title: microRNA data from mice hearts of 21 days post myocardial infarction versus sham control

status: Public on Feb 12 2017

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

summary:
microRNAs control cardiac remodeling post myocardial infarction, though the cellular and molecular mechanisms remain unclear.
We used microarrays to examine microRNA profiles in mice hearts 21 days after ligation of left anterior descending coronary artery (LAD) versus sham control.

overall_design: Myocardial infarction was induced by ligation of anterior descending coronary artery (LAD). Mice hearts 21 days after LAD (n=4) versus sham control were used for RNA extraction and hybridization on Affymetrix miRNA 4.0.

first: Lichan

last: Tao

first: Junjie

last: Xiao

first: Xinli

last: Li


title: Mistimed sleep disrupts circadian regulation of the human blood transcriptome - Heterozygotes

status: Public on Feb 08 2017

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

summary: 4 healthy volunteers without sleep disorders were resident in an environmental scheduling facility and participated in a forced-desynchrony protocol, in which the sleep-wake cycle and the associated fasting-feeding cycle is scheduled to a 28-hour period, of which one third (i.e. 9h 20min) is scheduled for sleep. Under these conditions, during which light levels in the waking episode are kept low and sleep is scheduled in darkness, the phase of the melatonin rhythm occurred at approximately the same clock time during the first (D1) and fourth (D4) 28-h cycle and there were no major changes in either the amplitude or the waveform of this rhythm. During D1 and D4 7 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 23 samples comprising 4 human subjects, for which 14 samples across multiple time-points/sleep condition were collected.

first: Carla

last: Moller-Levet

first: Simon

last: Archer

first: Giselda

last: Bucca

first: Ana

last: Slak

first: Renata

last: Kabiljo

first: June

last: Lo

first: Nayantara

last: Santhi

first: Malcolm

last: von Schantz

first: Colin

middle: P

last: Smith

first: D

middle: J

last: Dijk


title: microRNA expression data from a heterozygous Titin-deficient mouse model and wildtype controls

status: Public on Jan 31 2017

city: Tuebingen

first: Qifeng

last: Zhou

address: Otfried Mueller str.10

department: Cardiology

country: Germany

institute: University Hospital Tuebingen

summary:
Mutations in the sarcomeric protein titin are a major cause of human dilated cardiomyopathy. We have developed a knock-in mouse model that imitated a previously identified titin truncation mutation. The heterotygous Ttn-deficient mice develop features of DCM and therefore recapitulate the human phenotype.
To investigate the role of microRNAs in titin-based heart failure, we performed a miRNA screen in heterozygous Ttn-deficient mice and their wildtype littermate controls.

overall_design: Heterozygous Ttn knock-in mice and theit wildtype littermate controls were challenged with Angiotensin II infusion for 3 days. RNA was extracted and hybridized to Affymetrix microRNA microarrays.

first: Michael

last: Gramlich


title: Schistosomula exposed to HDAC inhibitor (Trichostatin A) [12hrs]

city: São Paulo

first: Leticia

last: Anderson

state: SP

address: Av. Vital Brasil, 1500

department: Parasitologia

country: Brazil

institute: Instituto Butantan

summary: HDACs inhibitors induces mortality in the parasite Schistosoma mansoni (schistosomula and adult worms), and became an interesting drug class for the development of new drugs to treat schistosomiasis. In order to understand the effect of histone hyperacetylation on the parasite, we tested the effect of the HDAC inhibitor Trichostatin A on schistosomula gene expression.

overall_design: Newly transformed schistosomula were exposed to 1 µM Trichostatin A or vehicle solution (ethanol) and kept in culture for 12 h. Three independent biological replicates were assayed for each condition.

first: Sergio

last: Verjovski-Almeida


title: Cutaneous Localization In Multiple Myeloma In The Context Of Bortezomib Resistance: How Myeloma Cells Escape From The Bone Marrow To The Skin?

status: Public on Feb 15 2017

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
A rare complication of multiple myeloma is a secondary extramedullary involvement, and the skin is one of the possible sites, due to the physiological homing of plasma cells (PCs) into the skin. The article reports a case of a relapsed refractory MM patient, who developed a cutaneous localization after 16 months from the diagnosis under Bortezomib treatment without a leukemic phase.  Patient was refractory to Bortezomib. We analyzed the gene expression profiles, the immunophenotypic and immunohistochemistry profiles of MM cells across the course of the disease at the bone marrow and skin localization. Data obtained were further expanded by an immunohistochemistry analysis on selected molecules in a large cohort of MM patients with cutaneous localization. In particular we focused on the expression of chemokines and chemokine receptors involved in the PC skin homing.
The mechanisms behind the extramedullary spread and the formation of localizations outside the BM are not completely understood. Several studies investigated the expression profile of myeloma cells in the extramedullary localization by immunohistochemistry without a prospective molecular and immunohistochemistry study across the progression of the disease and consequently the development of extramedullary localization. This case indicates that the skin homing of MM cells could be related to the high CCR10 expression of at the diagnosis and relapse and the loss of CXCR4 surface expression across the progression of the disease in the contest of Bortezomib resistance.
This data was further confirmed in a larger series of patients. Moreover, high expression of CD44, together with the down-regulation of CD54 and the lack of expression of CD56 by MM cells in the BM relapse with the re-acquisition of both antigens during the cutaneous relapse may be the mechanism that drives the escape from BM of PCs and their localization into the skin. Our data have identified a possible mechanism that drives the escape from BM of myeloma cells and their localization into the skin.

overall_design: To investigate the genes differentially expressed in malignant plasma cells of a patient with relapsed refractory MM patient, who developed a cutaneous localization, we performed gene expression profiling using Affymetrix GeneChip analysis of plasma cells purified from the bone marrow aspirates at diagnosis and relapse.

first: Nicola

last: Giuliani

first: Valentina

last: Marchica

first: Fabrizio

last: Accardi

first: Paola

last: Storti

first: Benedetta

last: Dalla Palma

first: Cristina

last: Mancini

first: Eugenia

last: Martella

first: Marina

last: Bolzoni

first: Katia

last: Todoerti

first: Chiara

last: Schifano

first: Sabrina

last: Bonomini

first: Antonino

last: Neri

first: Magda

last: Marcatti

first: Maurilio

last: Ponzoni

first: Franco

last: Aversa


title: Expression profiling feline peripheral blood monocytes identifies a transcriptional signature associated with type two diabetes mellitus

status: Public on Feb 06 2017

city: Brisbane

first: Katharine

last: Irvine

address: Translational Research Institute

country: Australia

institute: Mater Research Institute UQ

summary: Peripheral blood monocytes were isolated from 3 control and 3 diabetic cats using positive selection and expression profiled using the Affymetrix Feline 1.0ST array.

overall_design: Comparison of monocyte expression in cats with type 2 diabetes or controls (n=3 per group)


title: The histone demethylase KDM3A, and its downstream target MCAM, promote Ewing Sarcoma cell migration and metastasis

city: Aurora

first: Paul

last: Jedlicka

state: CO

department: Pathology, MS-8104

country: USA

institute: University of Colorado Denver Anschutz Medical Campus

summary:
Ewing Sarcoma is the second most common solid pediatric malignant neoplasm of the bone and soft tissue. Driven by EWS/Ets, or rarely variant, oncogenic fusions, Ewing Sarcoma is a biologically and clinically aggressive disease with a high propensity for metastasis.  Our laboratory has previously identified the Jumonji-domain H3K9 me 1/2 histone demethylase KDM3A as a novel oncogene downstream of EWS/Fli1, the most common oncofusion in Ewing Sarcoma. Herein, we uncover a role for KDM3A in the promotion of Ewing Sarcoma metastasis.
Using global gene expression profiling, we show that some of the most strongly regulated genes by KDM3A are those implicated in cell migration and metastasis, and demonstrate, using functional assays, that KDM3A promotes migration in vitro and metastasis in vivo. We further provide evidence that MCAM, one of the most strongly and consistently regulated genes by KDM3A, is an important effector of KDM3A pro-metastatic action. Our studies also show that KDM3A regulates MCAM expression both through a direct mechanism, involving modulation of H3K9 methylation at the MCAM promoter, and an indirect mechanism, via the Ets1 transcription factor.

overall_design: Biological triplicates of A673 cells were stably transduced with Scrambled shRNA control, or 1 of 2 different KDM3A knockdown shRNA sequences (KDM3A sh1 or sh2) for RNA extraction and hybridization on Affymetrix microarrays.

first: M

last: Sechler

first: Janet

middle: K

last: Parrish

first: Diane

last: Birks


title: Schistosomula exposed to HDAC inhibitor (Trichostatin A)

first: Leticia

last: Anderson

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

overall_design: Refer to individual Series


title: Expression data from mir-35-41(nDf50) mutant embryos grown at 25 degrees, compared to wild type

status: Public on Feb 09 2017

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

summary:
Gene expression in early animal embryogenesis is in large part controlled post-transcriptionally. Maternally-contributed microRNAs may therefore play important roles in early development. We have elucidated a major biological role of the nematode mir-35 family of maternally-contributed, essential microRNAs. We show that this microRNA family regulates the sex determination pathway at multiple levels, acting both upstream and downstream of her-1 to prevent aberrantly activated male developmental programs in hermaphrodite embryos. The predicted target genes that act downstream of the mir-35 family in this process, sup-26 and nhl-2, both encode RNA binding proteins, thus delineating a previously unknown post-transcriptional regulatory subnetwork within the well-studied sex determination pathway of C. elegans. Repression of nhl-2 by the mir-35 family is not only required for proper sex determination but also for viability, showing that a single microRNA target site can be essential. Since sex determination in C. elegans requires zygotic gene expression to read the sex chromosome karyotype, early embryos must remain gender-naïve; our findings show that the mir-35 family microRNAs act in the early embryo to function as a developmental timer that preserves naïveté and prevents premature deleterious developmental decisions.
The mir-35 family of microRNAs is essential for development. The mir-35-41(nDf50) allele deleted 7 of 8 mir-35 family members, and presents a hypomorphic phenotype in which embryonic lethality is temperature sensitive. To characterize the molecular phenotype associated with loss of mir-35 family function, we profiled gene expression in mir-35-41(nDf50) mutant embryos at both permissive (20) and restrictive (25) temperatures. (Refer to A microRNA family exerts maternal control on sex determination in C. elegans)

overall_design: Mixed-stage embryos samples were obtained by hypochlorite treatment of mixed-stage C. elegans cultures. Cultures were grown on NGM supplemented with chicken egg yolk, and upshifted from 20 to 25 degrees 24h before harvest.

