title: Affymetrix SNP array data for recurrent deletion in 19p in DLBCLs and BLs

status: Public on Dec 23 2013

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

summary: A single nucleotide polymorphism (SNP)-chip analysis of 98 cases of aggressive B-cell lymphomas revealed a recurrent deletion at 19p13 in 9 of the cases. Six further cases with deletions encompassing this region were found in array-comparative genomic hybridization data of 295 aggressive B-cell lymphomas from a previous study. Three cases even showed a homozygous deletion, suggesting a tumor suppressor gene in the deleted region. Two genes encoding members of the tumor necrosis factor superfamily were located in the minimally deleted region, i.e. TNFSF7 and TNFSF9. As no mutations were found within the coding exons of the remaining alleles in the lymphomas with heterozygous deletions, we speculate that the deletions may mostly function through a haploinsufficiency mechanism. The cases with deletions encompassed both diffuse large B-cell lymphomas and Burkitt lymphomas, and a deletion was also found in a Hodgkin lymphoma cell line. Thus, TNFSF7 and TNFSF9 deletions are recurrent genetic lesions in multiple types of human lymphomas.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from whole tissue. Copy number and LOH analysis of 500K SNP/250K SNP arrays was performed on 9 cases of aggressive B-cell lymphoma harboring the described deletion. Genotyping was performed using the BRLMM-algorithm. 20 normal references (10 of those hybridized to nsp-chips) extracted from healthy blood donors, used as normals in the analysis in addition to the HapMap references provided by Affymetrix, are included in the set.

first: René


title: MicroRNA expression data from high and low invasive A549 human lung adenocarcinoma cells

status: Public on Dec 08 2013

city: Kuala Lumpur

first: ho

middle: chai

last: san

state: Wilayah Persekutuan

address: Jalan Universiti

department: Department of Genetics and Molecular Biology

country: Malaysia

institute: University of Malaya

summary:
The major cause of cancer-related deaths in lung cancer patients is commonly attributed to its ability to metastasize to distant organs such as the bone, brain, liver and adrenal glands. The dysregulation in miRNA expression is believed to contribute toward the initiation and progression of metastasis through their capability to regulate target genes.
In this study, two NSCLC sub-cell lines possessing opposing migration and invasion properties were established using serial transwell invasion assays, followed by miRNA microarray to obtain the overview of miRNA expression as well as identify important playes in metastasis.

overall_design: High and low invasive A549 sub-cell lines were established from heterogeneous parental population and selected through seven generations. Three replicates were used for RNA extraction and miRNA microarray.

first: C

middle: S

last: Ho

first: S

middle: H

last: Yap

first: N

last: Phuah

first: L

middle: A

last: In

last: Hasima


title: microRNA expression in oral keratinocytes

status: Public on Nov 28 2013

city: Sheffield

first: Keith

middle: David

last: Hunter

state: South Yorkshire

address: Claremont Crescent

department: School of Clinical Dentistry

country: United Kingdom

institute: University of Sheffield

summary: This was a hypothesis generating experiment to look at miR expression in a range of oral keratinocytes, including normal, precancer and oral cancer samples.  The cells were cultures as per standard protocols (duplicate cultures) before assessment on the Affy miRNA array (1.0)

overall_design: one normal oral keratinocyte, one precancer, and 2 cancer samples, all in duplicate

middle: D

first: Craig

last: Murdoch

first: Daniel

middle: W

last: Lambert


title: Expression data from miRNAs in colorectal cancer tissues with and without liver metastasis

status: Public on Dec 10 2013

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

country: China

institute: Sun Yat-sen University Cancer Center

summary: The purpose of this study is to identify miRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 39 miRNAs were identified to be differentially expressed between 16 primary CRC tissues with liver metastases and 16 CRC tissues without liver metastases from 32 patients by Affymetric miRNA microarrays.

overall_design: 16 coloretcal cancer tissues with liver metastasis and 16 colorectal cancer tissues without liver metastasis were included in this study for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the differentially expressed miRNAs between colorectal cancer tissues with and without liver metastasis.

first: Rui-hua

last: Xu


title: Direct and indirect targets of the E2A-PBX1 leukemia-specific fusion protein

status: Public on Nov 23 2013

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

state: California

address: 1450 3rd Street, MC 0520

department: Epidemiology and Biostastics

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by genome tiling array

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: SNP arrays to detect copy number changes in t(1;19) E2A-PBX1 positive leukemias

summary:
The experiment was to detect the identity and range of copy number alterations in a subtype of childhood leukemia defined by t(1;19) translocaitons
The data will be presented in the manuscript "Direct and indirect targets of the E2A-PBX1 leukemia-specific fusion protein" to be published in PLOS One, authors Christofer Diakos, Yuanyuan Xiao, Shichun Zheng, Leo Kager, Michael Dworzak, Joseph L. Wiemels

overall_design: A series of leukemia DNAs were subjected to Affymetrix SNP 5.0 (Nsp) arrays

first: Christofer

last: Diakos


title: SNP array analysis of single cell genomes

status: Public on Dec 04 2013

city: Charlottesville

first: Michael

middle: J

last: McConnell

state: VA

address: 1340 Jefferson Park Ave

institute: University of Virginia

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

summary:
This study (McConnell, et al. Science 2012) used both SNP array and sequencing data to examine copy number variation in neuronal genomes.
Encolsed here are the SNP Array data from the 42 fibroblasts, 19 human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs), and 40 hiPSC-derived neurons that were reported in the manuscript.

overall_design: Copy number analysis was performed on .CEL files using Partek Genomics Suite with a custom single cell reference file.

middle: R

last: Lindberg

first: Kristen

last: Brennand

first: Julia

middle: C

last: Piper

first: Thierry

last: Voet

first: Chris

last: Cowing-Zitron

first: Svetlana

last: Shumilina

first: Roger

last: Lasken

first: Joris

last: Vermeesch

first: Ira

middle: M

last: Hall

first: Fred

last: Gage


status: Public on Nov 26 2013

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: The yeast expression vectors used to express AAE13 was constructed as follows: AAE13 (At3g16170) was amplified from the vector pENTR-AAE13. The amplified product was cloned into pCR®8⁄GW⁄TOPO® (Invitrogen). The resulting plasmid was combined with the Advanced Gateway destination vectors pAG305GPD-ccdB (Addgene, Boston, MA) in an attL X attR recombination reaction to generate the vectors pAG305GPD-AAE13. The integrating vector pAG305GPD-AAE13 was introduced into WAT11, which was also transformed empty vector pAG305GPD-ccdB as control (B1, B2, B3 and B4). The transgenic and control yeast cells were cultured in SD-drop out medium at 30 °C under shaken conditions, malonate was fed into cells at final concentration 0.2 mM when the value of OD600 reached at 0.1. The cells were harvested at mid-log phase.

overall_design: Two-condition experiment, Transgenic yeast (pAG305GPD-AAE13) vs. control yeast (pAG305GPD-ccdB). Biological replicates: 4 control replicates, 4 transgenic replicates.

first: Oliver

first: Yechun

last: Wang


title: MicroRNA expression of clear cell papillary renal cell carcinoma

status: Public on Oct 23 2013

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

institute: University of Oxford

summary: to see if CCPRCC has a distinct miRNA profile from CCRCC and PRCC

overall_design: miRNA v.2.0 chips on two portions of five CCPRCC cases (total 10 samples), three portions of two CCRCC cases and a further three CCRCC cases (total 9 samples), and five type I PRCC samples; a total of 24 samples

first: Charles

last: Lawrie


title: Affymetrix SNP array data for oral squamous cell carcinoma and oral dysplasia samples

status: Public on Oct 22 2013

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: medical

country: Japan

institute: Miyazaki university

summary: The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. Oral carcinogenesis is a multifactorial process involving numerous genetic changes that affect the activity of oncogenes, tumor suppressor genes and other classes of disease-related genes.Therefore, to identify the responsive genes for progression of oral dysplasia or OSCC, we here performed CGH analysis to DNA from oral dysplasia and OSCC by microdissection

overall_design: Copy number analysis of Affymetrix 250K SNP arrays was performed for 8 oral dysplasia samples, 8 oral squamous cell carcinoma samples, using microdissection

first: Kentarou

last: Nagai

first: Kazuhiro

last: Morishita


title: miRNA expression data from post-partum dairy cattle (Holstein Friesian) liver

status: Public on Oct 25 2013

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

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

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary:
High yielding dairy cattle undergo a state of NEB (negative energy balance) during the post-partum period when energy demand for lactation and maintenance exceeds energy intake. During this period in order to counteract NEB the liver under goes extensive metabolic and physiological change resulting in alteration in hepatic genes and miRNAs expression.
We used Affymetrix Multispecies miRNA-2_0 Array with miRBase version 15 coverage to assess the liver miRNA expression in SNEB (severe NEB)  and MNEB (mild NEB) Holstein Friesian cattle during the post-partum period.

overall_design: A NEB model of Holstein Friesian was established such that 12 post-partum cattle were randomly assigned to MNEB and SNEB groups depending on different feeding and milking regimes

first: Attia

last: Fatima

first: Sinead

last: Waters

first: Padraic

last: O'Boyle

first: Cathal

last: Seoighe


title: miRNAs expression of soleus response to simulated microgravity

status: Public on Nov 05 2013

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

institute: Astronaut Research and training Center

summary:
Identification of gravisensitive miRNAs expression in rat soleus muscle exposed to 7 and 14 days of Hindlimb suspension (HS) simulated microgravity. Microgravity causes muscle atrophy possibly due to muscle wasting overtake regeneration. Results provide insight into the molecular mechanisms regulating muscle atrophy.
The expression of 23 out of 174 miRNAs was found to change at least 2-fold of 7 and/or 14 days of TS. By using real-time PCR assays, we verified the microarray data using some of the expected genes.

