title: miRNA profiling of repeat kidney biopsies in Lupus Nephritis

first: Ilias

last: Alevizos

state: Maryland

address: 10 Center Dr., RM 1N110

country: USA

institute: National Institute for Dental and Craniofacial Research (NIDCR)

summary:
We aimed to identify miRNA biomarkers of renal injury in kidney biopsies from patients with lupus nephritis. MiRNA profiles of 8 patients were analyzed for correlation with various clinical features including Progression, Activity, Chronicity, and Time to Kidney Failure.
MicroRNAs (miRs) are promising biomarkers and are involved in pathogenesis of kidney diseases. We aimed to identify miR biomarkers of renal injury in kidney biopsies from patients with lupus nephritis and study their potential role in renal fibrosis. miR-150 was significantly increased in kidneys with high chronicity compared to low chronicity and it correlated positively with chronicity index scores and renal collagen I expression. In kidneys with high chronicity, miR-150 was found predominantly in proximal tubular cells (PTCs) and was moderately expressed in podocytes and to lesser degree in mesangial cells (MCs). We hypothesized that miR-150 increases fibrosis by downregulating a negative regulator of profibrotic proteins. Suppressor of cytokine signaling1 (SOCS1) is a predicted target of miR-150 and has shown antifibrotic role. After confirming that SOCS1 is a direct target of miR-150, we showed that transfection of a miR-150 analog downregulated SOCS1 protein and upregulated the profibrotic     proteins fibronectin, collagen I, collagen III, and TGF-β1 in both primary normal human renal PTCs and MCs. A similar effect was seen when using a SOCS1 siRNA to confirm that the effect of miR-150 on profibrotic proteins is mediated through SOCS1. Stimulation with TGF-β1 induced miR-150 increase in PTCs and human podocytes but not MCs. These results suggest that miR-150 might be a useful quantitative renal biomarker of kidney injury in lupus nephritis and that miR-150, which might be partially induced by TGF-β1, plays an important role in renal fibrosis by increasing profibrotic molecules through downregulation of SOCS1.

overall_design: FFPE kidney specimens (n=25) including baseline and repeated needle renal biopsies were from 14 patients with LN enrolled in IRB-approved protocols at the NIDDK between 1976 and 1999. The specimens were divided in two groups based on histological chronicity index (CI). CI ≥ 4 were categorized as having high degree of chronicity of chronic kidney injury. 18 kidneys from 8 patients including high CI (n=9) and low CI (n=9) were used for miR profiling by Affymetrix microRNA microarrays.

first: Hua

last: Zhou

first: Sarfaraz

middle: A

last: Hasni

first: Mayank

last: Tandon

first: Shyn-Ing

last: Jang

first: Jeffery

middle: B

last: Kopp

first: Howard

last: Austin

first: James

middle: E

last: Balow

first: Gabor

last: Illei


title: CCND2 rearrangements are the most frequent genetic events in Cyclin D1-negative mantle cell lymphoma [Affymetrix]

status: Public on Dec 19 2012

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

summary: Cyclin D1-negative mantle cell lymphomas (MCL) are not well characterized, in part due to the difficulties in their recognition. SOX11 has been recently identified as a reliable biomarker of MCL, also expressed in the cyclin D1-negative variant. We investigated 40 lymphomas with MCL morphology and immunophenotype, negative for cyclin D1 expression/t(11;14)(q13;q32) but SOX11-positive. These tumors presented clinically with generalized lymphadenopathy, advanced stage, and had a poor outcome (5-year overall survival 48%). Chromosomal rearrangements of the CCND2 locus were detected in 55% of the cases, with an IG gene as partner in 18/22 cases, in particular with light chains (10 IGK@, 5 IGL@). No mutations in the phosphorylation motifs of CCND1, CCND2 and CCND3 were detected. The global genomic profile and the high complexity of the 32 cyclin D1-negative SOX11-positive MCL analyzed by copy number arrays were similar to the conventional cyclin D1/SOX11-positive MCL. 17p deletions and high Ki67 expression conferred a significantly worse outcome to the patients. This comprehensive characterization of a large series of cyclin D1-negative MCL indicates that these tumors are clinically and biologically similar to the conventional cyclin D1-positive MCL and provides a basis for the proper identification and clinical management of these patients.

overall_design: This Series contains copy number analysis of 500K Affymetrix SNP arrays for five MCL (5 hybridizations of wih Nsp 250K array and 5 hybridizations with Sty 250K arrays, that combined are the 500K array).

first: Itziar

last: Salaverria

first: Silvia


title: Genome-Wide HDA18-Binding Sites in Arabidopsis Root Tips

status: Public on Nov 02 2012

city: Beijing

first: Linchen

last: Li

address: 5 Yiheyuan Road

department: College of Life Sciences

country: China

institute: Peking University

type: Genome binding/occupancy profiling by genome tiling array

summary: We found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase (HDAC) gene family member HDA18 exhibits altered H and N epidermal cell patterning. We then performed genome-wide location (ChIP-chip) analyses by using antibody against HDA18 in transgenic HDA18 overexpression Arabidopsis plants. These analyses identified statistically significant enriched DNA associated with HDA18. A total of 286 DNA fragments were enriched as putative HDA18 protein-binding sites.

overall_design: Root tips of P35S:HDA18 Arabidopsis plants (Col-0) ChIPed with HDA18 antibody vs. pre-immune mouse serum.