first: Victor

last: Ambros


title: LuCaP prostate cancer patient-derived xenografts reflect the molecular heterogeneity of advanced disease and serve as models for evaluating cancer therapeutics [GE]

status: Public on Jan 19 2017

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: In order to advance our understanding of prostate cancer biology and identify new effective treatments we have established and characterized multiple advanced prostate cancer patient-derived xenografts that mimic well the disease in patients.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 24 early and late passage LuCaP PCa xenograft lines. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines. Custom Agilent 415K whole human CGH microarrays were used to profile 33 LuCaP PCa xenograft lines.  Genomic DNA from tumors was hybridized against a pool of reference normal male DNA.

first: Eva

last: Corey

first: Holly

middle: M

last: Nguyen

first: Colm

last: Morrissey

first: Lisha

middle: G

last: Brown

first: Celestia

middle: S

last: Higano

first: Elahe

middle: A

last: Mostaghel

first: Xiaotun

last: Zhang

first: Lawrence

middle: D

last: True

middle: H

last: Lange

first: Peter

last: Nelson

first: Robert

middle: L

last: Vessella


title: LuCaP prostate cancer patient-derived xenografts reflect the molecular heterogeneity of advanced disease and serve as models for evaluating cancer therapeutics

type: Genome variation profiling by genome tiling array

first: Paul


title: Expression data from mir-35-41(nDf50) mutant embryos grown at 20 degrees, compared to wild type

overall_design: Mixed-stage embryos samples were obtained by hypochlorite treatment of mixed-stage C. elegans cultures. Cultures were grown on NGM supplemented with chicken egg yolk.


title: MicroRNA-664a-5p promotes neuronal differentiation of SH-SY5Y cells

status: Public on Feb 13 2017

city: Okayama

first: Kazunori

last: Watanabe

address: 3-1-1 tsushimanaka

country: Japan

institute: Okayama University

summary: MicroRNAs (miRNAs) belong to a class of small non-coding RNAs that play important roles in the transcriptional regulation of gene expression. A number of miRNAs are known to act as key regulator of diverse processes such as neuronal differentiation. In this study, we have attempted to identify novel miRNAs related to neuronal differentiation. 15 upregulated and 8 downregulated miRNAs were identified in SH-SY5Y cells treated with all-trans retinoic acid. We further showed that one of the upregulated miRNAs, miR-664a-5p promoted neuronal differentiation of SH-SY5Y cells. Herein, we report for first time the important role of miR-664a-5p in SH-SY5Y cells.

overall_design: To identify miRNAs related to neuronal differentiation of SH-SY5Y cells, we examined miRNA expression levels in undifferentiated SH-SY5Y cells and differentiated SH-SY5Y cells after 2 days and 14 days of retinoic acid treatment.

first: Ryuhei

last: Yamaji

first: Takashi

last: Ohtsuki


title: Human TNBC Cells 72h Treatment with 45nM OTSSP167 MELK Inhibitor vs. DMSO Control

status: Public on May 01 2017

city: Houston

first: Cecilia

middle: M.

last: Williams

state: Texas

address: 3605 Cullen Blvd

department: Center for Nuclear Receptors & Cell Signaling

institute: The University of Houston

summary: Microarray comparing TNBC cells treated for 72 hours with OTSSP167 MELK Inhibitor and control (DMSO)

overall_design: Two-condition arrays: MDA-MB-231 cells were treated with either 45nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).

first: Marisa

last: Simon

first: Fahmi

last: Mesmar


title: Schistosomula exposed to HDAC inhibitor (Trichostatin A) [24hrs]

first: Leticia

last: Anderson

overall_design: Newly transformed schistosomula were exposed to 1 µM Trichostatin A or vehicle solution (ethanol) and kept in culture for 24 h. Three independent biological replicates were assayed for each condition.

first: Sergio

last: Verjovski-Almeida


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila. [Agilent-018972]

status: Public on Feb 03 2017

city: Asahimachidori, Chuo-ku, Niigata-shi

first: Yohei

last: Nitta

state: Niigata

address: 757, Ichibancho,

institute: Niigata University

summary: Axonal branching is a fundamental requirement for sending electrical signals to multiple targets. However, despite the importance of axonal branching in neural development and function, the molecular mechanisms that control branch formation are poorly understood. Previous studies have hardly addressed the intracellular signaling cascade of axonal bifurcation characterized by growth cone splitting. Recently we reported that DISCO interacting protein 2 (DIP2) regulates bifurcation of mushroom body axons in Drosophila melanogaster. DIP2 mutant displays ectopic bifurcations in α/β neurons. Taking advantage of this phenomenon, we tried to identify genes involved in branching formation by comparing the transcriptome of wild type with that of DIP2 RNAi flies. A microarray analysis and a subsequent qRT-PCR experiment reviled that Glaikit (Gkt), a member of the phospholipase D (PLD) superfamily, is potentially a downstream target of DIP2. RNAi against gkt phenocopied the ectopic axonal branches observed in DIP2 mutant. Furthermore, a genetic analysis between gkt and DIP2 revealed that gkt acts in parallel with DIP2. In conclusion, we identified a novel gene underlying the axonal bifurcation process.

overall_design: The central brain was isolated at 24 hrs APF to compare the entire gene expression profiles of elav-Gal4/ UAS-dicer2;; UAS-DIP2-RNAi (DIP2 RNAi) with those of elav-Gal4/ UAS-dicer2 (control). The experiments were performed in four biological replicates.


title: Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes

status: Public on Jan 17 2017

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

summary: To find BRCA1-associated copy number abberations, the copy number profiles of Familial Basal-like BRCA1-mutated breast carcinomas were compared to Familial Basal-like carcinomas with no pathgogenic BRCA1/2 mutation. This led to the observation of unanticipated heterogeneity of the BRCA1 associated copy number profiles. Gene expression analysis on the same samples identified tumor infiltrating lymphocytes to be responsible for this observation. High number of infiltrating lymphocytes proved to be detrimental for copy number profiling efforts. After optimal sample selection, BRCA1-associated copy number abberations could be detected.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen primary breast tumors
Copy number analysis of Affymetrix  500K SNP arrays was performed for 120 famlial primary breast tumors. 90 Female HAPMAP samples (http://hapmap.ncbi.nlm.nih.gov/) with CEU ancestry were used as baseline.

first: Maarten

last: Massink

first: Quinten

last: Waisfisz

first: Hanne

last: Meijers-Heijboer


title: LuCaP prostate cancer patient-derived xenografts reflect the molecular heterogeneity of advanced disease and serve as models for evaluating cancer therapeutics [CGH]

first: Ilsa

last: Coleman

first: Eva

last: Corey

first: Holly

last: Nguyen

first: Colm

last: Morrissey

first: Lisha

last: Brown

first: Celestia

last: Higano

first: Elahe

last: Mostaghel

first: Xiaotun

last: Zhang

first: Lawrence

last: True


title: Enhanced transcriptomic responses in the Pacific salmon louse Lepeophtheirus salmonis oncorhynchi to the non-native Atlantic Salmon Salmo salar suggests increased parasite fitness

status: Public on Jan 25 2017

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

summary: This study investigates host-specific gene expression of the Pacific salmon lice, Lepeophtheirus salmonis oncorhynchii, while parasitizing a resistant host (Coho salmon), two susceptible hosts (Atlantic salmon, Sockeye salmon), and a population with-held hosts (starved), over 48 hrs.

overall_design: Adult female sea lice were allowed to attach to three different host populations (Atlantic, Coho and Sockeye salmon), or were kept in incubation chambers devoid of hosts (starved). At 0, 24, and 48 hours, individual lice were sampled for subsequent RNA analysis.

first: Laura

last: Braden

last: Sutherland

first: Simon

last: Jones


title: KSHV miRNA transfection and inhibition

first: Joseph

last: Ziegelbauer

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary:
Transcriptional profiling of BJAB cells transfected with KSHV miRNAs and BCBL cells treated with KSHV miRNA inhibitors.
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed or inhibited.

overall_design: Cells transfected with negative control miRNA compared to KSHV miRNAs or negative miRNA inhibitor compared to inhibitors to KSHV miRs.

first: Don

last: Ganem


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila.

first: Yohei

last: Nitta


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila. [Agilent-021791]


title: Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach

status: Public on Feb 17 2017

city: Miami

first: Denise

last: Yan

state: FL

address: 1601 NW 12th Ave

department: Otolaryngology

institute: University of Miami

summary: In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.

overall_design:
The microarray is composed of a fluidic manifold made of polycarbonate glued on the glass slide to introduce a dynamic hybridization for signal enhancement and acceleration of reaction kinetics. The tag probes containing a poly (dT) spacer and a 5' amino group are spotted with a SmartArrayer 136 spotter (CapitalBio) on the aldehyde-functionalized glass slides to capture the allele-specific PCR products.
100 deaf individuals and 59 normal individuals were analyzed.