overall_design: The tissue was collected from Sprague-Dawley rats (8 weeks of age) subjected to 7, 14days of TS. miRNA expression profile was determined in three groups: control (CN), TS for 7 days (TS-7), and TS for 14 days (TS-14).Three miRNA microarray chips were analyzed for mixture of four samples of each of the three groups.

first: H

last: Xu

first: F

last: Wu

first: Z

first: Y

last: Li


title: Analysis of circulating microRNAs in adrenocortical tumours

status: Public on Nov 19 2013

city: Budapest

first: Diana

middle: Rita

last: Szabo

address: Szentkirályi u. 46

country: Hungary

institute: Semmelweis University

summary: Differential diagnosis of adrenocortical adenoma and carcinoma is of pivotal clinical relevance, as the prognosis and clinical management of benign and malignant adrenocortical tumours is entirely different. Circulating microRNAs are promising biomarker candidates of malignancy in several tumours. In the present study we investigate circulating microRNAs in adrenocortical tumours and to evaluate their potential applicability as biomarkers of malignancy.

overall_design: For the miRNA profiling, 8 preoperative plasma samples obtained from patients with adrenocortical adenomas and carcinomas and were studied by microarray.

first: D

first: P

first: K

last: Racz

last: Igaz


title: miRNA expression data from human cell lines (Panc1 cells)

status: Public on Nov 20 2013

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary: The experiment aims to identify miRNAs that are regulated in response to TRAIL R1 si-RNA and TRAIL R2 si-RNA. The overall aim of the study was to identify mechanisms by which TRAIL death receptors may contribute to malignancy via inhibition of let-7 maturation.

overall_design: Comparison of TRAIL R1 si-RNA vs. control si-RNA and comparison of TRAIL R2 si-RNA vs. control

first: R

last: Hasler


title: Transcriptomic analysis of a nickel-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

status: Public on Sep 19 2013

city: TOULOUSE

first: CEREN

last: ALKIM

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

country: France

institute: INRA

summary: Nickel-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. The reference strain which was used to select this nickel-resistant mutant could not grow even at 0.5 mM NiCl2 whereas this mutant was shown to be resistant upto 5.3 mM NiCl2 concentration. Whole-genome microarray analysis might be promising to identify the nickel resistance mechanisms in the yeast cells.

overall_design: The reference Saccharomyces cerevisiae strain and the nickel-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which correspond to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

first: G

last: Küçükgöze

first: C

last: Alkım

first: U

last: Yılmaz

middle: I

last: Kısakesen

middle: P

last: Cakar


title: miRNA expression in primary renal carcinomas, subgrouped based on HIF1α expression

status: Public on Sep 30 2013

city: philadelphia

first: lijoy

last: mathew

state: pa

address: 438 brb II/III, curie blvd

institute: university of pennsylvania

summary:
Clear cell renal cell carcinoma (ccRCC), the most common type of renal cancer is often associated with inactivation of the tumor suppressor gene von-Hippel Lindau (VHL), leading to stable expression of hypoxia inducible factors, HIF1α and HIF2α. Although HIF1α functions as a tumor suppressor gene, majority of ccRCCs constitutively express HIF1α, stratifying VHL-deficient ccRCCs into groups which express either both HIF1α and HIF2α (H1H2) or HIF2α exclusively (H2).
MicroRNA (miRNA) profiling performed in these two ccRCC subtypes to identify novel molecular mechanisms.

overall_design: ccRCCs were classified into H1H2 and H2 subtypes by immunohostochemical staining of H1F1α  and  H1F2α expression. Five H1H2 tumor samples and eight H2 tumor samples were used for the study. Matched adjacent normal renal tissues were used as respective controls.

first: Priti

last: Lal

first: Celeste

last: Simon


title: microRNA profiling of lung adenocarcinomas, induced by cRaf overexpression in lung epithelium

status: Public on Sep 11 2013

city: Trento

first: Valerio

last: Del Vescovo

state: Trentino Alto Adige

address: via delle Regole 101

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

platform_organism:
Mus musculus
synthetic construct


title: Id1 knockdown in primary human glioma stem cells

status: Public on Sep 05 2013

city: Kaifeng

first: Xiong

last: Jin

state: Henan

address: Jin Ming Avenue

department: School of Pharmacy

institute: Henan University

summary: Abnormal activation of stemness factors is a crucial signature of cancer stem cells (CSCs), a highly tumorigenic subpopulation in malignant tumors. However, it is unclear whether multi-signaling pathways are activated in CSCs, as like normal stem cells. I would like to report that an inhibitor of differentiation 1 (ID1) activates intracellular multi-signaling involved in proliferation,  genesis, and maintenance of glioma stem cells (GSCs) by suppression of Cullin3, an E3 ubiquitin ligase that degrades Cyclin E and components of SHH and WNT signaling. ID1 inhibits BMP-dependent differentiation of GSCs by activation of BMPR2-targeting miR17/20a. ID1HIGH-Cullin3LOW signature correlates with a poor prognosis of GBM patients with a significant association to gene signatures enriched in EGF, WNT, SHH, and BMP signaling. Combinational inhibition of GSC intracellular multi-signaling network increases tumor-bearing mice survival. These results provide insights on molecular and cellular basis of GSC biology, and also suggest necessity of multi-signaling inhibition for GSCs therapy.

overall_design: Two human primary glioma stem cells (GSCs) such as GSC2 and GSC8 were isolated from two individual primary human glioma specimens.  The GSCs were directly transfected with pSuper-GFP-ID1-shRNA and pSuper-GFP-Scrambled-shRNA using FuGENE 6 reagent (Roche). The RNA extraction in these cells was used to analyze gene expression.

first: Xun


title: The role of the Hog1 and Slt2 MAP Kinases in the regulation of Saccharomyces cerevisiae gene expression upon stress by sulfuric acid

status: Public on Oct 18 2013

city: Recife

first: Rodrigo

middle: Mendonça

last: Lucena

state: Pernambuco

address: Av. Jorn. Aníbal Fernandes

country: Brazil

institute: Federal University of Pernambuco

summary: In our previous work, we had found that Saccharomyces cerevisiae needs of the Hog1 and Slt2 proteins to growth in a low pH environment caused by sulfuric acid, one of the stress factors during the process of ethanol production. Then was performed the gene-wide expression analysis in the hog1∆ and slt2∆ mutants in order to reveal the function of the Hog1p and Slt2p MAP Kinases in the regulation of S. cerevisiae global gene expression upon stress by sulfuric acid.

overall_design: BY4741 strain (Reference) and their derivate mutants hog1∆ and slt2∆ were grown for 1 h in YPD medium pH 2.5 adjusted with concentrated sulfuric acid

first: Lucena

last: Rodrigo

first: Elsztein

last: Carolina

first: Pita

last: Will

first: Paiva

last: Sergio

first: Simões

last: Diogo

first: Morais

last: Marcos


title: microRNA profiling of lung adenocarcinomas, induced by cRaf overexpression in lung epithelium (Affymetrix)

summary:
In this study we analyzed the expression of miRNAs in the lungs of SP-C/c-raf transgenic mice. The transgene is under the transcriptional control of the surfactant protein C (SP-C) promoter and consists of the oncogenically activated NH2-terminal deletion mutant c-Raf-1-BxB.
Overall this study aims at identifying miRNAs regulated in precursor lesions of lung cancer.

overall_design: Affymetrix platform was used to analyze and compare the miRNA expression pattern in RNA extracts derived from two different conditions, i.e. lung of wild type mice and lung of SP-C/c-raf mice expressing the c-Raf-1 transgene. Each gender and condition was tested separately using 6 different individuals from each group: male and female wild type mice (M WT and F WT) and male and female transgenic mice (M c-Raf and F c-Raf).

first: Tatiana

last: Meier


title: Rat Life Cycle Kidney Female Gene Expression Data

status: Public on Jul 31 2013

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

summary: The kidney functions in key physiological processes to filter blood and regulate blood pressure via key molecular transporters and ion channels. Sex-specific differences have been observed in renal disease incidence and progression as well as acute kidney injury in response to certain drugs. Although advances have been made in characterizing the molecular components involved in various kidney functions, the molecular mechanisms responsible for sex differences are not well understood. We hypothesized that the basal expression levels of genes involved in various kidney functions throughout the life cycle will influence sex-specific susceptibilities to adverse renal events.

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

first: Joshua

last: Kwekel


title: Rat Life Cycle Kidney Male Gene Expression Data

summary: The kidney is important for a number of physiological processes including blood filtering, blood pressure regulation and proper excretion of many drugs and xenobiotics. Age is a predisposing condition for susceptibility to chronic kidney disease and progression as well as acute kidney injury that may arise due to the adverse effects of some drugs. Age-related differences in kidney biology, therefore, are a key concern in understanding drug safety and disease progression.  We hypothesize that the underlying suite of genes expressed in the kidney at various life cycle stages will impact susceptibility to adverse drug reactions. Therefore, establishing changes in baseline expression data between these life stages is the first and necessary step in evaluating this hypothesis.