first: Cui

last: Liu

first: Shunong

last: Bai


title: Relevance of Chromosome 2p Gain in Early Binet Stage A Chronic Lymphocytic Leukemia (SNP)

status: Public on Oct 12 2012

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by chromosomal aberrations of prognostic significance. Recent studies showed that gain of chromosome 2p is a recurrent lesion in CLL. We investigated the 2p gain and its relationship with prognostic biomarkers in a prospective series of 287 early-stage CLLs (Binet A). The 2p gain was detected by FISH in 17 patients (6%) and further characterized by single nucleotide polymorphism-array. Overall, unfavorable cytogenetic deletions, i.e. del(11)(q23) and del(17)(p13) (P=0.002) as well as unmutated (UM) status of IGHV (P<1×10-4) and CD38 (P<1×10-4) and ZAP-70 positive expression (P=0.003) were significantly more prevalent in 2p gain cases. Furthermore, 2p gained patients showed a significantly higher occurrence of stereotyped HCDR3 sequences compared to 2p normal CLLs (P=0.009). Among the stereotyped subsets, the incidence of subset #1 in 2p positive patients was significantly higher than that found in the remaining CLLs (P=0.031). Finally, gene expression profiling analysis identified a number of genes significantly upregulated in 2p gain CLLs. Among those located at 2p, NCOA1 and ROCK2 are known for their involvement in tumor progression in several human cancers, whereas among those located in different chromosomes, CAV1 at 7q31.1 has been recently identified to play a critical role in CLL progression. Our study indicates that 2p gain is a recurrent lesion in early CLL, correlated with the major biological and cytogenetic risk markers of the disease. Moreover, we provide insights to define novel candidate genes that may play additional pathogenetic roles in CLL.

overall_design: This series of microarray experiments contains the genome-wide profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 10 patients (Binet stage A) showing 2p gain alteration. Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labeled DNA were hybridized on GeneChip Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).

first: Sonia

last: Fabris

first: Laura

last: Mosca

first: Giovanna

last: Cutrona

first: Marta

last: Lionetti

first: Gabriella

last: Ciceri

first: Marzia

last: Barbieri

first: Francesco

last: Maura

first: Serena

last: Matis

first: Massimo

last: Gentile

first: Anna

middle: G

last: Recchia

first: Emanuela

last: Pesce

last: Di Raimondo

first: Caterina

last: Musolino

first: Marco

last: Gobbi

first: Nicola

last: Di Renzo

first: Francesca

middle: R

last: Mauro

first: Maura

last: Brugiatelli

first: Fiorella

last: Ilariucci

first: Simonetta

last: Zupo

last: Angrilli

first: Gianni

last: Quintana

first: Ugo

last: Consoli

first: Giovanni

last: Bertoldero

first: Paolo

last: Di Tonno

first: Alberto

last: Fragasso

first: Stefano

last: Molica

first: Pellegrino

last: Musto

first: Maria

middle: C

last: Cox

first: Gianluca

last: Festini

first: Iolanda

last: Vincelli

last: Sacchi

last: Baldini

first: Agostino

last: Cortelezzi

last: Federico

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: CCND2 rearrangements are the most frequent genetic events in Cyclin D1-negative mantle cell lymphoma

first: Sílvia

last: Beà

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Itziar

last: Salaverria

first: Silvia


title: microRNA expression data in bronchial epithelial cells from healthy and asthmatic donors

status: Public on Oct 31 2012

city: Chapel Hill

first: Melanie

middle: J.

last: Jardim

state: NC

address: 104 Mason Farm Road

department: NHEERL

institute: U.S. EPA

summary:
Airway inflammation is the hallmark of asthma and suggests a dysregulation of homeostatic mechanisms. MicroRNAs (miRNAs) are key regulators of gene expression, necessary for the proper function of cellular processes.
We used miRNA microarrays to  compare the profiles of human bronchial epithelial cells from healthy and asthmatic donors

overall_design: Human bronchial epithelial cells were isolated from healthy and asthmatic donors.  RNA was extracted and miRNA expression was analyzed on Affymetrix miRNA microarrays. We sought to utilize miRNA expression as a tool for understanding underlying biological differences in BECs from healthy and asthmatic donors.

middle: J

first: Lisa

last: Dailey

first: David

last: Diaz-Sanchez


title: Expression data from normal melanocyte, melanoma cells and their exosomes (microRNA)

status: Public on Oct 10 2012

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

summary: Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression.

overall_design: Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines. RNA was quantified using Nanodrop ND-1000. The integrity of these total RNAs was assessed using Agilent 2100 Bioanalyzer. Total high-quality RNA was labelled. The miRNA array profiling was performed by using the Affymetrix GeneChip miRNA Array 1.0. Two different RNA preparations from two cell lines and their exosomes were used, except that only one RNA preparation was used for HEMa-LP exosome miRNA array. Due to the limited number of passages (approximately 10), adequate exosomal RNA and proteins from HEMa-LP cells for multiple analyses was not available.

first: Deyi

last: Xiao

first: Joanna

last: Ohlendorf

first: Yinlu

last: Chen

first: Douglas

middle: D

last: Taylor

first: Shesh

last: Rai

first: Sabine

last: Waigel

first: Wolfgang

last: Zacharias

first: Kelly

middle: M

last: McMasters


title: miRNA expression data from lean PCOS adipose vs BMI matched control women

status: Public on Sep 06 2012

city: Augusta

first: Yen-Hao

state: GA

address: 1459 Laney-Walker Blvd

department: OB/Gyn

institute: Georgia Health Sciences University

summary:
Why ~70% of women with polycystic ovary syndrome (PCOS) have intrinsic insulin resistance (IR), above and beyond that associated with body mass, including dysfunctional glucose metabolism in adipose tissue (AT), remains a fundamental question. In these experiments, we sought to explore the role of miRNAs in the AT of PCOS and matched controls. Analysis determined that PCOS AT has a differentially expressed miRNA profile, including upregulated miR-93. We observed a significant association between HOMA-IR, and GLUT4 and miR-93 expression in human AT. Our results point to a novel mechanism for regulating insulin-stimulated glucose uptake via miR-93, and demonstrate upregulated miR-93 expression in PCOS, possibly accounting for the IR of the syndrome, and also in non-PCOS women with IR.
We performed miRNA microarrays to determine PCOS-related miRNA expression in adipose derived from lean PCOS patients and matched control women.

overall_design: We analyized miRNA from total RNA extracted from subcutaneous (sc) adipose tissue from three lean PCOS patients and three matched control women.