first: Xue

middle: Z

last: Liu


title: Comparison of transcriptome between E .faecalis OG1RF and rnjB deletion mutant

first: Peng

last: Gao

address: SRB 301V, 1825 Pressler Street

department: IMM

institute: UTHealth

summary: To globally characterize the role of rnjB gene in E.faecalis, the transcriptome of ∆rnjB and OG1RF grown to exponential phase were compared using DNA microarray analysis

overall_design: RNA obtained from cultures of the OG1RF and the mutant strains was used in  two separate dye swap hybridization (one with parent-Cy3/mutant-Cy5 and the other with parent-Cy5/mutant-Cy3)

first: Gao

last: Peng

first: Harvey

last: Barrett


title: microRNA expression profiles of tumor-positive and tumor-negative sentinel lymph node biopsies from cutaneous melanoma patients

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: We analyzed microRNA profiles in archival FFPE sentinel node biopsy (SNB) from melanoma patients with different outcomes. Tumor-negative SNB (N), and tumor-positive SNB from patients with (PP) or without disease progression at 5 years follow-up (PN) were analyzed.

overall_design: This is a pilot  study assessing  24 sentinel node biopsies from 24 melanoma patients. Each biological group contains 8 samples.

first: Monica

last: Rodolfo

first: Loris

last: De Cecco


title: Modeling Transcriptional Rewiring in Neutrophils through the Course of Treated Juvenile Idiopathic Arthritis

status: Public on Feb 01 2017

city: Buffalo

first: kaiyu

last: Jiang

state: NY

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

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

summary: Neutrophils in children with the polyarticular form of juvenile idiopathic arthritis (JIA) display abnormal transcriptional patterns linked to fundamental metabolic derangements. These abnormalities include re-ordering of miRNA-RNA expression networks. In this study, we sought to determine the effects of therapy on miRNA-RNA networks in polyarticular JIA. We studied children with active JIA disease on therapy (ADM), children with inactive disease also on therapy (ID), and children with clinical remission on medication (CRM) using exon and miRNA microarrays and compared results to findings from healthy control (HC) children. We found substantial re-ordering of miRNA-RNA networks after the initiation of therapy. Each disease state was associated with a distinct transcriptional profile.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Total RNA and miRNA were extracted from isolated neutrophils from patients with JIA and healthy control children.

first: Kaiyu

first: Zihua

last: Hu

first: Mark

middle: B

last: Frank

first: Yanmin

last: Chen

first: James

middle: N

last: Jarvis


title: Zebrafish embryo: Control vs. Nrf2a overexpression

status: Public on Jan 13 2017

city: Nagoya

first: Shin'ichi

last: Akiyama

state: Aichi

address: 65 Tsurumaicho

department: Department of Nephrology

institute: Nagoya University Graduate School of Medicine

summary: We analyzed transcriptome profiles at 8 hours post fertilization of zebrafish embryo which were injected with/without nfr2a mRNA into a 1-cell stage embryo by using the Zebrafish gene expression microarray (MZH_Zebrafish_16k_v1.0).

overall_design: Two-condition experiment, uninjected  (control) vs. injected with Nrf2a mRNA (Test). Biological replicates: Triplicate design (3 controls and 3 tests), independently grown and harvested. Analytical replicates: Triplicates array analysis in biological experimental group #1. Duplicates array analysis in biological experimental group #2 and #3.

first: Vu

middle: T

last: Nguyen

first: Yuji

last: Fuse

first: Junya

last: Tamaoki

first: Masafumi

last: Muratani

first: Yutaka

last: Tamaru

first: Makoto

last: Kobayashi


title: Schistosomula exposed to HDAC inhibitor (Trichostatin A) [48hrs]

first: Leticia

last: Anderson

institute: Instituto Butantan

summary: HDACs inhibitors induces mortality in the parasite Schistosoma mansoni (schistosomula and adult worms), and became an interesting drug class for the development of new drugs to treat schistosomiasis. In order to understand the effect of histone hyperacetylation on the parasite, we tested the effect of the HDAC inhibitor Trichostatin A on schistosomula gene expression.

overall_design: Newly transformed schistosomula were exposed to 1 µM Trichostatin A or vehicle solution (ethanol) and kept in culture for 12 h. Three independent biological replicates were assayed for each condition.

first: Sergio

last: Verjovski-Almeida


title: Expressing profiles of small non-coding RNA in mouse models of oxygen-induced retinopathy (OIR)

status: Public on Feb 10 2017

city: Boston

first: Chi-Hsiu

last: Liu

state: MA

address: 300 Longwood Avenue

department: Ophthalmology

institute: Boston Children's Hospital

summary:
Pathologic ocular angiogenesis is a common cause of blindness in proliferative retinopathy. Small non-coding RNAs (sncRNAs) play critical roles in normal development and diseases, and their function in eye diseases and angiogenesis are increasingly recognized. In the present study, we aimed to identify the function and therapeutic potential of sncRNAs in retinopathy.
We used microarray to analyze the retinal expression profile of sncRNAs in a mouse oxygen-induced retinopathy (OIR) model that mimic human proliferative retinopathy.

overall_design: Total retinal RNAs including sncRNAs were isolated from P17 mouse OIR and normoxic retinas (n=3 per group) and applied to the Affymetrix GeneChip miRNA 2.0 array (GEO platform id: GPL14613). Each sample is a biological replicate.

first: Zhongxiao

last: Wang

first: Ye

last: Sun

first: John

last: SanGiovanni

first: Jing


title: Genes altered by L-asparaginase treatment in REH cells

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

institute: Tokyo Medical & dental univ.

summary: To identify genes affected by L-asparaginase, we treated with L-asparaginase 1U/ml. After 2 days, RNA was extracted, and then expression analysis was performed using agilent microarray.

overall_design: Expression microarray with L-asparaginase or non-treated REH cells were performed in duplicate.

first: Hiroyoshi

last: Takahashi

first: Johji

last: Inazawa


title: mRNA profile in CD4+ T cell in healthy control and Primay biliary cholangitis (PBC) [mRNA]

status: Public on Jan 06 2017

city: Chiba

first: Ryo

last: Nakagawa

address: 1-8-1, Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Chiba University

summary: Primary biliary cholangitis (PBC), formally known as primary biliary cirrhosis, is an autoimmune liver disease of unknown pathogenesis. Consequently, therapeutic targets for PBC have yet to be identified. As CD4+ T cells play a pivotal role in immunological dysfunction observed in PBC, we analyzed microRNA(miRNA) and mRNA expression in CD4+ T cells to investigate PBC pathogenesis and identify novel therapeutic targets.

overall_design:
Clinically and pathologically diagnosed 6 PBC patients and 6 healthy controls, who agreed to provide samples with written informed consent, were enrolled in this study. Total RNA was extracted from peripheral CD4+ T cells from PBC patients and healthy controls. All samples fulfilled the following criteria (RNA integrity number > 8.0, A260/A280 ratio; 1.9-2.2) by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a DU730 UV/Visible Spectrophotometer (Beckman Coulter, Brea, CA, USA). All samples profiled the expression of miRNA and mRNA by using Agilent microarray (SurePrint G3 human miRNA microarray kit 8×60K Rel.16.0 and SurePrint G3 human GE 8×60K microarray kit) according to manufacturer’s protocols.
mRNA profiling was performed using Agilent gene expression array platforms with RNAs isolated from  CD4+ T cell of  PBC  and healthy control.

first: N

last: Kato

first: R


title: HER2 FISH results in breast cancers with increased CEN17 signals using alternative chromosome 17 probes - reclassifying cases in the equivocal category.

status: Public on Jan 01 2017

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

summary:
AIMS:
HER2 testing of invasive breast cancer by in-situ hybridisation guides therapy decisions. Probing HER2 and cen17 simultaneously is supposed to reveal both a potential HER2 gene amplification and polysomy 17. However, a considerable number of breast cancer patients with quasi polysomy 17 are considered "equivocal" which is diagnostically meaningless. Moreover, patients with equivocal / false polysomic tumours are prevented from a potentially beneficial anti-HER2 treatment. Here we evaluated the RAI1, D17S122, and TP53 hybridisation markers to reliably indicate true polysomy and to accurately reclassify equivocal samples as HER2-positive.
METHODS AND RESULTS:
Samples with (n = 82) and without (n = 52) increased cen17 copy numbers and 78 evidently HER2-amplified specimens were analysed using dual and triple marker hybridisation probes. Selected putative polysomic samples were subjected to array-based comparative genomic hybridisation. We found that 37.8% samples with putative polysomy 17 did not show any gain in RAI1, D17S122, or TP53. Accordingly, aCGH revealed evidence for the presence of HER2/cen17 coamplification rather than for true polysomy in those cases. Reflex testing using alternate 17p markers reclassified up to 56.3% equivocal cases as HER2-positive and the combined assessment of a 17p and 17q locus allows the differentiation of true vs. false polysomy.
CONCLUSIONS:
An increased cen17 copy number does not necessarily reflect polysomy and reflex testing facilitates the reclassification of "equivocals". Nevertheless, the prognostic and predictive value of a HER2/cen17 coamplification versus HER2 gene amplification alone must still be prospectively evaluated. This article is protected by copyright. All rights reserved.

overall_design: Twelve DNA samples were extracted from formalin-fixed, paraffin-embedded (FFPE) tissue specimens, tissue cores, obtained from primary breast tumors. All samples were co-hybridized on SurePrint G3 Human CGH Microarrays against reference DNA samples obtained from peripheral blood of healthy female donor. To much the DNA fragment size distribution of test and reference samples prior to labeling and aCGH hybridization all reference samples were sheared to and average DNA fragment size of 500 bp. aCGH analysis was conducted to validate results of FISH analaysis that had been previously obtained for the same clinical samples.

first: Maria-Anna

last: Holszschuh

first: Sven

last: Hauke

first: Elisabeth

middle: C

last: Inwald

first: Bernhard

last: Polzer

first: Gero

last: Brockhoff


title: MicroRNAs related with the metastasis of human tongue squamous cell carcinoma

status: Public on Dec 31 2016

city: beijing

first: zhang

last: suwei

address: changping

country: China

institute: capitalbio

summary: MicroRNAs play a crucial role in tumorigenesis. However, the value of microRNAs in the diagnosis and treatment of tongue squamous cell carcinoma (TSCC) still await investigations. To identify the microRNAs associated with the metastasis of TSCC, we analyzed the transcriptomic difference between metastatic and the non-metastatic TSCC tissue. We identified a set of metastasis-related microRNAs with potential prognostic value.