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


title: Distinct Micro-RNA profiles are associated with severity of hepatitis C virus recurrence and acute cellular rejection after liver transplant

status: Public on Sep 17 2013

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

institute: kings college hospital

summary: Recurrent hepatitis C virus (rHCV) is universal post-liver transplantation (LT), with accelerated fibrosis rates compared to non-transplanted patients. rHCV is associated with increased mortality and morbidity post-transplant and is a leading indication for re-transplantation. We hypothesized that miRNA expression profiles from liver grafts can distinguish severity of HCV recurrence and differentiate this from acute cellular rejection (ACR).    Methods  Using microarrays, we characterized global microRNA (miRNA) expression from patients with slow HCV fibrosis progression (F<2 Ishak), fast HCV fibrosis progression (F≥2 Ishak), ACR and non-HCV transplanted patients. Selected miRNA were analysed by quantitative PCR (qPCR) using both liver tissue and serum samples.    Results  We demonstrated changes in miRNA expression in patients with slow HCV fibrosis progression that were anti-fibrogenic, anti-angiogenic and anti-inflammatory in comparison to patients with fast HCV fibrosis progression. miRNA-146a, miRNA-19a, miRNA- 20a and miRNA-let-7e expression were increased in the slow HCV fibrosis progression group. In addition, comparison of patients with fast HCV progression against patients with ACR identified pro-fibrogenic pathways.  qPCR analysis on liver tissue and serum confirmed the up-regulation of miRNAs in the slow HCV fibrosis progression group.    Conclusion  We demonstrate specific miRNA expression signatures that distinguish rate of progression of HCV recurrence and ACR post –liver transplantation. Pathway analysis indicates that specific miRNA may play a regulatory role in these processes. The miRNAs identified may act as potential biomarkers for HCV recurrence post-LT and help distinguish between ACR and recurrent HCV.

overall_design: We compared 29 patients in total; 11 patients with slow HCV fibrosis progression, 9 patients with fast HCV fibrosis progression, 5 patients with acute cellular rejection and 4 HCV negative patients with normal liver histology that acted as controls. RNA was extracted from archived histology samples of the RG and NRG and miRNA expression was analysed using the affymetrix Genechip miRNA 2.0 assays.

first: Deepak

last: Joshi

first: Siamak

last: Salehi

first: Helen

last: Brereton

first: Matthew

last: Arno

first: Alberto

last: Quaglia

first: Nigel

last: Heaton

first: John

last: O'Grady

first: Kosh

last: Agarwal

first: Varuna

last: Aluvihare


title: Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

status: Public on Aug 31 2013

city: Leuven

first: Barbara

last: De Coninck

address: Kasteelpark Arenberg 20

country: Belgium

institute: KU Leuven

type: Expression profiling by genome tiling array

summary: Although evidence accumulates on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. 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 treated with paraquat (PQ), an reactive oxygen species inducer and water (control), resulting in the identification of 92,844 and 86,272 transcriptionally active regions (TARs), respectively. Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a treshold, 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 PQ treatment compared to the control treatment, resulting in 176 TARS induced by PQ.

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

first: Delphine

last: Carron

first: Patrizia

last: Tavormina

first: Lander

last: Willem

first: David

last: Craik

first: Christine

last: Vos

first: Karin

last: Thevissen

first: Janick

last: Mathys

first: Bruno

last: Cammue


title: Expression data in Arabidopsis wild type, ahg2-1 and ahg2-1ags1-1 mutants

status: Public on Aug 09 2013

city: Yokohama

first: Motoaki

last: Seki

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

institute: RIKEN CSRS

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis wild type, ahg2-1 and ahg2-1ags1-1 mutants.

overall_design: The total RNA was prepared from 15-day-old Arabidopsis plants grown on the agar plates and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Yukio

last: Kurihara

first: Takashi

last: Hirayama

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Tetsuro

last: Toyoda

first: Yoshiki

last: Mochizuki


title: Rat Life Cycle Kidney Gene Expression Data

first: Vikrant

last: Vijay

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

overall_design: Refer to individual Series


title: CTCL and ATL cell lines, mir-150 transfected versus controls

status: Public on Jul 30 2013

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

summary: We examined the function of miR-150 in T-cell lymphomagenesis. We transfected GFP-control or GFP-miR-150 into several T-cell lymphoma lines and sought which genes were regulated by miR-150.

overall_design: To examine the function of miR-150 in T-cell lymphomagenesis, we first transfected GFP-control (Mock) or GFP-miR-150 into several T-cell lymphoma lines (ATN-1, HUT78, My-La, and HH). To detect genes commonly downregulated among these cells, we used the CodeLinkTM Human Whole Genome Bioarray platform with the criterion that the miR-150/GFP-control ratio must be <0.75 in all 3 CTCL lines.

first: Hiroyuki

last: Tagawa


title: MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS) miRNA

status: Public on Aug 02 2013

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: MicroRNAs are small noncoding RNA molecules that are involved in the control of gene expression. To investigate the role of microRNA in multiple sclerosis (MS), we performed global microarray analyses of mRNA and microRNA in peripheral blood T-cells from relapsing-remitting MS patients and controls. We identified 2,452 regulated genes and 21 regulated microRNA that differed between MS patients and controls. By Kolmogorov-Smirnov test, 20 of 21 regulated microRNA were shown to affect the expression of their target genes, many of which are involved in the immune system. LIGHT (TNFSF14) was a microRNA target gene significantly decreased in MS. The down-regulation of mir-494 and predicted mRNA-target LIGHT was verified by real-time PCR and we could demonstrate decreased serum levels of LIGHT in MS. Thus, regulated microRNA were significantly associated with both gene and protein expression of a molecule in immunological pathways. These findings indicate that microRNA may be important regulatory molecules in T-cells in MS.

overall_design: Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control and MS patients

first: Margareta

last: Jernas

first: CLAS

last: Malmestrom

first: MARKUS

last: Axelsson

first: Hans

last: Wadenvik

first: JAN

last: Lycke

first: Bob

last: Olsson


title: Epididymosomes convey different repertoires of miRNAs throughout the epididymis

status: Public on Jul 01 2013

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: Epididymosomes are small membrane vesicles (50-500nm) secreted by epididymal epithelial cells and involved in post-testicular sperm maturation. While their role in protein transfer to the sperm membrane is well acknowledged, we unveil here their capacity to vehicle microRNAs (miRNAs), which are potent regulators of post-transcriptional gene expression. Using a global microarray approach, we showed that epididymosomes providing from two discrete bovine epididymal regions (caput and cauda) possess distinct miRNA signatures. In addition, we established that miRNA repertoires contained in epididymosomes differ from those of their parent epithelial cells, suggesting that miRNA populations released from the cells may be selectively sorted. Binding of DilC12-labeled epididymosomes to primary cultured epididymal cells was measured by flow cytometry and indicated that epididymosomes from the median caput and their miRNA content may be incorporated into distal caput epithelial cells. Overall, these findings reveal that distinct miRNA repertoires are released into the intraluminal fluid in a region-specific manner and could be involved in a novel mechanism of intercellular communication throughout the epididymis via epididymosomes.

overall_design: We determined the miRNA profiles of epididymosomes isolated by perfusion from caput and cauda regions of the epididymis and compared it with the miRNA content of epididymal epithelial cells from the same regions.

first: Clémence

last: Belleannée

first: Robert

last: Sullivan


title: microRNA levels are altered in male and female mouse hearts: a role for miR-222

city: Bethesda

first: Delong

last: Liu

address: 10 Central Drive

department: NHLBI

institute: NIH

summary: To elucidate sex-dependent differences in miRNA expression

overall_design: Comparison of miRNA levels isolated from the ventricles of male and female mice

first: Anne

last: Deschamps


title: 10 Intellectual Disability samples for clinically relevant CNV detection

status: Public on Aug 01 2013

city: Nijmegen

first: Joep

last: de Ligt

address: Geert Grooteplein 10, 848

department: Human Genetics

country: Netherlands

institute: UMCN St Radboud

type: Genome binding/occupancy profiling by SNP array

summary: 10 patients with Intellectual Disability diagnosed with a clinically relevant copy number change, selected to assess the dection performance of alternative platforms.

overall_design: 10 Affymetrix arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Rolph

last: Pfundt

first: Nicole

last: de Leeuw

first: Jyane

middle: Y

last: Hehir-Kwa


title: MicroRNAs in neuronal differentiation

status: Public on May 29 2013

city: Omaha,

first: Sowmya

middle: V

last: Yelamanchili

state: NE

address: 985800 Nebraska Medical Center - DRC 1 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical center

summary: We used microarrays to detail the global programme of miRNA expression during neuronal differentiation

overall_design: To study changes in miRNA during neuronal differentiation

first: Howard

middle: S

last: Fox


title: miRNA profile of radioresistant pancreatic cancer cell lines

city: Shanghai

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

institute: Fudan University Shanghai Cancer Center

summary: We established radioresistant cell sublines, named as BxPC3/RR1 and BxPC3/RR2 which were derived from parental human pancreatic cancer cell line BxPC3. The miRNA expression profiles of the radioresistant pancreatic cancer cells were then compared with their parental cells.

overall_design: Three samples were analysed. miRNAs that were differentially expressed (increased or decreased in expression by ≥1.5-fold) between the radioresistant and parental cells were identified.


title: Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana

status: Public on May 12 2013

city: Rehovot

first: Noam

last: Leviatan

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Cold stress, which adversely affects plants growth and development, regulates the transcription and splicing of plants splicing factors. This affects the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions.