first: Saleh

last: Heneidi

first: Jung-Min

last: Lee

middle: W

last: Stepp

first: Lawrence

last: Layman

first: Gloria

last: Gamboa

first: Gregorio

last: Chazenbalk

first: Ricardo

last: Azziz


title: Genome-wide haplotyping of human single cells

status: Public on Oct 01 2012

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

summary: A method to infer genome-wide haplotypes from the analysis of one or two single (human) cells has tremendous applicative value. It would revolutionize not only preimplantation genetic diagnosis of in vitro fertilized human embryos in the clinic, but also animal breeding programs by enabling genome-wide quantitative trait loci selection at the embryonic level. In addition, it allows to further scrutinize drivers of haplotype diversity, mainly meiotic homologous recombination as well as somatic (homologous) recombination processes that occur often during (human) tumorigenesis.  We developed a generic approach to type genome-wide single nucleotide polymorphisms in single human cells and to reconstruct genome-wide haplotypes of single or dual cell derived genotypes. Genome-wide sequences of syntenic alleles were determined for EBV-transformed lymphoblastoid cells as well as human blastomeres. To this end, multiple displacement amplified DNA samples of single cells were hybridized to Affymetrix 250K SNP-arrays. Different algorithmic designs were subsequently developed to assess from the single cell-derived SNP-probe intensities the sequence of syntenic alleles and to pinpoint accurately the majority of parental homologous recombination sites using a linkage-based approach.

overall_design: In total 12 amplified single human lymphoblastoid cell DNA samples, 3 amplified single human blastomere DNA samples and 19 non-amplified genomic DNA samples extracted from blood were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718).  The non-amplified genomic DNA samples extracted from blood were derived from 19 different persons belonging to 4 different families. The sample names of these 19 samples are respectively Family1_Individual1, Family1_mother, Family1_father, Family1_MaternalGrandmother, Family2_Individual2, Family2_mother, Family2_father, Family2_MaternalGrandmother, Family2_MaternalGrandfather, Family3_Individual3, Family3_Individual4, Family3_mother, Family3_father, Family3_MaternalGrandmother, Family3_MaternalGrandfather, Family4_mother, Family4_father, Family4_PaternalGrandmother, Family4_PaternalGrandfather. These 19 non-amplified genomic DNA samples extracted from blood were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12.  The 12 amplified single lymphoblastoid cell DNA samples were derived from Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) of four different persons. Three  amplified single lymphoblastoid cell DNA samples from individual “Family1_Individual1”, three  amplified single lymphoblastoid cell DNA samples from individual “Family2_Individual2”, three  amplified single lymphoblastoid cell DNA samples from individual “Family3_Individual3” and three  amplified single lymphoblastoid cell DNA samples from individual “Family3_Individual4”. The samples names of these 12 are respectively: Family1_Individual1_SingleCell1, Family1_Individual1_SingleCell2, Family1_Individual1_SingleCell3, Family2_Individual2_SingleCell1, Family2_Individual2_SingleCell2, Family2_Individual2_SingleCell3, Family3_Individual3_SingleCell1, Family3_Individual3_SingleCell2, Family3_Individual3_SingleCell3, Family3_Individual4_SingleCell1, Family3_Individual4_SingleCell2, Family3_Individual4_SingleCell3. These 12 amplified single lymphoblastoid cell DNA samples were genotyped using (1) the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the ‘Genotyping console 3.0.1’ software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm of the APT-1.10.1 package (Affymetrix Power Tools) using the ‘birdseed-dev’ command which is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html).  The 3 amplified single human blastomere DNA samples were derived from three different human blastomeres that belong to the same in vitro fertilized embryo. This embryo was conceived in vitro by using sperm of person “Family4_father” and an oocyte from person “Family4_mother”. The sample names of these 3 amplified single blastomere DNA samples are respectively: Family4_Blastomere1, Family4_Blastomere2, Family4_Blastomere3. These 3 amplified single human blastomere DNA samples were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12.

first: Evelyne

last: Vanneste

first: Hilde

last: Peeters

first: Peter

last: Konings

first: Yves

last: Moreau

first: Jean-Pierre

last: Fryns

first: Thomas

last: D'Hooghe

first: Eric

last: Legius

first: Joris

last: Vermeesch


title: Changes of miRNA expression in granulocytes of patients with polycythemia vera (PV) and essential thrombocythemia (ET) receiving INCB018424 in a Phase 2 study

status: Public on Sep 26 2012

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

summary:
A global microRNA expression profile was obtained from gradient-purified granulocytes (>95% pure) collected at the time of screening and at cycle 4 of treatment
Protocol #18424-256 is a Phase 2 study of the JAK1 and JAK2 inhibitor INCB01842 in patients with advanced polycythemia vera (PV) and essential thrombocythemia (ET) refractory to hydroxyurea;

overall_design: The aim was to to determine whether treatment with INC180424 was associated with changes in the global microRNA expression profile we compared granulocytes collected at baseline (screening) and at cycle 4

first: Alessandro

last: Vannucchi

first: Rossella

last: Manfredini

first: Paola

last: Guglielmelli

first: Lisa

last: Pieri


title: Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [miRNA]

city: Bethesda

first: Steven

last: Kern

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

summary:
Normal human bronchial epithelial (NHBE) cells cultured in an air-liquid interface (ALI) system form a polarized, pseudostratified epithelium composed of basal, ciliated and goblet cells that closely resemble the in vivo airway epithelium structure. ALI cultures of NHBE cells provide a unique in vitro system to investigate airway epithelial biology, including developmental, structural and physiologic aspects. MicroRNAs (miRNAs) are short, single-stranded, non-coding RNAs of 20-23 nucleotides that down-regulate gene expression by either inducing degradation of target mRNAs or impairing their translation. They are phylogenetically well conserved, which probably implies an important role of miRNAs in biological processes. In this way, we wanted to shed some light on miRNA specific roles and the relationship with their mRNA targets during airway epithelium differentiation.
By using microarrays, we studied the changes in expression of microRNAs in normal human bronchial epithelial cells as they differentiate from an undifferentiated monolayer to a differentiated pseudostratified epithelium after 28 days of air-liquid interface (ALI) culture, when epithelial cells differentially express basal, ciliated and goblet cell markers.