overall_design: Using microarray-based technology, we have performed a microRNA expression analysis in 5 pairs of patients with TSCC


title: Expression data in Arabidopsis sad1mutant during heat stress

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

type: Expression profiling by genome tiling array

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in sad1 mutant during heat stress

overall_design: Ten-day-old seedlings of wild type (C24 accession) and sad1 mutant were subjected to 37 °C for 0, 2, and 6 h. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Masanori

last: Okamoto

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Kei

last: Iida

first: Yoshiki

last: Mochizuki

first: Tetsuro

last: Toyoda


title: DNA sequence properties that determine susceptibility to epiallelic switching [Affymetrix]

status: Public on Jan 09 2017

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genome-wide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability and provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci largely determine their susceptibility to epiallelic switching. The importance of this rule was confirmed by analyses of common epialleles in natural Arabidopsis accessions and verified in rice.

overall_design: RNA expression profiles of 3 met1-1 replicates, 3 met1-3 replicates and 6 wild type replicates.


title: microRNA profile in CD4+ T cell in healthy control and Primay biliary cholangitis (PBC) [miRNA]

first: Ryo

last: Nakagawa

overall_design:
Clinically and pathologically diagnosed 6 PBC patients and 6 healthy controls, who agreed to provide samples with written informed consent, were enrolled in this study. Total RNA was extracted from peripheral CD4+ T cells from PBC patients and healthy controls. All samples fulfilled the following criteria (RNA integrity number > 8.0, A260/A280 ratio; 1.9-2.2) by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a DU730 UV/Visible Spectrophotometer (Beckman Coulter, Brea, CA, USA). All samples profiled the expression of miRNA and mRNA by using Agilent microarray (SurePrint G3 human miRNA microarray kit 8×60K Rel.16.0 and SurePrint G3 human GE 8×60K microarray kit) according to manufacturer’s protocols.
miRNA profiling was performed using Agilent miRNA array platforms with RNAs isolated from  CD4+ T cell of  PBC  and healthy control.

first: N

last: Kato

first: R


title: MicroRNA expression data from bone marrow T cells of acquired aplastic anemia patients and healthy individuals

city: Jinan

first: Yuan-xin

last: Sun

address: 107 Wenhuaxi Rd

institute: Qilu hospital, Shandong University

summary:
Acquired aplastic anemia (AA) is an immune-mediated disease with active destruction of hematopoietic stem and progenitor cells by the cytotoxic T-cells in bone marrow. Aberrant expression of microRNAs in T-cells results in development of some autoimmune diseases.Screening the potential miRNAs which may play regulatory role in T cells of AA is meaningful to explore the mechanism of AA.
We used microarrays to screen the differential expression pattern of miRNAs in T cells of aplatic anemia patients to find the potential regulatory miRNAs.

overall_design: Bone marrow mononuclear cells were obtained by aspiration of the iliac crest of patients and healthy donors and prepared with the use of lymphocyte separation medium. CD3+ cells were positively selected from three SAA patients and three healthy controls by means of immunomagnetic activated cell sorting system. Affymetrix GeneChip microRNA 2.0 Array was used for detection of miRNA expression in CD3+ T cells of the six samples.

first: Jun

last: Peng

first: Hu

last: i Li


title: Leucocyte small nucleolar RNA and microRNA expression data from healthy control subjects of different age

status: Public on Nov 30 2016

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

summary: It has been observed that immune cell deterioration occurs in the elderly, as well as a chronic low-grade inflammation called inflammaging. These cellular changes must be driven by numerous changes in gene expression and in fact, both protein-coding and non-coding RNA expression alterations have been observed in peripheral blood mononuclear cells from elder people. In the present work we have studied the expression of small non-coding RNA (microRNA and small nucleolar RNA -snoRNA-) from healthy individuals from 24 to 79 years old. We have observed that the expression of 69 non-coding RNAs (56 microRNAs and 13 snoRNAs) changes progressively with chronological age. According to our results, the age range from 47 to 54 is critical given that is the period when the expression trend (increasing or decreasing) of age-related small non-coding RNAs  is more pronounced. Furthermore, age-related miRNAs regulate genes that are involved in immune, cell cycle and cancer-related processes, which had already been associated to human aging. Therefore, human aging could be studied as a result of progressive molecular changes, and different age ranges should be analysed to cover the whole aging process.

overall_design: 38 healthy controls were included in the study ranging from 24 to 79

first: M

first: H

last: Irizar

first: A

last: Gorostidi

last: Alberro

first: J

last: Ruiz-Martínez

last: Olascoaga

last: López de Munain

first: D

last: Otaegui


title: miRNA Expression Data from Ovarian Cancer Exosomes and Cells of Origin

status: Public on Nov 01 2016

city: Houston

first: Gabriel

last: Lopez-Berestein

state: TX

address: 1901 East Rd

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary: We used Affymetrix miRNA microarray to identify the oncogenic and tumor-suppressor miRNAs differentially expressed between exosomes and the originating cells.

overall_design:
Exosomes were isolated from 6 different ovarian cancer cell lines and one normal ovarian cell line (HIO180). Following miRNA isolation, samples were used for hybridization on Affymetrix microarrays.
Contributor: Noncoding RNA Program at the Center for Targeted Therapy, MD Anderson Cancer Center

first: Pinar

last: Kanlikilicer

first: Mohammed

last: Helmy Saber


title: Transcriptomic study on yeast expressing an intracellular antibody against acetylated-K9-H3 Histone

status: Public on Nov 14 2016

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

summary: Post-translational modifications (PTMs) of proteins, such as acetylation or phosphorylation, represent a huge untapped source of targets of great biological and therapeutic potential, but their validation can only be indirect. PTMs cannot be selectively hit by the powerful nucleic-acid based interference approaches. Antibodies represent a class of molecules that could be exploited to selectively target PTMs. However, currently it is not possible to systematically derive antibodies that selectively bind PTMs of a native protein and work intracellularly to achieve a native PTM-selective interference. We developed  the Post-translational Intracellular Silencing Antibody technology (P.I.S.A.), a new method for the selection of intrabodies targeting the native PTM version of proteins and their use for PTM targeting in cells. We used PISA to select an intrabody against acetylated-K9-H3 Histone (ScFv-58F). Microarray study is aimed at the investigation of ScFv-58F-specific changes in gene expression in yeast, in comparison to yeast expressing a control intrabody (ScFv-112A, anti-acetyl-Integrase, selected with PISA), and to a wild type yeast.

overall_design: Total RNA extracted from L40 Saccharomyces cerevisiae strain was used for this gene expression study by Agilent microarray. Three experimental groups were analyzed, overall n=12 RNA samples: yeast stably expressing ScFv-112A anti-HIV1 acetylated Integrase intrabody; yeast stably expressing ScFv-58F anti-acetylated H3 Histone intrabody; wild type yeast.

first: Michele

last: Chirichella

first: Simonetta

last: Lisi

last: Fantini

first: Martina

last: Goracci

first: Rossella

last: Brandi

first: Renata

last: Cerna

first: Mara

last: D'Onofrio

first: Cristina

last: Di Primio

first: Antonino

last: Cattaneo


title: MiRNA Expression Profiling in Cisplatin Resistance Human Gastric Cancer Cell Lines and Their Parental Cell Lines

status: Public on Sep 05 2016

city: Nanjing

first: Yajie

last: Zhang

address: 140 Hanzhong Road

department: Cell biology

institute: Nanjing Medical University

summary: Cisplatin is the first-line agent utilized for the clinical treatment of a wide variety of solid tumors including gastric cancer. However, the intrinsic or acquired cisplatin resistance is often occurred in patients with gastric cancer and resulted in failure of cisplatin therapy. In order to investigate if miRNA involves in cisplatin resistance of human gastric cancer, we first screened and compared the expression of miRNAs between cisplatin resistant gastric cancer cell lines SGC-7901/DDP and BGC-823/DDP and their sensitive parental cells by miRNAs microarray.

overall_design: Total miRNAs expression was examined in SGC-7901,SGC7901/DDP,BGC-823,BGC-823/DDP four cell lines.

first: Wenxia

last: Xu

first: Pan

last: Ni

first: Aiping

last: Li

first: Jianwei

last: Zhou

first: Shan


title: ARA-PEPs : a repository of putative sORF-encoded peptides in Arabidopsis thaliana

status: Public on Dec 23 2016

city: Leuven

first: Vera

middle: van

last: Noort

address: Kasteelpark Arenberg 20, bus 2460

department: Microbial and Molecular systems

country: Belgium

institute: KU Leuven

summary: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). There is increasing evidence for the translation of these sORFs into bioactive peptides. Yet only a few small peptides are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of small peptides, we have developed ARA-PEPs, a repository and webserver of putative peptides encoded by sORFs in the Arabidopsis genome from in house Tiling arrays, RNA sequencing and from publicly available datasets. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChip® Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves inoculated with Botrytis cinerea (BC). Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a threshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after BC treatment compared to the control treatment, resulting in 195 BC induced TARs.

overall_design: Botrytis cinerea treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

first: Rashmi

middle: R

last: Hazarika

first: Barbara

last: De Coninck

first: Janick

last: Mathys

first: Bruno

middle: P

last: Cammue

last: van Noort


title: miRNA Expression data from murine hearts of transgenic Clock delta 19/delta 19 mice (Clock mice) and wild type (WT) mice at 4 and 21 months of age

city: Guelph

first: Faisal

middle: James

last: Alibhai

state: ON

address: 50 Stone Rd East

department: Biomedical Sciences

institute: University of Guelph

summary:
Mice are on a C57Bl/6J background strain
The micorarray approach allows the investigation of changes in miRNA expression between Clock Mutant and Wild Type mice.