overall_design: Two-week old Arabidopsis seedlings grown on agar were subjected to 24 hours of cold (4°C) treatment under long day conditions. Control and cold-treated plants were harvested at the same time to ensure that observed differences would not be due to circadian clock effects on transcripts. Total RNA from four biological repeats were used for microarray hybridization.

last: Fluhr


title: Molecular phenotyping of the idiopathic interstitial pneumonias [miRNA]

status: Public on Jun 21 2013

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary:
Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses.
Methods: We collected transcriptional and miRNA profiles on lung tissue from 167 subjects with IIP and 50 non-diseased controls.  Differential expression of individual transcripts and miRNAs was identified using an ANCOVA model incorporating the clinical diagnosis of each subject as well as age, gender, and smoking status.  Validation was performed in an independent cohort of 131 IIPs and 39 non-diseased controls.
Results: Our results demonstrate a substantial degree of overlap in mRNA and miRNA signatures of clinical subtypes of IIP.  However, we identify two subtypes of IPF/UIP based on a strong molecular signature associated with expression of cilium genes.  We demonstrate that elevated expression of cilium genes is associated with more extensive microscopic honeycombing, more fibroblastic foci, higher expression of the airway mucin gene MUC5B, and better survival in an independent cohort of IPF/UIP patients.  Moreover, we identify miRNAs involved in the regulation of cilium-associated gene expression that contribute to novel molecular subphenotypes of IPF.
Conclusions: While subtypes of IIP are related biologically with similar transcriptional profiles, expression of cilium genes appear to identify two unique clinical presentations of IPF/UIP.

overall_design: 167 subjects with IIP and 50 non-diseased controls with no replicates

first: Ivana

last: Yang

first: Chris

last: Coldren

first: Sonia

last: Leach

first: Elissa

last: Murphy

first: Jia

last: Lin

first: Rachel

last: Burton

first: Steve

last: Groshong

first: Carlyne

last: Cool

first: Gregory

last: Cosgrove

last: Lynch

first: Kevin

middle: K

last: Brown

first: Marvin

last: Schwarz

first: Tasha

middle: E

last: Fingerlin

middle: A


title: A systematic evaluation of miRNA: mRNA interactions involved in the migration and invasion of breast cancer cells [miRNA Array]

status: Public on Jun 03 2013

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: In this study we performed a systematic evaluation of functional miRNA-mRNA interactions associated with the aggressiveness of breast cancer cells using a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction, and functional assays. Analysis of the miRNA expression identified 11 miRNAs that were differentially expressed, including 7 down-regulated (miR-200c, miR-205, miR-203, miR-141, miR-34a, miR-183, and miR-375) and 4 up-regulated miRNAs (miR-146a, miR-138, miR-125b1 and miR-100), in aggressive cell lines when compared to normal and less aggressive cell lines. Transient overexpression of miR-200c, miR-205, and miR-375 in MDA-MB-231 cells led to the inhibition of cell migration and invasion. The integrated analysis of miRNA and mRNA expression identified 35 known and novel target genes of miR-200c, miR-205, and mir-375, including CFL2, LAMC1, TIMP2, ZEB1, CDH11, PRKCA, PTPRJ, PTPRM, LDHB, and SEC23A. Surprisingly, the majority of these genes (27 genes) were target genes of miR-200c, suggesting that it plays a more important role in regulating the aggressiveness of breast cancer cells. We characterized one of the target genes of miR-200c, CFL2, and demonstrated that CFL2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous miR-200c. Tissue microarray analysis further revealed that CFL2 expression in primary breast cancer tissue correlated with tumor grade. To our knowledge, this study is the first systematic screening of functional miRNA target genes in aggressive breast cancer cells. The results obtained from this study may improve our understanding of the role of these candidate miRNAs and their target genes in relation to breast cancer aggressiveness and ultimately lead to the identification of novel biomarkers associated with prognosis.

overall_design: Affymetrix miRNA 1.0 arrays were performed according to the manufacturer's directions on small RNA extracted from 12 breast cancer cell lines including 4 aggressive cell lines, 6 less aggressive cell lines and 2 imortalized breast epithelium cell lines

first: Daya

last: Luo

first: Nikki

last: Harvel


title: Affymetrix SNP array data for hepatocellular carcinoma and their adjacent liver tissue samples

city: shanghai

first: Zeguang

last: Han

address: No.351,Guoshoujing Rd.,Zhangjiang Hi-Tech Park

institute: Chinese National Genome Center at Shanghai

summary:
Chromosomal DNA copy number alterations are a hallmark of human malignancies, including hepatocellular carcinoma (HCC). However, which oncogenes or tumor suppressors located on regions with DNA copy number aberration may contribute to HCC initiation and progression still remain obscure. Here we performed a genome-wide DNA copy number analysis on human HCC samples to identify novel potential oncogenes or tumor suppressors with DNA copy number aberrations.  Genome-wide DNA copy numbers analysis was performed with single nucleotide polymorphism micoarray. RT-PCR and immunohistochemical staining were employed to evaluate the NOXIN expression in HCC samples. Colony formation, cell cycle analysis and tumor xenograft assays were performed to assess the role of NOXIN in HCC cells. Reciprocal co-immunoprecipitation experiments were used to detect the interaction between NOXIN and DNA polymerase a primase. Genome-wide DNA copy number analysis on 43 paired HCC samples indentified the smallest DNA amplification region containing NOXIN, along with the elevated transcript. NOXIN overexpression was significantly associated with HCC tumor stage. Enforced NOXIN promoted cellular proliferation, colony formation, cell migration and in vivo tumorigenicity, whereas RNA interference against NOXIN can attenuate these effects. Interestingly, NOXIN overexpression can accelerate the G1-S transition of cell cycle progression through enhancing DNA synthesis in HCC cells, as indicated by bromodeoxyuridine incorporation. Furthermore, NOXIN can interact with DNA polymerase a, implying that NOXIN may promote de novo DNA synthesis via affiliating formation of DNA polymerase-primase complex.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from hepatocellular carcinoma and adjacent liver tissue samples.

overall_design: Copy number analysis of Affymetrix 500K SNP arrays was performed for 43 hepatocellular carcinoma tissue samples, which their adjacent liver tissues were used as references for copy number inference.

first: Jian

last: Huang


title: miRNAs in renal transplantation

status: Public on Jun 14 2013

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

summary: Sixty-five selected post-transplant biopsy samples (30 acute cellular rejection (AREJ 15 Banff-1, 15 Banff-2), 11 antibody mediated rejection (ABMR), 14 DGF, 10 PBx - protocol management biopsies - controls) were analyzed by using the Affymetrix GeneChip® miRNA Array.

overall_design: comparison between control group (protocol biopsies 3 month after TX) and indication biopsies (AREJ, ABMR and DGF)

first: Heinz

last: Regele

first: Paul

last: Perco

first: Alexander

last: Kainz

first: Afschin

last: Soleiman

first: Ferdinand

last: Mühlbacher

first: Bernd

last: Mayer

first: Rainer

last: Oberbauer


title: Expression data from primary tissue, human oral mucosa (miRNA data)

status: Public on May 06 2013

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

institute: University Clinic of Schleswig Holstein

summary: The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets.

overall_design: 7 cases (OLP) and 7 controls (healthy individuals). Genome wide mRNA and miRNA screening, linking both datasets (see summary).

last: Häsler


title: Affymetrix SNP array data for xenografted transient abnormal myelopoiesis samples

status: Public on Mar 01 2013

city: Tokyo

first: Aiko

last: Sato-Otsubo

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

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

summary: Transient abnormal myelopoiesis (TAM) is a clonal pre-leukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, IL-2Rγnull mice. In serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from murine bone marrow (hCD45 sorted) or human peripheral blood samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for xenografted TAM samples of 3 patients. There are also 3 samples from TAM patients in remission, which were used as references for copy number inference.

first: Seishi

last: Ogawa

first: Kenichi

last: Yoshida

first: Yusuke

last: Okuno

first: Satoshi

last: Saida

first: Ken-ichiro

last: Watanabe


title: MicroRNA expression data from Bcl-xL silenced A549 lung adenocarcinoma cells

status: Public on May 18 2013

city: Kuala Lumpur

first: Norahayu

last: Othman

address: Institute of Biological Science, Department of Genetics and Molecular Biology, Faculty of Science, University Malaya

department: Genetics & Molecular Biology

institute: University Malaya

summary:
Bcl-xL is an anti-apoptotic protein that is frequently found to be overexpressed in non-small cell lung cancer leading to an inhibition of apoptosis and poor prognosis. Recently, the role of miRNAs in regulating apoptosis and cell survival during tumorigenesis has become evident, with cancer cells showing perturbed expression of various miRNAs.
We utilized miRNA microarrays to determine if miRNA dysregulation in bcl-xL silenced lung adenocarcinoma cells could be involved in regulating apoptotic behavior, and identified dysregulated miRNAs with putative targets involved in signal transduction pathways regulating apoptosis, cell proliferation and cell progression.

overall_design: Short interfering RNA-based transfection of A549 was carried out inducing a reduction in bcl-xL expression levels. 24 hours post-transfection total RNA was isolated using TRIzol reagent and hybridized onto  Affymetrix GeneChip miRNA Arrays.  A global miRNA expression profile was then established, which compared total RNA, extracted from siRNA-transfected and non-transfected A549 cells.  All experiments were carried out with three independent biological replicates.