overall_design: Normal human bronchial epithelial cells were cultured in an air-liquid interface (ALI) system and harvested at three different time-points: subconfluent, confluent and day 28 of ALI. Samples were processed for total RNA (including small RNAs) extraction and hybridization on Affymetrix microarrays.  All the experiments were performed by triplicate.

first: Asuncion

last: Martinez-Anton

first: Milena

last: Sokolowska

first: A

middle: S

last: Davis

first: Sara

last: Alsaaty

first: Jeffery

middle: K

last: Taubenberger

first: Junfeng

last: Sun

first: Robert

middle: L

last: Danner

first: Michael

last: Eberlein

first: Carolea

last: Logun

first: James

middle: H

last: Shelhamer


title: In vivo and in vitro investigations of heterozygous nebulin knock-out mice reveal similarities with mild human form of nemaline myopathy

status: Public on Sep 01 2012

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

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

platform_organism:
Mus musculus
synthetic construct


title: MicroRNA expression data from human renal cell cancer subtypes

status: Public on Oct 03 2012

city: Erlangen

first: Sven

last: Wach

address: Glueckstrasse 6

department: Dept. of Urology

institute: University Hospital, Friedrich-Alexander-University Erlangen-Nuernberg

summary: MicroRNAs play a vital role in the process of tumorigenesis. To identify and characterize miRNA Expression in renal cell cancer, we performed microarray based screening of miRNA expression profiles in clear cell, papillary type 1 and papillary type 2 renal cell cancer.

overall_design: We selected cases of confirmed clear cell, papillary type 1 and papillary type 2 renal cell carcinoma and generated pairs of tumor and corresponding normal tissue by manual microdissection.

first: Arif

last: Ekici

first: Andre

last: Reis


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

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

country: Austria

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

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae W303


title: Profiles of genomic instability in high-grade serous ovarian cancer (HGSC) predict treatment outcome

city: Boston

first: Zhigang

last: Wang

state: MA

address: 450 Brookline Ave SM936A

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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

summary:
Profiling of loss of heterozygosity (LOH) in HGSC, subcrouping HGSC by LOH-based clustering  and comparing to the LOH profiles of triple-negative breast cancer [previously submitted; GSE19594].
Study for the correlation of LOH burdern and LOH-based subgroups to clinical response to platinum-based chemotherapy in patients suffered from HGSC.

overall_design: SNP data (Affymetrix GenChip 250K SNP Nsp) from 47 high grade serous ovarian cancer were generated and used for LOH and copy number analysis, LOH-based hierarchical clustering to subclassify HGSC, and comparison to the chromosomal alterations in high grade brest cancer. The associstion between LOH-based subgroups and LOH burden and clinical resposne to platinum-based chemotherapy was investigated. The results were validated in two independent public opening datasets.

first: Nicolai

last: Birkbak

first: Aedín

last: Culhane

first: Ronny

last: Drapkin

first: Joyce

last: Liu

first: Aquila

last: Fatima

first: Ruiyang

last: Tian

first: Kathryn

last: Daniels

first: Huiying

last: Piao

first: Alexander

last: Miron

first: John

last: Quackenbush

first: Ross

last: Berkowitz

first: J

last: Iglehart

first: Ursula

last: Matulonis


title: miRNA Expression data from maize young leaf and developing seed

status: Public on Aug 07 2012

first: Mingming

last: Kang

address: No. 2 Yuanmingyuan West Rd,

institute: China Agricultural University

summary: miRNAs of at least 2 times expression level higher in seeds were all from the miR319, miR171 and miR166 family. In leaves, most up-regulated miRNAs included miR399a/c/d/e, miR408, miR159c/d, miR156k/j, miR160a/b/c/d/e and miR164a/b/c/d

overall_design: We intend to identify the up-regulated miRNAs in maize seed and screen for key miRNAs involved in maize seed development

first: Qian

last: Zhao

first: Dengyun

last: Zhu

first: Jingjuan

last: Yu


title: Role of microRNAs on the pattern of gene expression in the different segments of human epididymis.

status: Public on Jul 01 2012

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary:
BACKGROUND: The molecular mechanisms resulting in the establishment of regionalized gene expression in the human epididymis involve numerous and complex regulatory elements that have not yet been fully elucidated. Interestingly, more than 200 microRNAs (miRNAs) have been identified in the human epididymis that could be involved in the regulation of mRNA stability and post-transcriptionnal expression in this organ.
METHODS: Using a global miRNA microarray approach, we investigated the correlation between the miRNA signature and the gene expression profile found in three distinct regions (caput, corpus and cauda) of human epididymides from 3 donors. In silico prediction of transcript miRNA targets was performed in silico using TargetScan and Miranda software’s. To experimentally verify some of these data, FHCE1 immortalized epididymal cell lines were cotransfected with mimics microRNAs and plasmid constructs containing the 3’UTR of target genes downstream of the luciferase gene.
RESULTS: We identified 35 miRNAs differentially expressed between the different segments of the epididymis (fold change > 2, P < 0.01). Among these miRNAs, miR-890, miR-892a, miR-892b, miR-891a, miR-891b belonging to the same cluster located on the X chromosome and specifically expressed in epididymal tissues, are significantly more expressed in the corpus and cauda regions compared to the caput. Interestingly, a strong negative correlation (r= -0,89, P <0.001) was found between the pattern of expression of miR-892b and its potential mRNA target Esrrg (Estrogen Related Receptor Gamma), with miR-145 and Cldn10 mRNA (r= -0,92, P<0.001) and with miR-145 and Cftr mRNA (r= -0,69, P<0.05). We confirmed that miR-145 and miR-892b inhibit the expression of the luciferase reporter via Cldn10 and Esrrg 3’ UTRs respectively, whereas miR-145 does not affect the expression of luciferase after its co-transfection with the plasmid containing the Cftr 3’UTR.
CONCLUSION: Overall, our study shows that the expression of miRNAs is segmented along the different regions of the human epididymal duct and correlates with the pattern of target gene expression in these regions. Therefore, epididymal miRNAs may be in charge of the maintenance of gene expression profile in the epididymis that dictate segment-specific secretion of proteins and establish physiological compartments that directly or indirectly affect sperm maturation and fertility.