overall_design: There are a total of 12 samples, 3 from Clock Mutant 4 month, 3 from Wild type 4 month, 3 from Clock mutant 21 month and 3 from Wild Type 21 month. Animals were sacrificed at 6 hours into the light phase (ZT 6).

first: Tami

last: Martino


title: miRNA expression data from mice Ago2-amygdala

status: Public on Sep 30 2016

city: Rehovot

first: Alon

last: Chen

address: 234 Herzel St.

department: Neurobiology

country: Israel

institute: The Weizmann Institute of Science

summary:
In this study we aimed to uncover which miRNAs are changed in the Ago2-amygdala complex following chronic social defeat in mice
We used microarrays to determine which miRNAs are changed in the Ago2-amygdala complexof mice following chronic social defeat compared to control

overall_design: Mice were subjected to chronic social defeat. 8 days following the end of the protocol, mice were sacrificed and amygdala was collected. The amygdala was immunoprecipitated using Ago2 beads and RNA was extracted to microarray.

first: Naama

last: Volk


title: MicroRNA deregulation in laryngeal squamous cell carcinoma cell lines

status: Public on Sep 19 2016

city: Hong Kong island

first: Zeng Hong

address: Lab block, No. 21, Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

summary:
Cancer of the larynx is the second most common upper-aerodigestive cancer, and laryngeal squamous cell carcinoma (LSCC) is the major histological form. However, the molecular mechanism within LSCC progression remains poorly understood. MicroRNA-based target therapy is a promising approach in cancer therapy and offers multiple advantages as compared with the conventional treatment modalities. Hence, there is a need to identify the key microRNA involved in the progression of LSCC.
We used GeneChip miRNA 2.0 array to profile the global microRNA deregulation in LSCC.

overall_design: LSCC cell lines (SNU46, SNU899 and SNU1076) and human normal epithelial cultures (HOK1, HOK2 and HTEpiC) derived from head and neck region were selected for RNA extraction. RNA quality was evaluated using Agilent 2100 Bioanalyser. RNA sample with a RIN value over 8 was selected for hybridization on Affymetrix miRNA geneChip 2.0 arrays. MicroRNA with P < 0.05 and 1.5-fold difference were considered as differentiated microRNA in LSCC.

first: John

first: Thian

middle: S

last: Wong

first: Wei

last: Gao


title: Title: Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a

status: Public on Oct 28 2016

city: Philadelphia

first: Satish

last: Rattan

state: PA

address: 1025 Walnut St., Room 320 College

department: Medicine

institute: Thomas Jefferson University

summary: A comprehensive –omic, computational, and physiological approach was employed to examine the (previously unexplored) role of microRNAs (miRNAs) as regulators of IAS smooth muscle contractile phenotype and basal tone. MicroRNA profiling, genome wide expression, validation and network analyses were employed to assess changes in mRNA and miRNA expression in IAS smooth muscles from young vs. aging rats. Multiple miRNAs, including rno-miR-1, rno-miR-340-5p, rno-miR-185, rno-miR-199a-3p, rno-miR-200c, rno-miR-200b, rno-miR-31, rno-miR-133a and rno-miR-206 were found to be up-regulated in aging IAS. qRT-PCR confirmed the up-regulated expression of these miRNAs and down regulation of multiple, predicted targets (Eln, Col3a1, Col1a1, Zeb2, Myocd, SRF, Smad1, Smad2, RhoA/ROCK2, Fn1, Sm22-v2, Klf4, and Acta2) involved in regulation of SM contractility. Subsequent studies demonstrated an aging-associated increase in the expression of miR-133a, corresponding decreases in RhoA, ROCK2, MYOCD, SRF and SM22α protein expression, RhoA-signaling, and a decrease in basal and agonist (U-46619 (thromboxane A2 analog))-induced increase in the IAS tone. Moreover, in vitro transfection of miR-133a caused a dose-dependent increase of IAS tone in strips, which was reversed by anti-miR-133a. Lastly, in vivo perianal injection of anti-miR-133a reversed the loss of IAS tone associated with age. This work establishes the important regulatory effect of miRNA-133a on basal and agonist-stimulated IAS tone. Moreover, reversal of age-associated loss of tone via anti-miR delivery strongly implicates miR dysregulation as a causal factor in the aging-associated decrease in IAS tone, and suggests miR-133a is feasible therapeutic target in aging-associated rectoanal incontinence.

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Three rats (Fischer 344) provided by the National Institutes of Aging of three different age groups (6 months, 18 months, and 26 months of age) were used for these studies.  The smooth muscle cells (SMCs) from the internal anal sphincter (IAS) from above different age groups were isolated using collagenase dispersion method.  The cells were subjected to RNA collection; and RNA from these samples were used for mRNA microarray analysis.  For another sets of studies, from another batch of Fischer 344 rats (of 6 months, 18 months, and 26 months of age), the IAS SMCs were isolated and their miRNA fractions using miRVana miRNA Isolation kit following the manufacturer’s protocol were collected for miRNA microarray analysis.

first: Jagmohan

last: Singh

first: Ettickan

last: Boopathi

first: Sankar

last: Addya

first: Isidore

last: Rigoutsos

first: Raymond


title: Transplant tissue specfic exosome platform for noninvasive monitoring of immunologic rejection [miRNA]

status: Public on Oct 18 2016

first: Prashanth

last: Vallabhajosyula

address: 3400 Spruce Street

institute: University of Pennsylvania

summary: In transplantation, there is a critical need for non-invasive biomarker platforms for monitoring immunologic rejection. We hypothesized that transplanted tissues release donor specific exosomes into recipient circulation/ bodily fluids, and that the quantitation and profiling of their intra-exosomal cargoes would constitute a novel biomarker platform for monitoring rejection.  We tested this hypothesis in a human into mouse xenogeneic islet transplant model, and validated the concept in clinical settings of islet and renal transplantation.  In the xenogeneic model, islet transplant exosomes in recipient blood were quantified over long-term follow-up using anti-human leukocyte antigen (HLA) antibody that is only expressed on human islets (p=1.6x10-14).  Transplant islet exosomes were purified using anti-HLA antibody conjugated beads and their cargoes contained bona fide islet endocrine hormone markers insulin, glucagon, and somatostatin.  Rejection led to significant decrease in transplant islet exosome signal (p=4x10-15), along with distinct changes in its microRNA and proteomic profiles prior to appearance of hyperglycemia.  In the clinical settings of islet (n=5) and renal (n=5) transplantation, donor exosomes with respective tissue specificity for islet β cells and renal epithelial cells were reliably characterized in recipient plasma over follow-up (up to 5 years; p=0.0001).  Collectively, these findings demonstrate the biomarker potential of transplant exosome characterization for providing a non-invasive window into the conditional state of the transplant tissue.

overall_design: We assessed an in vivo read-out of TISE cargo as compared to its transplanted human islet tissue counterpart. Transplant islet exosomes from two independent experiments were analyzed.  Small RNA microarray profiling of islet exosomes and islet graft tissue was performed. Next, we attempted small RNA profiling of R (rejection)-xeno samples, but because of the low TISE levels from a single sample we had to pool transplant islet exosomes from 5 animals for microarray analysis.

first: Laxminarayana

last: Korutla

first: Andreas

last: Habertheuer

first: Ming

last: Yu

first: Susan

last: Rostami

first: Chao-Xing

last: Yuan

first: Sanjana

last: Reddy

first: Chengyang

last: Liu

first: Varun

first: Brigitte

last: Koeberlein

first: Jennifer

last: Trofe-Clark

first: Michael

last: Rickels

first: Ali

last: Naji


title: Profile of microRNAs in human umblical vein endothelial cells (HUVECs)

status: Public on Aug 31 2016

city: Lexington

first: Banrida

last: Wahlang

state: KY

address: 900 S Limestone Street Rm 559

department: UK Superfund Research Center

institute: University of Kentucky

summary: Polychlorinated biphenyl exposure alters the expression profile of microRNAs in HUVECs

overall_design: Primary human endothelial cells (HUVECs) were exposed to the commercial PCB mixture, Aroclor 1260, at 10 µM. After a 16-h exposure, RNA was extracted and hybridized on Affymetrix microarrays. Samples were analyzed using Affymetrix GeneChip® miRNA 4.0 arrays for high throughput detection.


title: Affymetrix SNP array data for muscular dystrophy samples

status: Public on Nov 04 2016

city: Mexico City

first: Juan Carlos

last: Zenteno

state: In the USA or Canada, please select...

address: Chimalpopoca 14

country: Mexico

institute: Institute of Ophthalmology "Conde de Valenciana"

summary: Genome-wide homozygosity mapping was employed for identification of the locus involved in autosomal recessive muscular dystrophy highly prevalent in a small community.

overall_design: Affymetrix SNP array was performed for a pool of three samples from individuals with an autosomal recessive form of muscular dystrophy.

first: Juan


title: Smooth muscle cell mineralocorticoid receptor regulation of vascular microRNAs with aging

status: Public on Jul 29 2016

city: Boston

first: Iris

last: Jaffe

address: 800 Washington Street

institute: Tufts Medical Center

summary:
We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic miRNA to examine the effect of age on vascular miRNA alterations in the presence and absence of SMC-MR.
For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

overall_design: Total miRNA was extracted from young (3-4 mo) and aged male (12mo) MR-intact and SMC-MR-KO mice to investigate aging-induced alterations in vascular miRNA expression

middle: J

last: DuPont


title: Hepatocytic parental progenitor cells of rat small hepatocytes

status: Public on Sep 08 2016

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

summary:
We analyzed gene expression of hepatocytic parental progenitor cells in a population of small hepatocytes.
The hepatocytic parental progenitor cells possess self-renewal capability. These cells maintain the ability to differentiate into mature hepatocytes.

