpha 2, both targets of hsa-miR-215, were up-regulated in pterygium by 3.01- and 3.11-fold, respectively. These changes were confirmed in the protein levels using immunofluorescent staining. Derangement of hsa-miR-766 and hsa-miR-215 may cause dysregulation of matrix rearrangement, cell proliferation and adhesion proteins, resulting in pterygium formation. Targeting miRNA may be a possible therapeutic approach in this disease.

overall_design: 3 pterygium samples and 3 matched conjuctiva samples from patients diagnosed with primary pterygium. A pool of all 6 samples was used as the common reference.

first: Louis

last: Tong