overall_design: Normal human epididymides from three donors of 26–50 years of age, were collected and dissected into 3 anatomical regions (caput, corpus and cauda).A cross-comparison between the miRNA signature found in different segments was performed using GeneChip miRNA Array 1.0 (Affimetrix, Santa Clara, CA).

first: Clémence

last: Belleannée

first: Véronique

last: Thimon

first: Daniel

last: Cyr

first: Christine

last: Légaré

first: Louis

last: Garneau

first: Robert

last: Sullivan


title: Affymetrix SNP array data for DNA copy number analysis of supernatant DNA

status: Public on Jul 09 2012

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

summary: DNA contained in the supernatant of cultured malignant cells as well as from plasma/serum of cancer patients is able to transform recipient immortal murine NIH3T3 cells. We demonstrate for the first time that human circulating DNA is able to drive tumor progression in an immunocompetent colon carcinogenesis rat model and that treatment with DNAse I/proteases has antitumor effects in a xenograft nude mice model. DNA copy number analysis of the DNA purifed from the supernatat of SW480 cell cultures was analyzed to determine if specific regions of the genome are represented in this fraction.

overall_design: We hybridized genomic DNA from parental SW480 cells, the DNA isolated from supernatant of SW480 cells, onto the 500K Affymetrix genotyping array set, following the manufacturer´s instructions, and compared their DNA copy number profile against a common reference generated using data from the International HapMap project.

first: Alfonso

last: González


title: Deregulation of miRNAs in Infant Outflow Tract Myocardium of Non-syndromic Tetralogy of Fallot

status: Public on Aug 15 2012

city: Shanghai

first: jin

last: zhang

address: 130# Dong'An Road, R307 Ming Dao building

institute: Fudan University

summary: Tetralogy of Fallot (TOF) is one of the most common heart defects in children and the underlying mechanisms remain elusive. miRNAs are a recently discovered class of regulators of gene expression and are becoming increasingly recognized as important regulators of heart development and function. The objective of the present study was to identify miRNAs that are abnormally expressed in clinical infant outflow tract myocardium tissues of TOFs.

overall_design: Microarray was used to analyze miRNA expression profiles in infant outflow tract myocardium tissues of TOFs and paired normal ones.

first: Jin

last: Zhang

first: Duan

last: Ma


title: The Role of the E2F1 transcription factor in the innate immune response to systemic LPS [miRNA]

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Our recent study of gene expression in mice treated with LPS systemically identified the E2F1 transcription factor as a novel regulator of innate immune response in lung, liver, and spleen tissue. Our follow up studies showed that RNAi-mediated inhibition or E2F1 gene deficiency lead to reduced inflammatory response to LPS in vitro and in vivo. Furthermore, a clear role for the role of miRNAs in the regulation of innate immune response to LPS has emerged.  In the current study, we further examined B6;129E2F1-/- and B6x126 F2 mice in the systemic LPS model and used gene expression profiling to identify a defect in the coagulation cascade that contributes to increased morbidity of B6;129E2F1-/- mice despite their reduced systemic inflammatory response. We also studied miRNA expression profiles identified miRNAs that are differentially expressed in B6;129E2F1-/- but not B6x129 F2 mice.

overall_design: 32 mice (4-6) per group, E2F+/+ or E2F-/- genotype, treated with saline or LPS, 6 or 20 hrs

first: Laura

last: Warg

first: Judy

last: Oakes

first: Rachel

last: Burton

first: Holly

last: Rutledge

first: Steve

last: Groshong

first: Ivana

middle: V

last: Yang


title: Non-allelic homologous recombination between retrotransposable elements is a major driver of de novo unbalanced translocations.

status: Public on Jul 13 2012

first: Caroline

last: Robberecht

institute: Catholic University Leuven

summary: Large scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo translocations and mapped the breakpoints in 9. Surprisingly, in contrast to balanced translocations, we identify non-allelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding implicates (retro)transposons to be a major driver of genomic rearrangements and exposes a profoundly different mutational mechanism compared to balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements.

overall_design: In total 36 non-amplified genomic DNA samples  (12 patients plus parents) extracted from blood or amniocytes were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718).

first: Thierry

last: Voet

first: Masoud

middle: Z

last: Esteki

first: Beata

last: Nowakowska

first: Joris

last: Vermeesch


title: In vivo and in vitro investigations of heterozygous nebulin knock-out mice reveal similarities with mild human form of nemaline myopathy [miRNA]

first: Carsten

last: Sticht

summary: In the present study, we used a multimodal approach including protein and gene expression analysis and combined in vivo and in vitro measurements of force production. Overall, we aimed at investigating the functional impact of the expression of a single nebulin allele.

overall_design: Comparison of the miRNA expression profile of quadriceps in 3 nebulin wild type mice with 3 nebulin heterozygous mice.

first: C

last: Gineste

first: J

last: De Winter

last: Kohl


title: Expression data from bladder tumors and adjacent normal tissues

status: Public on Jul 07 2012

first: qinsong

last: zeng

address: 168 Changhai Road

institute: Changhai Hospital

summary:
miRNAs are involved in cancer development and progression,acting as tumor suppressors or oncogenes. Half of the human miRNAs are located in cancer-associated genomic regions and can function as tumor suppressor genes or oncogenes depending on their targets
miRNA profiling was performed on paired bladder cancer tissues and differentially expressed miRNAs were identified in BC and adjacent noncancerous tissues of any disease stage/grade.

overall_design: Ten paired bladder cancer tissues (5 low-grade non-muscle-invasive bladder cancer[NMIBC] and 5 high-grade muscle-invasive bladder cancer[MIBC]) were sent to CapitalBio Corp. (Beijing) for noncoding RNA microarray analysis. The microarray analysis was done as described on the Web site of CapitalBio. NMIBC samples include 07A, 19A, 23A, 24A and T63 while coresponding pairs include 07B, 19B, 23B, 24B and 63. MIBC samples include 10A, 20A, 21A, 34A and 49A while coresponding pairs include 10B, 20B, 21B, 34B and 49B.