overall_design: Primary rat small hepatocytes were isolated from fresh livers by using collagenase perfusion method and cultured in serum-free medium. Nine days after plating, colonies were treated with a separation solution and CD44+  cells were isolated by using MACS methods.The sorted CD44+ cells were cultured in Matrigel-coated dishes and passaged every 4 weeks. Second passage cells were cultured for 14 days and then treated with Matrigel-overlay for 7 days. As a control, mature hepatocytes were isolated from fresh livers.

first: Toshihiro

last: Mitaka


title: Dysregulation of hepatic microRNA expression profiles with Clonorchis sinensis infection

status: Public on Oct 14 2016

city: harbin

first: su

last: han

address: xuefu road

department: parasite

institute: harbin medical university

summary:
Clonorchiasis remains an important zoonotic parasitic disease worldwide. The molecular mechanisms of host-parasite interaction are not fully understood. Non-coding microRNAs (miRNAs) are considered to be key regulators in parasitic diseases. The regulation of miRNAs and host micro-environment may be involved in clonorchiasis, and require further investigation.
MiRNA microarray technology and bioinformatic analysis were used to investigate the regulatory mechanisms of host miRNA and to compare miRNA expression profiles in the liver tissues of Clonorchis sinensis-infected rats and controls.A total of eight miRNAs were downregulated and two were upregulated, which showed differentially altered expression profiles in the liver tissue of C. sinensis-infected rats. Further analysis of the differentially expressed miRNAs revealed that many important signal pathways were triggered after infection with C. sinensis, which were related to clonorchiasis pathogenesis, such as cell apoptosis and inflammation, as well as genes involved in signal transduction mechanisms, such as pathways in cancer and the Wnt and Mitogen-activated protein kinases (MAPK) signaling pathways.This dysregulation in miRNA expression may contribute to the etiology and pathophysiology of clonorchiasis. These results also provide new insights into the regulatory mechanisms of miRNAs in clonorchiasis, which may present potential targets for future C. sinensis control strategies.

overall_design: We collected liver from control and 3 weeks post-infection with clonorchis sinensis of rat, respectively.

first: Su

last: Han

first: Qiaoran

last: Tang

first: Xi

last: Lu

first: Rui

last: Chen

first: Yujuan

last: Shen

first: Yihong

last: Li

first: Jing

last: Shu

first: Xiaoli

last: Zhang

first: Jianping

last: Cao


title: Profile of miRNA in Bovine corpora lutea

status: Public on Sep 03 2016

city: UNIVERSITY PARK

first: Samar

middle: and animal

last: Maalouf

state: Pennsylvania

address: 324 Henning Building

department: Animal Science

institute: Pennsylvania state university

summary: The corpus luteum (CL), an ovarian transient gland, develops from the remnants of the ovulatory follicle and produces progesterone, required for maintenance of pregnancy in mammals. The development of the CL is characterized by the differentiation of granulosal and thecal cells into luteal cells, cell hypertrophy and hyperplasia. As the CL matures, growth ceases and the tissue acquires the ability to undergo regression in response to luteolytic signals (prostaglandin F2alpha). The regulators of this transition are poorly understood. MicroRNA, posttranscriptional regulators of tissue development and function, are hypothesized to play a role during these processes. The goal of this study was to profile the expression of microRNA (miRNA) in the corpus luteum (CL) of Holstein cows at two time points of the estrous cycle (early-cycle (Day4) and midcycle (D9-12); day0= day of estrus) in order to investigate their role in regulating CL development and function.

overall_design:
Sample size = 6 animals and two time points (3 animals per time point).
The aim was to compare the expression of miRNA between the early-cycle (Day4) and midcycle (days9-12) CL
The three cows designated for early-cycle time point received an injection of gonadotropin releasing hormone (GnRH; Factrel; Zoetis, Florham Park, NJ) to synchronize the ovulation of a dominant follicle, and were slaughtered 4 days later to collect a day 4 CL.
The three cows designated for midcycle time point were observed after CIDR removal to determine the onset of estrus, and on days 9-12 of the estrous cycle, the CL was collected by culpotomy.

middle: W

first: Courtney

last: Smith

first: Joy

last: Pate


title: Expression data from zebrafish embryos

status: Public on Dec 06 2016

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Zebrafish embryos are sensitive to chemical substance and often used as a in vivo model for enviromental toxicology research.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance

platform_organism:
Danio rerio
synthetic construct

overall_design: Zebrafish embryos were selected at early development stages for RNA extraction and hybridization on Affymetrix microarrays. We tested the expression data of zebrfish embryos treated with  PM2.5

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: Re-expression of fetal IGF2 as a target for hepatocellular carcinoma therapy

status: Public on Nov 03 2016

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Non-coding microRNAs (miRNAs) mainly regulate the expression of targeted genes by regulating mRNA degradation or repressing their protein translation. MiRNA microarray profiling was then performed on 218 human HCC tumors samples, 10 samples from adjacent cirrhotic non-tumoral tissue, 10 samples from healthy liver and 12 HCC cell lines. In this study we investigated which miRNAs were differentially expressed in HCC compared to cirrhotic non-tumoral tissue and healthy liver.

overall_design: miRNA transcriptomic profile from 218 HCC, 10 Cirrhotic (CH) and 10 considered Normal patients. Also 12 derived Liver cell lines were included

first: A

last: Villanueva

first: I

last: Martinez-Quetglas

first: R

last: Pinyol

first: J

middle: M

last: Llovet


title: Affymetrix SNP array data for ovarian dysgenesis samples

status: Public on Aug 18 2016

city: Jerusalem

first: Ephrat

last: Levy-Lahad

address: Shmu'el Bait 12

institute: Shaare Zedek Medical Center

summary:
Ovarian development and maintenance are poorly understood, but diseases affecting them can offer insights into their underlying mechanisms. XX-female gonadal dysgenesis (XX-GD) is a rare, genetically heterogeneous disorder characterized by underdeveloped, dysfunctional ovaries with subsequent lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism. We used SNP arrays to perform homozygosity mapping in order to detect informative genomic regions which are homozygous and shared among affected individuals. This analysis identified genomic regions in which the mutated gene causing the XX-GD phenotype in the affected individuals may reside.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

overall_design: Homozygosity mapping of Affymetrix 250K SNP arrays was performed for 2 female cousins affected with XX-Ovarian dysgenesis.

first: Sharon

last: Zeligson

first: Paul

last: Renbaum

first: David

last: Zangen

first: Ariella

last: Weinberg-Shukron


title: Microarray Analysis of chemosensitivity in Hypopharyngeal Squamous Cell Carcinoma

status: Public on Aug 16 2016

first: Jugao

last: Fang

address: No. 1 Dongjiao Min Xiang, Dongcheng District

institute: Capital University of Medical Sciences attaches to Beijing Tongr

summary: OBJECTIVE: To investigate the differentially expressed genes and miRNAs related to the chemosensitivity of hypopharyngeal squamous cell carcinoma （HSCC）by microarrays and miRNA arrays.   METHODS: 1. A total number of 21 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (12 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis  2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.  3. Prediction and analysis of target genes of differentially expressed miRNAs: TargetScan, PITA and microRNAorg methods were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. Considering the result of microarrays, the intersection of the predicted target genes and the genes screened by microarrays would be analyzed by bioinformatics, which were considered as genes regulated by different miRNAs.  RESULTS: 1. Analyzed by microarrays, there were 1579 genes significantly related to the sensitivity to chemotherapy; Among these 1579genes, 815 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 764 presented the contrasting pattern.   2. Analyzed by miRNA arrays, there were 24 genes significantly related to the sensitivity to chemotherapy; Among them, 6 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 18 presented the contrasting pattern. TargetScan, PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. There were 613 putative target genes corresponding to the 24 significant miRNAs. Among them, six genes(MAPK14, ADCY1, GSTM4, CDC42, JUN, GPX6) were statistically and biologically different related to the sensitivity to chemotherapy. And among the 24 significant miRNAs, miR-193b-3p、miR-211-3p、miR-4253、miR-4496、miR-6738-5p could regulate them.  CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in hypopharyngeal squamous cell carcinoma by microarrays and miRNA arrays. The result will contribute to the understanding of the molecular basis of hypopharyngeal squamous cell carcinoma and help to improve diagnosis and treatment.

first: Haizhou

last: Wang

first: Meng

last: Lian


title: miRNA expression in different tissues from different breeds of chicken

status: Public on Sep 01 2016

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

institute: South China Agricultural University

summary: Affymetrix GeneChip miRNA Array was used to globally identify different expression miRNAs in hypothalamus, liver, breast muscle and abdominal fat between commercial broilers and indigenous chickens at seven-week old with hypertrophic pectoral muscle or normal pectoral muscle.

overall_design: A total of 24 microarrays were performed on 4 tissues with 3 replications from 2 different breeds at the 7-week old age.