first: Lionel

last: In

first: Noor

last: Hasima

first: Jennifer

last: Harikrishna


title: Lymph node CD4+ T cell miRNA expression data from naïve C57BL/6J and C57BL/6J-ChrY^SJL

status: Public on May 28 2013

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

summary: Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J background, we show that susceptibility to two diverse animal models of autoimmune disease, including experimental allergic encephalomyelitis (EAE) and experimental myocarditis, correlates with the natural variation in copy number of Sly and Rbmy multicopy ChrY genes. In the B6 background, ChrY possesses gene regulatory properties that impact both genome-wide gene expression and the presence of alternative splice variants, but not miRNA expression in pathogenic CD4+ T cells. An inverse correlation exists between the number of Sly and Rbmy ChrY gene copies and the number of significantly upregulated genes in immune cells, thereby supporting a link between copy number variation of Sly and Rbmy and the ChrY genetic element exerting regulatory properties. Thus, these data establish ChrY as a member of the regulatory genome in mammals due to its ability to regulate gene expression and alternative splicing in immune cells linked to disease.

overall_design: Three biological replicates for each strain were pooled from the axillary, brachial, and inguinal lymph nodes from 5 mice for each replicate. RNA was isolated from CD4+TCRB+ FAC sorted cells.

first: Emma

middle: H

last: Wall

first: Julie

last: Dragon

first: Naresha

last: Saligrama

first: Dimitry

middle: N

last: Krementsov

first: Mohamad

last: Moussawi

first: James

middle: F

last: Zachary

first: Sally

last: Huber

first: Elizabeth

last: Blankenhorn

first: Cory

last: Teuscher


title: Serum microRNA expression as an early marker for breast cancer risk in prospectively collected samples from the Sister Study cohort

status: Public on May 08 2013

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

institute: NIH/NIEHS

summary:
microRNAs are small, non-coding, single-stranded RNAs between 18-22 nucleotides long that regulate gene expression. Expression of microRNAs is altered in tumor compared to normal tissue; there is some evidence that these changes may be reflected in the serum of cancer cases compared to healthy individuals. This has yet to be examined in a prospective study where samples are collected before diagnosis.
We used Affymetrix arrays to examine serum miRNA expression profiles in 410 participants in the Sister Study, a prospective cohort study of 50,884 women. All women in the cohort had never been diagnosed with breast cancer at the time of enrollment.

overall_design: We compared global miRNA expression patterns in 205 women who subsequently developed breast cancer and 205 women who remained breast cancer-free.

first: Ashley

last: Godrey

first: Clarice

last: Weinberg

first: Robert

last: Getts

first: Paul

last: Wade

first: Lisa

last: DeRoo

first: Dale

last: Sandler

first: Jack

last: Taylor


title: Genome-wide identification of genes involved in tolerance to isopropanol in Saccharomyces cerevisiae

status: Public on May 13 2013

city: Yokohama

first: Akane

last: Misaizu

address: 1-13-5 Fukuura kanazawa-ku

institute: Kirin Holdings Company, Limited

summary: We performed massive screening of the genes in yeast that were involved in the tolerance to isopropanol using the non-essential genes deleted yeast collection, and identified sixty-five disruptants that grew slower than the wild type strain in the presence of isopropanol. The isopropanol sensitive mutants were tested to know their behaviour under other alcohol stresses. Besides, we conducted microarray analysis to reveal the transcriptional response to isopropanol stress in yeast. Our results certainly provide new insights into yeast response to C3 alcohol isopropanol.

overall_design: Strain BY4743 was used in this test. The prepared cells were inoculated into 120 ml of fresh media (YPD without isopropanol, and YPD with 20 g/l or 40 g/l of isopropanol) in 500-ml Sakaguchi-flasks. They were cultivated for 3 h at 30°C with 130-rpm shaking. At least three independent experiments were performed at each concentration of isopropanol.

first: Shigehito

last: Ikushima


title: Mouse embryonic fibroblast (MEF) cells after 2, 3 or 4 days of inducible genetic deletion of Dicer1

status: Public on May 10 2013

city: Cambridge

first: Di

last: Wu

state: MA

address: Statistics Department, Science Center, 1 Oxford Street

institute: Di Wu

summary: To investigate the suitable  normalization for  miRNA arrays from samples with global miRNA decrease. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs.

overall_design: In this work, we analyzed the miRNA profiles of samples with global miRNA decrease using Affymetrix miRNA microarrays, following the inducible genetic deletion of Dicer1. We also analyzed previously published miRNA profiling in cancer samples with global miRNA decrease.

first: Michael

last: Gantier


title: Successful and failed human liver regeneration are characterized by the coordinated expression of distinct microRNAs

city: london

first: siamak

last: salehi

address: denmark hill

institute: kings college hospital

summary: The liver’s remarkable capacity to regenerate allows it to carry out vital life-supporting functions despite unrelenting pathogen and toxin-induced injury. Unchecked, this capability also leads to cirrhosis, a burgeoning global disease burden. Existing animal models only partially recapitulate human liver regeneration, which hitherto has not been systematically studied. We investigated human liver regeneration in a unique model of liver transplantation. Here we show coordinated changes in expression of microRNA (miRNA) during regeneration that drive proliferation, innate immunity and angiogenesis. Failed regeneration is associated with distinct miRNAs enforcing cell cycle inhibition and DNA methylation. The miRNA expression associated with successful or failed regeneration when recapitulated in vitro, triggered expression of cardinal regeneration-linked genes promoting cell cycle entry or inhibition, respectively. Furthermore, inhibition of three miRNAs whose downregulation is associated with successful regeneration, induced proliferation in vitro. Our data indicate that human liver regeneration is orchestrated by distinct miRNAs determining cell cycle fate. Their manipulation may obviate the need for transplantation by enforcing successful regeneration in the liver and other solid organs.

overall_design:
We compared a group of seven patients with successful regeneration (RG) after auxiliary liver transplant (ALT) to four patients who also had ALT but failed to regenerate (NRG). Regeneration was quantified by volume expansion using radiographic imaging; functional recovery was assessed using nuclear isotope scanning and hepatocellular regeneration using histology. Based on histological assessment, three time points were selected for both groups (RG and NRG). Biopsies were taken at the time of transplant and at different intervals post-transplant. Since sample acquisition was driven by clinical necessity, widely discrepant time intervals existed between T=1, T=2 and T=3 for the patients. RNA was extracted from archived histology samples of the RG and NRG, and miRNA expression was analysed using the Affymetrix GeneChip miRNA 1.0 assays.

This submission does not include NRG samples taken at time point 3.

first: Siamak

last: Salehi

first: Helen

middle: C

last: Brereton

first: Mathew

middle: J

last: Arno

first: David

last: Darling

first: Alberto

last: Quaglia

first: Nigel

last: Heaton

first: Varuna

middle: R

last: Aluvihare


title: Noncoding RNA expression profiling of cisplatin-resistant cells derived from the A549 lung cell line (miRNA)

status: Public on Jan 15 2013

city: Beijing

first: Yong

last: Yang

address: baijiazhuang street 8

institute: ccmu

summary: To determine the signaling networks that are dysregulated in cisplatin-resistant non-small cell lung cancer, noncoding RNA expression data were obtained from, and compared between, the lung adenocarcinoma cell line, A549, and its cisplatin-resistant derivative, A549/CDDP.

overall_design: Noncoding RNA expression data from a cisplatin-sensitive lung adenocarcinoma cancer cell line (A549) were collected and compared to noncoding RNA expression data from a cisplatin-resistant cell line (A549/CDDP). 3 independent experiments were completed for both the sensitive and resistant cell lines.

first: Hui

last: Li

first: Jie

last: Liu

first: Jun

last: Wang


title: Identification of SHORT VEGETATIVE PHASE putative targets through whole-genome expression analysis

status: Public on Apr 23 2013

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary:
SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase.
We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are regulated by SVP by means of Arabidopsis Tiling 1.0R Arrays (Affymetrix) during the two distinct phases of development.

overall_design: Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. To evaluate the amount of SVP expression in the vegetative phase we used svp-41 single mutant and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and svp-41 agl24-2 ap1-12 triple mutant inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.

first: Veronica

last: Gregis

first: Alice

last: Sessa

last: Andrés

first: Rosalinda

last: Guerra

first: Julieta

last: Mateos

first: Stefano

last: Torti

first: Giulio

last: Pavesi

first: Federico

last: Zambelli

first: Gian

middle: M

last: Prazzoli

first: Paul

last: Grini

first: Lucia

last: Colombo

first: Sara

last: Simonini

first: Katrine

last: Bjerkan

first: George

last: Coupland

first: Martin

last: Kater


title: Expression data of multiple sclerosis patients receiving Interferon-beta therapy [miRNA-2_0]

status: Public on Apr 24 2013

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary:
The purpose of this study was to investigate the expression dynamics of mRNAs and microRNAs in response to subcutaneous IFN-beta-1b treatment (Betaferon, 250 µg every other day) in patients with clinically isolated syndrome (CIS) suggestive of multiple sclerosis (MS) or relapsing-remitting type of the disease (RRMS).
By using Affymetrix microarrays, we obtained microRNA expression profiles of peripheral blood mononuclear cells from 3 patients within the first month of IFN-beta treatment.

overall_design:
EDTA blood samples were taken from all patients immediately before first IFN-beta injection as well as after 1 month.
Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted, labeled and hybridized to Affymetrix GeneChip miRNA 2.0 arrays to quantify the expression of small non-coding RNA transcripts.
This GEO entry provides the GeneChip miRNA 2.0 microarray data.