first: Chuanliang

last: Xu

first: Qinsong

last: Zeng


title: The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [At35b_MR]

status: Public on Jun 18 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

type: Expression profiling by genome tiling array

summary: Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation.   Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root.   Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described.  To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date.

overall_design: 2 tissues X 3 treatments X 3 biological replicates

first: Nam-Hai

last: Chua

first: Jongchan

last: Woo

first: Cameron

last: MacPherson

first: Huan

last: Wang

first: Takatoshi

first: Matthew

last: Hannah

first: Xiu-Jie

first: Vladimir

last: Bajic


title: Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse and implications for therapy

status: Public on Jun 12 2012

city: Oxford

first: Thomas

last: Roberts

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression and are implicated in wide-ranging cellular processes and pathological conditions including Duchenne muscular dystrophy (DMD). We have compared differential miRNA expression in proximal and distal limb muscles, diaphragm, heart and serum in the mdx mouse relative to wild-type controls. Global transcriptome analysis revealed muscle-specific patterns of differential miRNA expression as well as a number of changes common between tissues, including previously identified dystromirs. In the case of miR-31 and miR-34c, up-regulation of primary-miRNA transcripts, precursor hairpins and all mature miRNAs derived from the same transcript or miRNA cluster strongly suggests transcriptional regulation of these miRNAs. The most striking differences in differential miRNA expression were between muscle tissue and serum. Specifically, miR-1, miR-133a and miR-206 were highly abundant in serum but down-regulated or modestly up-regulated in muscle, suggesting that these miRNAs are promising disease biomarkers. Indeed, the relative serum levels of these miRNAs were normalised in response to peptide-PMO mediated dystrophin restoration therapy. This study has revealed further complexity in the miRNA transcriptome of the mdx mouse, an understanding of which will be valuable in the development of novel therapeutics and for monitoring their efficacy.

overall_design: Male WT C57/B10 and male mdx C57/B10  mice (n=4) were sacrificed at eight weeks of age. The heart, quadriceps femoris, and diaphragm were dissected and flash frozen in liquid nitrogen-cooled isopentane. Samples were homogenised using Precellys 24 (Bertin Technologies, France), and RNA was extracted using TRIzol reagent (Invitrogen) as according to the manufacturer’s instructions.

first: K

last: Blomberg

first: Graham

last: McClorey

first: Samir

last: Andaloussi

first: Caroline

last: Godfrey

first: Corinne

last: Betts

first: Thibault

last: Coursindel

first: Michael

last: Gait

middle: I

last: Smith

last: Wood


title: The Role of the E2F1 transcription factor in the innate immune response to systemic LPS

first: David

last: Schwartz

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

overall_design: Refer to individual Series

first: Laura

middle: A

last: Warg

first: Judy

last: Oakes

first: Rachel

last: Burton

first: Holly

last: Rutledge

first: Steve

last: Groshong

first: Ivana

last: Yang


title: Identification and comparative analysis of microRNAs associated with low-N tolerance in rice genotypes

status: Public on May 25 2012

city: New Delhi

first: ALTAF

last: AHMAD

state: Delhi

address: Faculty of Science

department: Department of Botany

country: India

institute: Jamia Hamdard (Hamdard University)

summary:
Micro-RNA associated with low-N tolerance have been identified in rice (Oryza sativa) genotypes on the basis of differential expression of miRNA in low-N tolerant and low-N sensitive genotypes of rice. Since, miRNAs emerged as key players in plant responses and adaptation to stress, identification of low-N responsive miRNAs and their targets could help to uncover the molecular mechanisms of N-deficiency tolerance in plants.
We used affymetrix based GeneChip miRNA_2.0 Array to detail the global programme of miRNA expression variation in low-N tolerant (IC-547557) and low -N sensitive (Vivek Dhan).

overall_design: Low-N tolerant and low-N sensitive rice genotypes were grown using the nutrient medium containing  2 mM K2SO4, 2 mM MgSO4, 1 mM CaCl2, 0.3 mM NaH2PO4, 40 µM Fe-EDTA, 9 µM MnCl2, 25 µM Na2MoO4, 20 µM H3BO3, 1.5 µM ZnSO4, and 1.5 µM CuSO4. The nitrogen in the form of NH4NO3 was maintained as 0.01 mM (low-N condition). The pH of the nutrient solutions was adjusted to 6.0 and the solutions were changed every three days.  Twenty-day-old plants were sampled for expression studies of miRNA.

first: Altaf

last: Ahmad

first: Lata

last: Nischal


title: MicroRNAs may indirectly regulate other microRNAs

status: Public on Apr 09 2012

city: Atlanta

first: Shubin

last: Shahab

address: 310 Ferst Drive

department: Biology

institute: Georgia Institute of Technology

summary: MicroRNAs (miRNAs) are a class of regulatory RNAs that control the expression of genes critical to cell function. Ectopic expression of miRNAs has been shown to result in genome-wide changes in patterns of gene expression. While the reasons for these global alterations in gene expression patterns have been attributed to the ability of miRNAs to target multiple genes, and/or to induce indirect effects downstream of target genes, the molecular basis of indirect effects of miRNA regulation remains poorly understood. In this study, we demonstrate the potential of miRNAs to regulate other miRNAs. Using miRNA microarray analysis, we show that over 70 different miRNAs are differentially expressed ( ≥1.4 fold, FDR ≤ 5%) in human ovarian cancer cells after transfection with a single miRNA (miR-7). We present evidence that a major component of miR-7-induced changes in levels of miRNAs is the indirect consequence of miR-7-mediated alterations in levels of protein-coding genes (e.g., transcription and splicing factors) that exert trans-regulatory control on miRNAs.