first: Qinghua

last: Nie


title: miRNA expression profiling in neural differentiated mouse embryonic stem cells (mESCs) under exposure to sodium valproate and sodium arsenite

status: Public on Aug 01 2016

city: Baltimore

first: Lena

last: Smirnova PhD

state: MD

address: 615 North Wolfe St

department: School of Public Health

institute: The Johns Hopkins University

summary:
Studying chemical disturbances during neural differentiation of mES cells has been established as an alternative in vitro testing approach for the identification of developmental toxicants. miRNAs represent a class of small regulatory RNA molecules, which bind to target mRNAs thereby repressing their translation. Many studies have shown an essential role of miRNAs in regulation of gene expression during development and ESC differentiation. Thus, neural differentiation of ESC in vitro allows investigating the role of miRNAs in chemical-mediated developmental toxicity. We analyzed the expression of miRNAs and transcriptomics changes during neural differentiation of mESC exposed to the developmental neurotoxicant sodium valproate (VPA).  A total of 110 miRNAs and 377 mRNAs were identified differently expressed in neural differentiating mES cells under VPA treatment (300µM) compared to solvent control on day 16 of differentiation. Analysis of miRNA expression revealed that valproate switches the lineage specification from neural to myogenic differentiation (upregulation of muscle-enriched miRNAs mir-206, mir-133a and mir-10a and downregulation of neuro-specific miRNAs mir-124a, mir-128 and mir-137). The findings on the miRNA level could be confirmed on mRNA level (induction of expression of myogenic regulatory factors (MRFs) as well as muscle specific genes (Actc1, calponin, myosin light chain, asporin, decorin) and repression of genes involved in neurogenesis (Otx1 and 2, Zic3, 4, 5)) as well as morphologically by immunocytochemistry. The observed results were VPA specific and most probably due to inhibition of histone deacetylase (HDAC) activity of VPA for two reasons: (i) we did not observe any induction of muscle specific miRNAs in neural differentiating ES cells exposed to the unrelated developmental neurotoxicant sodium arsenite; (ii) expression of muscle specific mir-206 and muscle enriched mir-10a was similarly increased in cells exposed to a structurally different HDAC inhibitor, trichostatin A (TSA). Furthermore, using our in vitro cell system we could confirm an aberrant expression of known VPA target genes and genes involved in neural tube closure. We conclude that miRNA expression profiling is a suitable molecular endpoint for developmental neurotoxicity. Observed lineage shift into myogenesis, where miRNAs play a significant role, could be a major developmental neurotoxical mechanism of VPA.
We used microarray approach to identify altered miRNA expression in neural differentiated mES cells exposed to two known developmental neurotxicants and epigenetic active substances, sodium valproate (VPA) and sodium arsenite (As)

overall_design: mES cells line W4 were induced to differnetiate to neurons under exposure to VPA and As for 16 days. RNA for microarrays was collected on day 16 of differentiation from three biological replicates of solvent controls (PBS was used as a solvent for VPA and H20 for As) or substance treated cells.

last: Smirnova

first: Michael

last: Bonin


title: MicroRNA Expression data from transgenic mice

status: Public on Jul 15 2016

city: Taipei

first: Kung-Hao

last: Liang

address: Tung Hwa North Road

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
This study aimed to evaluate the change of liver status in the presence of hepatitis B viral proteins
We evaluated the microRNA expression profiles of liver tissues of transgenic mices carrying wild type or mutant viral surface proteins

overall_design: We checked the differential microRNA expressions in different transgenic mice, each with three biological replicates


title: miRNAs array analysis of HepG2 cells under oxidative stress

first: Yuan

last: LUO

state: Beijing

address: No. 30 Fucheng Road, Haidian District

institute: Air Force General Hospital, PLA, P. R. China

summary:
Some latest studies have cast new light on the complicated interplay network between inflammation, oxidative stress, cancer and microRNAs. Although publications in the past decade have described the involvement of miRNAs in almost all kinds of physiological and pathological processes, little is known about the specific mechanisms of the interaction between oxidative stress and miRNAs.
We examined the changes of the miRNAs expression profiles in HepG2 cells upon treatment with different concentrations of H2O2.

overall_design: HepG2 cells were seeded in 10 cm dishes and cultured as usual until they reached 80% confluence. To verify whether miRNAs could be modulated by oxidative stress, we stimulated HepG2 cells with H2O2 to develop a cell model of oxidative stress. Specifically, we chose 30 and 600 μM of H2O2 as low and high concentration for miRNAs profiling, respectively. After stimulating HepG2 cells for 24 h, H2O2-induced changes in the miRNAs expression profiles were analyzed by the Affymetrix microRNA 4.0 Array.

first: Yaping

last: TIAN


title: Screening and validation of lncRNAs and circRNAs as miRNA sponges [cell lines, miRNA-2_0]

status: Public on Jul 06 2016

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.

overall_design: The expressions of miRs were examined in HEK-293, HUVEC and Hs68 cells.

first: Giuseppe

last: Militello


title: Screening and validation of lncRNAs and circRNAs as miRNA sponges [siRNA, miRNA-2_0]

overall_design: The expressions of miRs were examined in HEK-293 cells that were LINC00324- or LOC400043-silenced using siRNA.


title: Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer  [Affymetrix]

status: Public on Jun 30 2016

city: HOUSTON

first: Hyun-Sung

last: Lee

address: One Baylor Plaza

institute: BAYLOR COLLEGE OF MEDICINE

summary: Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge.  We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics.  We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns.   We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC.

overall_design:
Clinical study
ESCC tumor samples vs. ESCC normal samples

first: Yong-Sun

first: Ju-Seog


title: Towards a new standardized method for circulating miRNAs profiling in clinical studies: Interest of the exogenous normalization to improve miRNA signature accuracy

city: Caen cedex 05

first: Christophe

last: DENOYELLE

address: 3 Avenue général Harris BP 5026

department: Centre de Lutte Contre le Cancer François Baclesse

country: France

institute: Université de Caen Normandie

summary:
In our study, we proposed first to reduce the profiling variability by selecting the miRNA isolation kit offering the higher input RNA concentration for microarray profiling and second to control the profiling step variability by adapting the widely used exogenous normalization of the validation step to the profiling one. The new strategy proposed could improve the overlap between independent studies using microarray profiling, but also potentially with other high-throughput methods, to finally identify pertinent miRNA signatures in biofluids.
Because this project is only a methodological study, the cohort of serum and plasma samples used in this study were all obtained from patients with FIGO stages III/IV serous ovarian cancer.   This study was approved by the ethics committee Nord-Ouest III [CPP N° 2011-02] and national authorities (AFSSAPS N°B110260-20). Plasma samples were obtained from the Comprehensive Cancer Center F. Baclesse biological collections that have been declared (# DC-2010-1243) to the French Ministry of Research and Superior Education. Prior to scientific use of samples and data, patients were appropriately informed and asked to consent in writing, in compliance with French and European regulations.

overall_design: 13 samples of serum from patients with homogeneous clinical status were used to purify circulating miRNAs. Purified miR levels were assessed by qPCR and by hybridization on Affymetrix miRNA V4 arrays. Arrays data were normalized by different methods. Comparison between the data from qPCR and arrays were performed to identify the best normalization approach.

first: N

last: Vigneron

first: M

last: Meryet-Figuiere

first: A

last: Guttin

first: J

last: Issartel

first: B

last: Lambert

last: Briand

last: Leconte

first: S

last: Lheureux

last: Clarisse

last: Krieger

first: F

last: Joly

first: P

last: Gauduchon

first: L

last: Poulain

first: C

last: Denoyelle


title: Functional gene expressions of continuously cultured Nitrosomonas europae after ZnO nanoparticles exposure and recovery incubation

status: Public on Jun 24 2016

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

institute: Southeast University

summary: To further explore the biotoxicity mechanisms of zinc oxide nanoparticles (ZnO NPs) and the recovery strategies of the accordingly impaired Nitrosomonas europaea (N. europaea, ATCC 19718) cells, a genome-sequenced model ammonia-oxidizing bacterium (AOB) commonly detected in the activated sludge of biological wastewater treatment plants, whole-genome microarray analysis was applied to retrieve the induced transcriptional responses, after their physiological and metabolic activities were revealed.

overall_design: The whole-genome expressions were measured after exposure to 50 ppm ZnO NPs and 12-hrs recovery incubation when the ammonia removal rate (ARA) declined by 10% in the chemostat bioreactor. Three independent experiments were performed for each experiment.

first: Ran

last: Yu


title: Expression data from 9-day-old rat Sertoli cells and MBP-treated rat Sertoli cells

status: Public on Jun 09 2016

city: Shanghai

first: Xiaoqin

last: Yin

state: Shanghai

address: No. 355 Luding Road, Shanghai 200062, P.R.China.

department: Shanghai Children’s Hospital

institute: School of medicine, Shanghai Jiao Tong University

summary:
Low-dose MBP can stimulated 9-day-old Sertoli cells proliferation and activated proliferation related signal pathway.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Rat Sertoli cell were selected from rat testis for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the differentially expressed genes and miRNAs in 0.1mM MBP and  solvent treated Sertoli cells, respectively.

first: Dongmei

last: Li


title: microRNA expression profile related to lymph node status in women with stage grade 1-2-3 endometrial cancer

status: Public on Jun 01 2016

city: Paris

first: Geoffroy

last: CANLORBE

address: 4, rue de la Chine

department: Department of Obstetrics and Gynaecology

institute: Tenon University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), University Pierre and Marie Curie, Paris 6

summary:
The aim of this study was to evaluate whether microRNA profiles of grade 1 – 2 or 3 endometrioid adenocarcinomas can be related to nodal status and used as a tool to adapt surgical staging in early-stage EC.
MicroRNA expression were assessed in twelve formalin-fixed paraffin-embedded (FFPE) EC primary tumors with positive lymph node and in 36 FFPE EC primary tumors with negative lymph node, matched for grade, stage and lymphovascular space involvement status.

overall_design: Total RNA was extracted using the miRNeasy FFPE Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions. The 36 specimens of negative LN status were pooled by 3 in accordance with the matching criteria. Microarray analysis was conducted on 48 distinct specimens: Twelve specimens with positive LN and 36 specimens with negative LN. Microarray hybridization on miRNA 4.0 chips (Affymetrix) was conducted at the genomic platform of the Institut Cochin, Paris.

last: Canlorbe

first: Céline

last: Méhats

first: Sébastien

last: Jacques


title: The impact of tacrolimus on hepatic mirnas

status: Public on May 24 2016

city: Hangzhou

first: Qi

last: Ling

state: Zhejiang

address: 79 Qingchun road

department: Suegery

institute: Zhejiang University

summary:
we aimed to evaluate the impact of tacrolimus on the expression of hepatic mirnas. HepG2 cells were treated with 0, 5, 20 ng/ml tacrolimus and RNA was extracted.
We used microarrays to detail the global programme of mirna expression.

overall_design: HepG2 cells were treated with 0, 5, 20 ng/ml tacrolimus for 24 hrs and RNA was extracted. The expression of mirnas were compared between low-dose tacrolimus group and control, high-dose tacrolimus and control.