first: Dirk

last: Koczan

first: Uwe

last: Zettl


title: Identification of miRNAs specific for prostate cancer (PCa)

status: Public on Mar 29 2013

city: VALENCIA

first: JOSE

middle: ANTONIO

last: LOPEZ-GUERRERO

address: C/PROF. BELTRAN BAGUENA, 8

department: LABORATORY OF MOLECULAR BIOLOGY

country: Spain

institute: FUNDACION INSTITUTO VALENCIANO DE ONCOLOGIA

summary: The purpose of this study are:  - To identify new biomarkers specific for prostate cancer (PCa) that can be used as diagnostic markers in the urine of individuals with high probability of PCa (abnormal PSA and/or digital rectal examination).  - To validate the utility of these new biomarkers, as well as others already known such as PCA3, fusion gene TMPRSS2-ERG, GOLPH2 and SPINK1.  - To establish a prediction model for the diagnosis of PCa based on the expression of these biomarkers.  - To validate this model within the framework of an opportunist programme of early diagnosis.  - Within the framework of this programme, to associate a series of social-demographic, antropometric, life-style and occupational variables for establishing a risk model predictor that could be associated with the model based on the biomarkers.

overall_design: Methodology: The study is divided in three phases based on three different cohorts of patients:  -Phase 1. Identification of biomarkers. This phase includes 60 patients (10 normal prostates and 50 PCa). Form these tumors a screening of miRNAs will be performed.  -Phase 2. Validation of the new biomarkers and others already known by means qRT-PCR on urine samples from 300 patients (200 with histological diagnosis of PCa and 100 with an histological negative result).  -Phase 3. Prospective validation in a prospective cohort iof 1065 patients included in an opportunist programme of early detection of PCa.

first: Jose

last: Lopez-Guerrero


title: Impact of nutrient unbalances on wine alcoholic fermentation: nitrogen excess enhances yeast cell death in lipid-limited must

status: Public on Mar 31 2013

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

summary: In this work we evaluated the impact of nutritional unbalances, as lipids/nitrogen unbalances, on wine yeast survival during alcoholic fermentation. We showed that lipids limitations (actually ergosterol limitation) lead to a rapid loss of viability during the stationary phase of fermentation but that cell death rate is strongly modulated by the amount of nitrogen sources. Yeast survival is reduced when an excess of nitrogen is available in lipid-limited fermentations. Such rapid dying yeast cells fermenting with high nitrogen level and lipids-limited amounts displayed a low storage of carbohydrate trehalose and glycogen compared to nitrogen limited cells. Consistently, examination of the cells stress response using an HSP12 promoter-driven GFP expression showed that lipids limitation triggered a weaker stress response than nitrogen limitation. We examined the involvement of nitrogen signalling pathway in the triggering of cell death using a sch9-deleted strain. We showed that deletion of SCH9 restored a high yeast viability indicating that the signaling pathway acting through Sch9p is involved in the enhanced cell death triggered by nitrogen excess. In addition we showed that various nitrogen sources provoked cell death but that histidine and proline did not trigger a similar effect. As a whole our data indicate that lipids limitation does not elicit a transcriptional program leading to a stress response which protects yeast cells and that nitrogen excess triggers cell death through a modulation of this stress response, but not by HSP12. These results point a potential negative role of nitrogen in fermentation which has until now never been described and taken into account in the management of alcoholic fermentations.

overall_design: 2 conditions with 2 biological replicates compared: 59A and 59A-Sch9

first: Catherine

last: Tesniere

first: Pierre

last: Delobel

first: Martine

last: Pradal


title: Expression data of multiple sclerosis patients receiving Interferon-beta therapy

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Differences in miRNA Detection Levels are Technology and Sequence Dependent [Affymetrix array]

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

summary: We undertook an integrative technological approach to compare miRNA detection capability of three high-throughput commercial platforms.

overall_design: We artificially introduced human precursor, 2’-O-methyl modified and mature spiked-in miRNAs in a controlled fashion into native human placenta total RNA.

first: Shirley

last: Horn-Saban

first: Yisrael

last: Parmet

first: Ester

last: Feldmesser


title: microRNA signature is altered in both human epididymis and seminal microvesicles following vasectomy.

status: Public on Feb 25 2013

city: Quebec

first: Ezequiel

last: Calvo

address: 2705 Boul. Laurier

institute: CRCHUL

summary:
BACKGROUND: Vasectomized men who wish for restoration of fertility commonly face problems to conceive despite high surgical success rates of vasovasostomy, a surgery routinely used to retrieve duct patency. In human, vasectomy has consequences on the epididymal transcriptome and is responsible for non-reversible changes that affect the biochemical parameters and functions of ejaculated sperm in vasovasotomized men. Since microRNAs (miRNAs) are key regulators of post-transcriptional gene expression, we explored the consequences of vasectomy on miRNA pattern in the human epididymis and determined the repercussion and reversibility of these changes in seminal microvesicles (SMVs) from semen of vasovasostomized men.
METHOD: miRNA signatures from a unique set of human epididymal segments (caput, corpus, cauda) provided by controls and vasectomized donors as well as miRNA content of SMVs isolated from semen of normal, vasectomized and vasovasostomized donors were determined by using high-throughput microarray technology. Epididymal miRNA signature was correlated with gene expression profiles by employing an integrated genomic approach.
RESULTS: While the segmented pattern of miRNA expression was maintained along the human epididymis following vasectomy, the array of miRNAs from each anatomical region significantly differed between normal and vasectomized donors. Greatest changes were observed in cauda epididymidis and were negatively correlated with transcription factors. Vasectomy also impacted expression of miRNAs found in SMVs from normal donors, including miRNAs of epididymal origin contained in epididymosomes. Among seminal miRNAs sequelae, 52 were reversible according to miRNA expression level following duct patency retrieval. In contrast, 66 of miRNAs found in SMVs were not retrieved in SMVs after vasovasostomy.
CONCLUSION: We showed that vasectomy has a substantial impact on the miRNA signature of the epididymis and SMVs, and that vasovasostomy does not restore all molecular players found in normal fertile individuals. According to the critical role played by miRNAs in the control of male fertility, we believe that miRNA sequelae occurring upstream and downstream of the vasectomy site may be in part responsible for the reduced fertility outcome reported after surgically successful vasectomy reversal.

overall_design: Human epididymides from 3 control (26, 47 and 50 years old. GEO accession number GSE35522) and 3 vasectomized donors (45, 47 and 48 years old), were collected and dissected into 3 anatomical regions (caput, corpus and cauda). Seminal microvesicles (SMVs) were isolated from the semen of normal (pool of 3 donnors), vasectomized (pool of 3 donnors) and vasovasostomized donors (pool of 5 donnors). A cross-comparison between the miRNA signature found in different segments and seminal vesicles was performed using GeneChip miRNA Array 2.0 (Affimetrix, Santa Clara, CA).

first: Clémence

last: Belleannée

first: Christine

last: Légaré

first: Véronique

last: Thimon

first: Robert

last: Sullivan


title: MicroRNA expression profiling of small-intestine neuroendocrine tumors and human neuroendocrine tumor cell lines

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

institute: Université catholique de Louvain

summary: Small intestinal neuroendocrine tumors (SI-NETs) arise from serotonin-producing enterochromaffin cells. SI-NETs are often well-differentiated tumors and most patients have regional or distant metastases at initial presentation. MicroRNAs (miRs) are post-transcriptional regulators which are important in diverse biological processes and can function as tumor suppressor genes or oncogenes. This study aims to identify an exclusive SI-NETs miR profile that may have a critical role in development, diagnosis, prognosis and progression of these malignancies.

overall_design: Five human NET cell lines, one octreotide-treated CNDT2.5 cells, one microdissected normal enterochromaffin cells, three snap-frozen normal ileum specimens and 15 SI-NET specimens at different stage of malignancy, five primary tumors, five mesentery metastases and five liver metastases, were included in this study. Total RNA was hybridized onto Affymetrix GeneChip® miR arrays for genome-wide profiling. Array data summarization, normalization, and quality control were performed using miRNA QC Tool software.

first: Su-Chen

last: Li

first: Cécile

last: Martijn

first: Ahmed

last: Essaghir

first: Ricardo

last: Lloyd

first: Kjell

last: Öberg

first: Valeria

last: Giandomenico


title: SNP microarray-based PGS significantly improves the clinical outcome for translocation carriers

status: Public on Mar 11 2013

city: changsha

first: xiong

last: bo

address: xiangya road

institute: xiangya

summary: This was a retrospective comparison study of SNP-based preimplantation genetic screening (SNP-PGS) and FISH-based preimplantation genetic diagnosis (FISH-PGD) for 575 couples in total with chromosome translocations, including 169 couples treated by SNP-PGS between October 2011 and August 2012, and 406 couples treated by FISH- PGD between January 2005 and October 2011. In total, 773 blastocysts obtained from 169 couples were biopsied and frozen, embryo transfer was carried out on the balanced embryos. The PGS results and pregnancy outcomes were compared with those of FISH-PGD for 406 translocation carriers with 3,968 embryos biopsied on day 3. Of the 773 biopsied blastocysts, reliable SNP-PGS results were obtained for 717 (92.76%). For Robertsonian translocation carriers, the rate of normal/balanced embryos, embryos with translocation-related abnormalities, and embryos with abnormalities unrelated to a translocation were 57.80%, 23.39% and 18.81%, respectively. In reciprocal translocation carriers, the rate of normal/balanced embryos, embryos with translocation-related abnormalities and embryos with abnormalities unrelated to translocation were 35.47%, 52.10% and 12.42%, respectively. There was no significant differences in patient age, basal endocrine level and the average number of retrieved oocytes and good quality day 3 embryos before biopsy in the SNP-PGS group compared with the FISH-PGD group. The number of embryos biopsied in the FISH-PGD group was higher than in the SNP-PGS group. However, the pregnancy rate with successful delivery per oocyte retrieval and the implantation rate were both lower in the FISH-PGD group than in the SNP-PGS group. The spontaneous abortion rate was higher in the FISH-PGD group than in the SNP-PGS group.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on whole genome amplification product of trophectoderm cells, which were collect from blastocysts biopsy. The results of SNP array were used to determine if the biopsied blastocyst have aneuploidy or unbalanced chromosomes.