overall_design: HEY cells were transfected with either hsa-miR-7 (2 biological replicates) or a negative control miRNA, miR-NC (2 biological replicates), and then grown in 6-well plates for ~48 hours. The difference in miRNA expression pattern between the miR-7-transfected cells and the miR-NC-transfected cells was determined using an Affymetrix GeneChip miRNA Array.

first: Lilya

last: Matyunina

first: John

middle: F

last: Mcdonald


title: miRNA expression profile of pre-transfected HEY cells

summary: MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We wanted to quantify the levels of endogenous miRNAs in pre-transfected HEY ovarian cancer cells to identify the highly expressed miRNAs. It was previously established that transfection of small RNAs can globally perturb gene expression, and one mechanism responsible for such alterations may involve de-repression of targets of endogenous miRNAs because of the saturation of the RISC complexes by the exogenously administered small RNA (Khan et al., 2009. Nat Biotechnol 27, 549-555). By measuring the levels of miRNAs in the pre-transfected HEY cells, we wanted to determine the miRNAs most highly expressed in HEY cells, and therefore, most likely to experience the effects of such competition.

overall_design: miRNAs were collected from duplicate wells of HEY cells grown in 6-well plates after ~64 hours of seeding (~1.5E5 cells/well). The miRNA expression pattern was determined using an Affymetrix GeneChip miRNA Array.


title: Natural variation in Arabidopsis thaliana transcriptomes

status: Public on May 22 2012

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

summary: A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana.  Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels.  To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays.  Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes.  The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions.  Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.

overall_design: Wild type accessions Col-0 were grown on soil at 16°C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0R®). Three biological replicates were performed for each accession.

first: Jesse

last: Hollister

first: Lisa

first: Ya-Long

last: Guo

first: Detlef

last: Weigel

first: Brandon

last: Gaut


title: Familial dominant diarrhea caused by an activating GUCY2C mutation is also associated with inflammatory bowel disease

status: Public on Apr 10 2012

city: Bergen

first: Torunn

last: Fiskerstrand

address: Jonas Lies vei

department: Center for medical genetics and molecular medicine

country: Norway

institute: Haukeland University Hospital

summary: BACKGROUND   Familial diarrheas are mostly severe recessive diseases. Here we describe the clinical picture and dominant genetic cause of a novel disease in 32 members of a Norwegian family. The  chronic diarrhea is of early onset, relatively mild, and is combined with increased susceptibility to intestinal inflammation, ileus and oesophagitis.  METHODS   Whole genome SNP-analysis was used to identify a single candidate locus for dominant diarrhea on chromosome 12, followed by sequencing of the GU2CY gene. This encodes guanylyl cyclase 2C, an intestinal receptor for bacterial heat-stable enterotoxins and the peptides uroguanylin and guanylin. Functional studies of a missense mutation were performed after heterologous expression of the mutant receptor in HEK293T cells. The therapeutic response to metformin, an inhibitor of the cystic fibrosis transmembrane regulator (CFTR), was investigated in 5 patients.   RESULTS   We identified heterozygosity for the first described pathogenic human mutation (c.2519G>T ) in the GUCY2C gene. The mutant receptor showed increased cGMP production in response to its ligands. This may cause hyperactivation of the CFTR and consequent increased chloride and water secretion from the enterocytes, resulting in chronic diarrhea. Treatment with the CFTR-inhibitor metformin significantly reduced the frequency of stools in affected individuals by 34-45%.   CONCLUSIONS   Increased GC-C signaling disturbs normal bowel function, as shown by the diverse symptoms in our patients, and seems to have a pro-inflammatory effect, either through increased Cl- secretion or additional effects of elevated cellular cGMP. The importance of genetic variants in the GC-C-CFTR-pathway for conditions like Crohn’s disease and IBS should be further explored.

overall_design: Linkage analysis  was performed (Allegro v 2.0) using Affymetrix 250K SNP arrays according to the manufacturer's directions on DNA extracted from  peripheral blood samples. This accession number contains the data for 25 individuals of family branch A  in the article.


title: Influence of RNA Labeling on Expression Profiling of MicroRNAs

city: Duarte

middle: S.

last: Kaddis

state: CA

address: 1500 East Duarte Road

department: Diabetes and Cancer Discovery Science

institute: City of Hope

summary: Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data quality.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Human brain/lung samples were each labeled in duplicate, at 1.0ug, 0.5ug, 0.2ug, and 0.1ug of total RNA, using two microRNA labeling kits (Genisphere Biotin and Biotin-HSR) that utilize the same labeling procedure but differ in the composition of the labeling reagent used to label the microRNA molecules in the samples.  A total of 32 arrays were used for this experiment. Additionally, synthetic microRNA spike-in experiments were also performed to establish the signal dynamic range of the microarray using the Biotin-HSR labeling kit. Two-fold serial dilution samples were prepared that contained from 5000 to 4.88 attomoles of miRNA.  A total of 12 arrays were used for this experiment, including a negative control sample.

first: Daniel

last: Wai

first: Jessica

last: Bowers

first: Nicole

last: Hartmann

first: Lukas

last: Baeriswyl

first: Sheetal

last: Bajaj

first: Michael

last: Anderson

first: Robert

last: Getts

first: Timothy

last: Triche


title: MicroRNA expression data from IL13-induced allergic airway inflammation of mice lungs

status: Public on Feb 23 2012

city: Los Angeles

first: Aik

middle: T

last: Ooi

address: 650 Charles E Young Dr S, Factor 9-240

department: Pediatrics

institute: UCLA

summary:
Epigenetic changes have been implicated in pathogenesis of asthma. We sought to determine if IL13, a key cytokine in airway inflammation and remodeling, induced miRNAs expression changes in the airways in conjunction with its transcriptional gene regulation.
For our studies, we used a well-characterized transgenic mouse model of allergic airway inflammation induced by IL13. In this model, IL13 is conditionally overexpressed in the mouse lung when treated with doxycycline. Upon IL13 induction, these mice showed inflammatory cell infiltration, pronounced emphysema, increased pulmonary compliance, lung volume enlargement, mucus metaplasia, and increased expression of matrix metalloproteinases and cathepsins in the lung.