first: Shusen

last: Zheng


title: SNAI1 overexpression effect on MCF-10A mammary epithelial cell line (miRNA)

status: Public on May 27 2016

first: Zhihua

last: Liu

address: NO.17 Nanli, Panjiayuan Road, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
SNAI1 is a key transcription factor in the EMT process, that is considered as the initial step of metastasis. The microRNAs(miRNAs) invovled in SNAI1-induced EMT may play important roles in regulating the process of metastasis.
We used microarrays to establish the miRNAs both upregulated and downregulated in SNAI1-induced EMT process.

overall_design: MCF-10A mammary epithelial cells were transfected with either SNAI1 (L) or a control vector (C) were harvested for RNA extraction and hybridization on Affymertix microarrays. 3 biological repetitions were done for microarray analysis.

first: Yun

last: Zhan


title: Expression data for xenograft tumor treated with IL-6 or siCUL4A.

status: Public on May 16 2016

city: Changsha

first: Weiguo

last: Ren

state: Hunan

address: No.216, Tongzipo, Yuelu District

institute: hird Xiangya Hospital of Central South University

summary: The miRNAs expression was altered with the treatment with IL-6 or siCUL4A in xenograft tumor of human colon adenocarcinoma cell line HCT116 cells. And various miRNAs induced by IL-6 also may contribute to tumor growth .

overall_design: Using a Affymetrix® GeneChip® miRNA Arrays platform, we analyzed the  miRNA expression levels in tumorous tissues of xenograft tumor that were treated with IL-6 or siCUL4A.

first: Xiayu

last: LI

first: Jian

last: Ma

first: Shourong

last: Shen


title: Epitope mapping of a monoclonal antibody directed against Neisserial Heparin Binding Antigen by peptide microarray

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

institute: GSK Vaccines

summary: The aim of the study was to determine the epitope targeted by 31E10/E7 mouse monoclonal antibody (mAb) and the cross-reactivity to linear peptide epitopes of 10 different Neisserial Heparin Binding Antigen (NHBA) variants. mAb 31E10/E7 was diluted at 1:200 and incubated on a custom PepStar Peptide Microarray platform printed with 560 different peptides in three independent experiments.

overall_design: A panel of 560 peptides (15-mer overlapping peptides with an offset of 4 amino acids) covering the entire sequence of ten different NHBA variants (p1, p2, p3, p5, p10, p17, p18, p20, p21 and p29) were printed in triplicate on a custom PepStar Peptide Microarray. Process-control peptide (GGSGGGSDYKDDDDK) and mouse IgG were distributed in each array copy as controls. mAb 31E10/E7 was profiled for anti-mouse IgG specific analysis of reactivity to the peptide epitopes

first: Marco

last: Bruttini


title: Epitope mapping of a monoclonal antibody directed against Neisserial Heparin Binding Antigen

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

platform_organism:
Neisseria meningitidis
Neisseria meningitidis serogroup B

overall_design: Refer to individual Series


title: Reconstructing gene regulatory networks of tumorigenesis [SNP]

status: Public on May 13 2016

city: Illkirch; Strasbourg

first: Valeriya

last: Malysheva

address: 1 rue Laurent Fries

institute: IGBMC

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

summary: The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. These TFs are involved in the regulation of divers processes, including cell differentiation, immune response and establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes, which are not only co-regulated but also functionally related. Further decortication of TF targets enabled us to define potential key regulators of cell transformation, which are engaged in RNA metabolism and chromatin remodelling. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of gene regulatory networks that are altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

overall_design: Affymetrix SNP arrays (250K) were performed according to the manufacturer's directions on DNA extracted from BJ, BJEL and BJELM cells

middle: A

last: Mendoza-Parra

first: Mohamed

last: Ashick

last: Saleem

first: Hinrich

last: Gronemeyer


title: Possible Genetic Basis for Failure of a Robotic-Assisted Laparoscopic Sacrocolpopexy

city: Basking Ridge

first: Deanne

last: Taylor

state: NJ

address: 140 Allen Road

institute: Reproductive Medicine Associates of New Jersey

summary: Sacrocolpopexy has been dubbed the “gold standard” repair for apical pelvic organ prolapse (POP).  This study sought to determine a genetic cause for sacrocolpopexy failure by comparing genotypes from 10 women who suffered from early POP reoccurance after sacrocolpopexy surgery, versus 40 randomly selected women with long term success after the same procedure.  We objectively defined early overt failure after robotic-assisted laparoscopic sacrocolpopexy as having a pelvic organ prolapse quantification system examination (POP-Q) of stage III or IV occurring in more than one compartment within six months after surgery.  All medical records identified during this process were then reviewed by a panel of urogynecology attendings and fellows to select patients who were truly clinical outliers.    By this method we identified 10 patients (cases) who experienced early overt surgical failure.  We also randomly selected 40 controls from our research database which includes greater than 500 patients who underwent robotic-assisted laparoscopic sacrocolpopexy during the same time period and had been objectively and subjectively assessed for ≥ 12 months with surgical success at ≥ 12 months that did not  undergo prolapse re-operation or re-treatment.  Demographics and peri-operative details were compared between cases and controls.  Exclusion criteria for controls included use of other graft material besides polypropylene mesh, prior surgery for prolapse involving graft material, and conversion to laparotomy.  DNA from the 10 cases and 40 controls was isolated from buccal swabs and genotyped on a single nucleotide polymorphism (SNP) array that contains 250,000 markers (NspI 250K SNP array, Affymetrix, Santa Clara, CA).  All women in this study identified as Caucasian.    All subjects provided written informed consent to study participation and data release.   This was a case-control study approved by the Institutional Review Board at the Atlantic Health System in Morristown New Jersey (R11-10-004).

overall_design: This case-control study compared single genotypes of 10 cases to 40 controls. All subjects were identified as Caucasian. Cases were women who experienced early overt POP recurrence after robotic sacrocolpopexy, and controls were randomly selected women with long term success after the same procedure.

first: Sarah

last: St. Louis

first: Richard

last: Scott Jr.

first: Christa

last: Lewis

first: Charbel

last: Salamon

first: Jennifer

last: Pagnillo

first: Nathan

last: Treff

first: Patrick

last: Culligan


title: Circulating let-7 levels in plasma correlate with hepatic fibrosis progression in chronic hepatitis C

status: Public on May 01 2016

city: North Bethesda

first: Kentaro

last: Matsuura

state: Maryland

address: 5411 McGrath Blvd.

department: Department of Transfusion Medicine

institute: National Institutes of Health

summary:
Circulating microRNAs show great promise as novel noninvasive markers for the state of disease progression in chronic hepatitis C (CHC).
We performed circulating miRNA expression analysis to identify circulating miRNAs associated with disease progression in the natural course of chronic HCV infection using a prospectively followed and well-characterized HCV-infected blood donor cohort.

overall_design: We analyzed miRNA expression patterns of human mature miRNAs in plasma in 48 subjects including 16 healthy controls, 16 CHC patients with mild fibrosis: Ishak fibrosis score 0, and 16 with significant fibrosis: Ishak fibrosis score 3-6 using Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Santa Clara, CA).

first: Havey

last: Alter


title: miRNA expression of myeloma cell lines under hypoxia

status: Public on Apr 29 2016

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

summary: By using world wildly used myeloma cell lines (RPMI8226, KMS-11, KMS-12BM, and MM.1S), we conducted whole miRNA screening against the cells that were subjected by chronic hypoxia condition.

overall_design: We compared four myeloma cell lines (RPMI8226, KMS-11, KMS-12BM, and MM.1S) cultured under hypoxia with cultured under normoxia (48hr) to find new important miRNAs of myeloma.

first: Hiroyuki

last: Tagawa


title: Epitope mapping of a monoclonal antibody directed against Neisserial Heparin Binding Antigen by protein microarray

first: Erika

last: Bartolini

summary: The aim of the study was to determine the epitope targeted by 31E10/E7 mouse monoclonal antibody (mAb). mAb 31E10/E7 was diluted at 1:2000 and incubated on a non-commercial Protein Microarray platform printed with NHBA specific recombinant protein fragments and full length NHBA of different variants.

overall_design: mAb 31E10/E7 was profiled for anti-mouse IgG specific analysis of reactivity to the spotted proteins. Three independent experiments were performed.

last: Bruttini


title: miRNA expression of myeloma patient samples under hypoxia

summary: We conducted whole miRNA screening against the MM patients bone marrow (sorted by CD38++) cells that were subjected by chronic hypoxia condition.

overall_design: We compired four primary myeloma samples cultured under hypoxia with cultured under normoxia (48hr) to find new important miRNAs of myeloma.


title: Effects of bedrest and hypoxia on human skeletal muscle miRNA expression

status: Public on May 04 2016

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary:
The present study concerns the effects of 21 days of sustained recumbence (bedrest) and hypoxia, alone and in combination, on skeletal muscle microRNA expression.
14 male subjects participated in 3 experimental campaigns in a counterbalanced fashion: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulatory confinement (HAMB), both hypoxic conditions with FO2 = 0.141 and PIO2 = 90 ± 0.4 mmHg, equivalent to an altitude of ≈ 4000 m). Each intervention (bedrest or ambulatory confinement) lasted 21 days, and the interventions were separated by a 4-month wash-out/recovery period. The order in which each subject undertook the interventions is denoted 'Intervention_order'  Throughout both bedrest interventions, each subject remained in a horizontal position at all times. He was allowed one pillow for the head and to occasionally lean on an elbow while eating or being transferred to a gurney. Muscular exercise was prohibited. During the HAMB confinement, each subject was allowed to move freely within the hypoxic area. To mimic a normal level of physical activity subjects performed 30 minutes of low-to-moderate-intensity exercise twice daily.    Muscle samples from Vastus lateralis.

overall_design: Biospy material sufficient for anlaysis was avialable for 72 observations, another 4 were excluded due to technical problems with the array hybridisation, leaving in total 68 observations.