first: Yue

middle: Q

last: Tan

first: Guang

middle: X

last: Lu


title: Role of pp-ips in rpd3 complex and the environmental stress response (ESR)

status: Public on Mar 22 2013

city: tucson

first: jeremy

last: worley

state: az

address: 1007 e. lowell st.

department: MCB

institute: university of arizona

summary: Cells respond to stress and starvation by adjusting their growth rate and enacting stress defense programs.  In eukaryotes this involves inactivation of TORC1, which in turn triggers downregulation of ribosome and protein synthesis genes and upregulation of stress response genes.  Here we report that the highly conserved inositol pyrophosphate second messengers (including 1-PP-IP5, 5-PP-IP4, and 5-PP-IP5) are also critical regulators of cell growth and the general stress response, acting in parallel to the TORC1 pathway to control the activity of the class I HDAC Rpd3L.  In fact, yeast cells that cannot synthesize any of the PP-IPs mount little to no transcriptional response in osmotic, heat, or oxidative stress.  Furthermore, PP-IP dependent regulation of Rpd3L occurs independently of the role individual PP-IPs (such as 5-PP-IP5) play in activating specialized stress/starvation response pathways.  Thus, the PP-IP second messengers simultaneously activate and tune the global response to stress and starvation signals.

overall_design: 2-condition experiments. Includes the responses of wild-type (ACY 044) and mutant yeast strains (all are W303 background) to log growth and stress conditions. This series of microarrays were performed on null mutants of various genes in the inositol pyrophosphate synthesis pathway, including several members of the Rpd3L histone deacetylase complex. All mutants were made in W303 strain, MatA yeast, using standard techniques (homologous recombination). Several stress conditions were tested, including heat-shock, oxidative (H2O2), and osmotic stress (0.375M KCl). Cells in mid-log growth were subjected to stress for 20 minutes. In one instance the TOR inhibitor rapamycin was added to determine whether PP-IPs act above/at or below TORC1 in activating the ESR. Taken together, these microarrays show the role of the inositol pyrophosphate synthesis pathway in activating the ESR in stress.

first: Jeremy

first: Xiangxia

last: luo

first: Andrew

middle: p

last: capaldi


title: Analysis of direct target genes regulated by AS1 and AS2

status: Public on Mar 06 2013

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

summary: Analysis of tiling array data identified 358 genomic regions commonly enriched by the AS1 and T7 antibody datasets.

overall_design: AS1 antibody data set (AS1 antibody versus mock) and the T7 antibody data set (T7 antibody versus mock)

first: Mayumi

last: Iwasaki

first: Chiyoko

last: Machida


title: Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.

city: College Park

first: Jianhua

last: Zhu

state: MD

address: 2102 Plant Sciences Building

department: Plant Science and Landscape Architecture

institute: University of Maryland

summary: Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

overall_design: Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were subjected to cold stress at 4°C for 12 h. Total RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.

first: Qingmei

last: Guan

first: Jianmin

last: Wu

first: Yanyan

last: Zhang

first: Changhua

last: Jiang

first: Renyi

last: Liu

first: Chenglin

last: Chai


title: Genome-wide analysis of the cytosine methylation profile in Arabidopsis thaliana crown galls

status: Public on Feb 18 2013

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

type: Methylation profiling by genome tiling array

summary:
Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth.
All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files.

overall_design: mCIP of gDNA from crown galls vs. mCIP of gDNA from inflorescence stalks (3 biol. replicates each)

first: Jochen

last: Gohlke

first: Rosalia

last: Deeken


title: microRNA profiling in paired human prostate cancer and benign prostate tissue

status: Public on Feb 05 2013

city: New York

first: Pei-Chun

last: Lin

state: NY

address: 1300 York Ave

department: Pathology and Laboratory Medicine

institute: Cornell Weill Medical College

summary: To determine the altered microRNA expression signature in human prostate cancer compared to benign prostate tissue. To determine the altered mRNA expression signatures upon overexrpession miR-31 in prostate cancer cells.

overall_design: Two condition experiments:1) Total RNA from 21 pairs of prostate cancers and matched benign prostate tissues were collected and processed for microRNA detection. 2) In LNCaP prostate cancer cells, miR-31 was overexpressed and compared to control miR-NC.

first: Pei

first: Ya-lin

middle: L

last: Chiu

first: Samprit

last: Banerjee

first: Francesca

last: Demichelis

first: Mark

last: Rubin


title: MiRNA expression profiling in bone-marrow-derived neutrophils of lcn2 deficient mouse

status: Public on Jan 31 2013

city: Cleveland

first: Zhuoming

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

summary:
Lipocalin 24p3 (24p3) is a neutrophil secondary granule protein. 24p3 is also a siderocalin, which binds several bacterial siderophores. It was therefore proposed that synthesis and secretion of 24p3 by stimulated macrophages or release of 24p3 upon neutrophil degranulation sequesters iron-laden siderophores to attenuate bacterial growth. Accordingly, 24p3-deficient mice are susceptible to bacterial pathogens whose siderophores would normally be chelated by 24p3. Specific granule deficiency (SGD) is a rare congenital disorder characterized by complete absence of proteins in secondary granules. Neutrophils from SGD patients, who are prone to bacterial infections, lack normal functions but the potential role of 24p3 in neutrophil dysfunction in SGD is not known. Here we show that neutrophils from 24p3-deficient mice are defective in many neutrophil functions. Specifically, neutrophils in 24p3-deficient mice do not extravasate to sites of infection and are defective for chemotaxis. A transcriptome analysis revealed that genes that control cytoskeletal reorganization are selectively suppressed in 24p3-deficient neutrophils. Additionally, small regulatory RNAs (miRNAs) that control upstream regulators of cytoskeletal proteins are also increased in 24p3-deficient neutrophils. Further, 24p3-deficient neutrophils failed to phagocytose bacteria, which may account for the enhanced sensitivity of 24p3-deficient mice to both intracellular (Listeria monocytogenes) and extracellular (Candida albicans, Staphylococcus aureus) pathogens. Interestingly, Listeria does not secrete siderophores and additionally, the siderophore secreted by Candida is not sequestered by 24p3. Therefore, the heightened sensitivity of 24p3-deficient mice to these pathogens is not due to sequestration of siderophores limiting iron availability, but is a consequence of impaired neutrophil function.
Key words: Lipocalin, 24p3, neutrophils, cell motility, chemotaxis, MIRNA-362-3p

overall_design: To address the role of lipocalin 2 in regulating miRNA expression profiling in neutrophils derived from mouse bone marrow, we performed microarray analysis of miRNAs in wild type (N=2) and lcn2 knockout (N=2) neutrophils.

first: L

last: Devireddy

first: Z


title: Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.

first: Jianhua

summary: Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under normal growth conditions to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

overall_design: Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) under normal conditions were harvested for total RNA isolation. RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.

first: Qingmei

first: Jianmin


title: miRNA expression profiling in squamous cell carcinoma (SCC)

status: Public on Jan 18 2013

city: Melbourne

first: Charbel

last: Darido

state: Vic

address: 99 Commercial road

country: Australia

institute: Monash University

summary: Despite its prevalence, the molecular basis of squamous cell carcinoma (SCC) remains poorly understood. We recently identified the developmental transcription factor Grhl3 as a potent tumor suppressor of SCC, and demonstrated that targeting of Grhl3 by a miR-21-dependent proto-oncogenic network underpins SCC in humans. Reduced levels of GRHL3 and its target gene PTEN are evident in human skin, and head and neck SCC, associated with increased expression of miR-21, which targets both tumor suppressors. Our data defines the miR-21-GRHL3-PTEN-axis as a critical tumor suppressor pathway in SCC.

overall_design: Total RNA was isolated from two SCC primary tissue samples and their matched normal skin controls.


title: Gene Expression Profiling In Murine Retina Neovascularization Models

status: Public on Dec 05 2012

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: In order to find out the vital genes during retinal neovascularization (RNV), we set up OIR (oxygen-induced retinopathy; induced with 75%±2% oxygen) and wild-type C57BL/6J murine models. We observed the retinal vascular growth process daily both in OIR and wild-type mice through retinal flat-mount, and isolated total retinal RNA at different time points (P8, P9, P12, P13, P30) both in OIR and wild-type mice for gene expression analysis.

overall_design: At least three different retinae were accessed at each time point for observing the retinal vascular growth process. Ten neural retinae from five mice were harvested and pooled into one sample for gene expression analysis. Three biological replicates were used for each time point. Dye-swaps were performed.

first: Xia

last: Yang

first: Xiaoguang

last: Dong

first: Changkai

last: Jia

first: Yiqang


title: Detailed genome-wide SNP analysis of major salivary carcinomas localizes subtype-specific chromosome sites and oncogenes of potential clinical significance

status: Public on Feb 21 2013

city: Houston

first: Li

last: Zhang

state: TX

address: 1400 Pressler st, unit 1410

department: Bioinformatics and COmputational Biology

institute: The University Of Texas MD Anderson Cancer Center

summary: We searched the head and neck pathology database at The University of Texas MD Anderson Cancer Center (Houston, Texas) to identify all patients with SGCs who had been treated surgically from 1995 to 2008. Twenty cases from each tumor type, ACCs, MECs, and SDCs were selected based on the availability of at least 1.0 gm of fresh frozen tumor tissues. Seventeen salivary gland tissues (10 from matching tumor cases and 7 from neck resections from patients with other diseases) were used as control (Supplemental Table 1). The 20 ACCs had previously been included in our earlier comparative genomic hybridization analysis. 32 The tissues had been harvested immediately after resection by experienced head and neck pathologists, placed in liquid nitrogen, and stored at -80°C until use. Frozen sections of each tissue specimen were evaluated for  tumor content and quality. Specimens with more than 20% of host non-neoplastic elements in any given sample underwent macrodissection to enrich the tumor percentage to more than 80%. One ACC tumor was disqualified because of excessive stroma; of the 59 tumor specimens, 14 had undergone mass dissection to remove non-tumor elements. All tissues were obtained according to an institutional review board-approved protocol for non-mucosal head and neck cancer. DNA extraction: Fresh-frozen tissue was processed using the Gentra Puregene tissue kit (QIAGEN, Valencia, CA). In brief, normal and tumor tissues were carefully dissected, and proteinase K was immediately added for cell digestion. After protein precipitation, DNA was precipitated using isopropanol, followed by a 70% ethanol washing procedure. Purified DNA was dissolved and eluted in DNA hydration solution and stored at -80°C. The quality of DNA was assessed using electrophoresis and nano-drop measurement. A 260/280 wavelength ratio of at least 1.8 was used to qualify specimens for analysis. Microarray analysis: We used the Affymetrix 250k Nsp SNP array (Affymetrix, Inc., Santa Clara, CA) to survey the genotype and DNA CNA copy number data for 59 tumor specimens and 17 healthy salivary gland specimens. Each array contains 261,563 SNP sites, which are approximately uniformly distributed throughout the genome. The SNP site mapping information was provided by Affymetrix, Inc., using human genome sequence version NCBI36/hg18. Two samples were repeatedly sampled to assess data reproducibility.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen tissues.
Copy number analysis of Affymetrix 250k NSP arrays was performed for 76 samples, 19 ACC samples, 20 SDCs, 20 MECs and 17 controls.

first: Pierre

last: Saintigny

first: Yoshitsugu

last: Mitani

first: Nianxiang

first: Carlos

last: Caulin

first: Randal

middle: S

last: Weber

first: Pulivarthi

last: Rao

first: Scott

last: Lippman

first: Merrill

last: Kies

first: Adel

last: El-Naggar


title: Identification of microRNAs specifically expressed in HCV-associated hepatocellular carcinoma

status: Public on Feb 20 2013

city: Bethesda

first: Patrizia

last: Farci

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary:
Background: Several studies have investigated the association of miRNAs with hepatocellular carcinoma (HCC) but the data are not univocal.

Methods: We performed a microarray study of miRNAs in hepatitis C virus (HCV)-associated HCC and other liver diseases and healthy conditions.

Results and Conclusions: The simultaneous comparison of different liver diseases and normal livers allowed the identification of 18 miRNAs exclusively expressed in HCV-associated HCC, with sensitivity and specificity values of diagnostic-grade.

overall_design: A total number of 76 liver specimens obtained from 43 patients were analyzed: 26 liver specimens obtained from 10 patients with HCV-associated HCC, including 9 specimens from the tumor area (HCC) and 17 specimens from the surrounding non-tumorous tissue affected by cirrhosis (HCC-CIR); 18 specimens from 10 patients with HCV-associated cirrhosis without HCC (CIR); 13 specimens from 4 patients with HBV-associated acute liver failure (ALF); 12 specimens from 12 liver donors (LD); and 7 from normal liver of 7 subjects who underwent hepatic resection for liver angioma (NL).

first: Giacomo

last: Diaz

first: Marta

last: Melis

first: Ashley

last: Tice

first: David

last: Kleiner

first: Lopa

last: Mishra

first: Fausto

last: Zamboni


title: Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy (microRNA)

status: Public on Dec 01 2012

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

country: Sweden

institute: Lund University

summary:
To increase our understanding of epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient.
We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation.

overall_design: comparison of trisomy 8 cells with disomic as well as reference fibroblasts

first: Bertil

last: Johansson


title: MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP) [miRNA]

status: Public on Jan 22 2013

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: MicroRNA are small non-coding RNA molecules that regulate gene expression. To investigate the role of microRNA in ITP, we performed genome-wide expression analyses of mRNA and microRNA in T-cells from ITP patients and controls. We identified 1,915 regulated genes and 22 regulated microRNA that differed between ITP patients and controls. Seventeen of the 22 regulated microRNA were linked to changes in target gene expression; 57 of these target genes were associated with the immune system, e.g. T-cell activation and regulation of immunoglobulin production. CXCL13 and IL-21 were two microRNA target genes significantly increased in ITP. We could demonstrate increased plasma levels of CXCL13 and others have reported increased plasma levels of IL-21 in ITP. Thus, regulated microRNA were significantly associated with both gene and protein expression of molecules in immunological pathways. We suggest that microRNA may be important regulatory molecules involved in the loss of tolerance in ITP.

overall_design: Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control and ITP patients.

first: Margareta

last: Jernås

first: Hans

last: Wadenvik

first: Bob

last: Olsson


title: Yeast transcriptomics in sugarcane-based ethanol fermentation

status: Public on Nov 27 2012

city: Recife

first: Marcos

middle: Antonio

last: Morais

address: Av. Moraes Rego, 1235

department: Department of Genetics

institute: Federal University of Pernambuco

summary: The present work aimed to compare the transcriptome of three major ethanol-producer Saccharomyces cerevisiae strains in Brazil when fermenting sugarcane juice for fuel ethanol production. This was motivated by the reports presenting physiological and genomics differences among them, and by the attempt to identify genes that could be related to their fermentation capacity and adaptation for different industrial processes.

overall_design: Two-condition experiment, T0h vs. T6h fermetations assay. Biological replicates: 3 T0h replicates, 5 T6h replicates.

first: Morais

last: Marcos

first: Paiva

last: Sergio

first: Tavares

last: Jose

first: Elsztein

last: Carolina

first: Pita

last: Will

first: Lucena

last: Rodrigo

first: Souza

last: Rafael

first: Balbino

last: Valdir


title: Differential miRNA expression profiles in the first and third trimester human placentas

status: Public on Dec 14 2012

city: Shreveport

first: Yuping

last: Wang

state: LA

address: 1501 Kings Highway

department: Ob/Gyn

institute: LSUHSC-Shreveport

summary: To investigate the role of miRNA in the placental development, we analyzed miRNA expression profiles in the first and third trimester human placentas. Total RNA was isolated from 12 placentas (6 from first trimester and 6 from third trimester). miRNA expression profiles were determined by Affymetrix GeneChip 2.0 miRNA Microarray.

overall_design: Using miRNA microarray to determine miRNA expression profiles in the human placenta between first and third trimester pregnancies.

first: Y

last: Gu

first: J

last: Sun

first: L

last: Groome


title: miRNA expression in untreated HCT116, HT-29 and SW480 colon cancer cell lines

status: Public on Nov 09 2012

city: Oslo

first: Lina

last: Cekaite

state: Norge (+47)

address: Ullernchausseen 70

department: Molecular Oncology

country: Norway

institute: Oslo University Hospital, Radiumhospitalet

summary: miRNA expression in untreated colon cancer cell lines

overall_design: Three colon cance cell lines, HCT116, HT-29, SW480

first: Rolf

middle: I

last: Skotheim

first: Ragnhild

last: Lothe


title: Transcriptome of lsm8-1 mutant using whole genome tiling arrays

status: Public on Jan 16 2013

city: Pozuelo de Alarcón

first: Tamara

last: Hernández-Verdeja

state: Madrid

address: Autovia M-40, Km 38

department: Centre for Plant Biotechnology and Genomics

institute: Universidad Politécnica de Madrid

summary: Characterization of gene expression and intron retention in lsm8-1 mutants.

overall_design: Pooled 2 week old rosettes of Col-0 (3 biological replicates) and lsm8-1 mutants (3 biological replicates).

first: Carlos

last: Perea-Resa

first: Julio

last: Salinas


title: The yeast PP2A-CDC55 phosphatase regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 [Time course 2]

status: Public on Nov 06 2012

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

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

summary: The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. This argues for a Msn2/4 specific function of PP2A-Cdc55.

overall_design: Time course of 0, 10 20 and 30 minutes hyperosmolarity treated yeast cells of msn2msn4 or msn2msn4cdc55 genetic background, both carrying plasmid pMsn2pMsn2DNES; reference hybridization: untreated W303 msn2msn4 pMsn2pMsn2DNES labelled with Cy3

last: Schüller

first: Andriy

last: Petryshyn

first: Eva

last: Klopf