overall_design: The CC10-rtTA-IL13 transgenic (TG) and wildtype (WT) mice were treated with doxycycline for seven days. Mice were euthanized and the left upper lobes from all mice were removed for RNA extraction using the TRIzol method.

first: Sonal

last: Ram

first: Alan

last: Kuo

first: Derek

last: Nickerson

first: Jennifer

last: Gilbert

first: Weihong

last: Yan

first: Matteo

last: Pellegrini

first: Talal

last: Chatila

first: Brigitte

middle: N

last: Gomperts


title: Expression data in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

status: Public on May 03 2012

city: Yokohama

first: Yukio

last: Kurihara

state: Kanagawa

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

department: CSRS

country: Japan

institute: Riken

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis  fry1-6, xrn2-4, xrn3-3 and xrn4-6 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: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Tetsuro

last: Toyoda

first: Motoaki

last: Seki


title: Genome-wide maps of circulating miRNA biomarkers for Ulcerative Colitis

status: Public on Feb 21 2012

city: Santa Clara

first: Radha

last: Duttagupta

address: 3450 Central Expressway

department: Applied Research

institute: Affymetrix

summary:
Circulating miRNAs has recently emerged as clinically relevant blood-based biomarkers for disease detection, tracking and prediction. The stability of these species combined with easy accessibility in circulation makes them attractive candidates for rapid and economic surveillance of broad spectrum disorders requiring invasive diagnosis.In this work we directly assess the utility of non-invasive blood-based biomarkers as an alternative strategy to accurately predict incidences of Ulcertaive Colitis.
Whole genome miRNA expression levels in Microvescicles , Peripheral Blood Mononuclear Cells (PMBC) and platelets from a cohort of 20 Ulcerative Colitis patients and 20 normal individuals were measured using Affymetric microarrays.

overall_design: 20 cases/controls in three fractions

first: Sharon

last: DiRienzo

first: Roger

last: Jiang

first: Jessica

last: Bowers

first: Jeremy

last: Gollub

first: Keith

last: Kearney

first: David

last: Rudolph

last: Kao

first: Tom

last: Stamato

middle: C

last: Jones


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA

status: Public on Jul 04 2012

city: Manchester

first: Jan

last: Taylor

address: Wilmslow Road

department: Bioinformatics

institute: Paterson Institute for Cancer Research

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

platform_organism:
Homo sapiens
synthetic construct

first: John

last: Hall

first: Janet

first: Amanda

last: Eustace

first: Helen

middle: R

last: Valentine

first: Joely

middle: J

last: Irlam

first: Crispin

last: Miller

first: Catharine

last: West


status: Public on Mar 12 2012

first: Stefan

last: Henz

address: Spemannstrasse 37-39

department: Department of Molecular Biology

overall_design: Wild type accessions Col-0, Bur-0 and C24 were grown on soil at 23°C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0R®). Three biological replicates were performed for each accession.

first: Korbinian

last: Schneeberger

first: Stephan

last: Ossowski

first: Felix

last: Ott

first: Juliane

middle: D

last: Klein

first: Lisa

middle: M

last: Smith

first: Jun

last: Cao

first: Joffrey

last: Fitz

first: Norman

last: Warthmann

first: Christa

last: Lanz

first: Daniel

last: Huson

first: Detlef

last: Weigel


title: Affymetrix SNP array data for paediatric ependymoma and constitutional DNA

status: Public on Feb 09 2012

city: Nottingham

first: John-Paul

last: Kilday

address: Derby Road

department: CBTRC

institute: University of Nottingham

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

summary:
Background: The high incidence of recurrence and unpredictable clinical outcome for paediatric ependymoma reflect the imprecision of current therapeutic staging and need for novel risk stratification markers. Gain of chromosome 1q has been reported as a frequent aberration and correlate of adverse outcome in ependymoma. We therefore evaluated a prognostic role for 1q25 gain across three age-defined European clinical trial cohorts of paediatric intracranial ependymoma.
Methods: The frequency of 1q gain in paediatric ependymoma was assessed across 51 tumours (42 primary, 9 recurrent) using Affymetrix® 500K SNP arrays. Gain of 1q25 was evaluated by interphase FISH (iFISH) across 189 primary intracranial ependymomas from children treated on the CCLG/SIOP CNS9204 (n = 60) and BBSFOP (n = 65) adjuvant chemotherapy trials, or with primary post-operative radiotherapy (SIOP CNS9904/RT group, n = 64). Results were correlated with clinical, histological and survival data.
Findings: Gain of 1q was the most frequent imbalance in primary (7/42, 17 %) and recurrent ependymomas (3/9, 33 %). Gain of 1q25 was the strongest independent predictor of tumour progression in both CNS9204 (HR 3·36, p = 0·0009) and BBSFOP (HR 4·10, p = 0·0009) trial cohorts. In contrast, 1q25 gain was not prognostic for the older CNS9904/RT only group (PFS: p = 0·37, OS: p = 0·95). Clinical variables implicated in adverse outcome amongst cohorts included incomplete tumour resection and posterior fossa location.
Interpretation: This is the first study to prospectively identify then validate a prognostic genomic marker for childhood ependymoma across independent prospective trial groups. 1q25 gain predicts progression in primary chemotherapy cohorts but not those treated by post-operative radiotherapy. We propose 1q25 gain is incorporated as an adverse marker into future European chemotherapeutic clinical trial design.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from flash frozen tumour specimens and patient-matched peripheral blood
Copy number analysis of Affymetrix 500K SNP arrays was performed for DNA from 51 ependymomas and 40 constitutional DNA samples.
Analysing broad genomic aberrations in 51 paediatric ependymomas, looking particularly at 1q gain.

first: Richard

last: Grundy


title: Heterosis of Arabidopsis C24 x Col hybrids is associated with increased photosynthesis capacity.

status: Public on Mar 06 2012

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

country: Australia

institute: CSIRO

summary: Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1).  Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS).  At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid.  Many of these genes are involved in chlorophyll biosynthesis and photosynthesis.  The rate of photosynthesis was constant per unit leaf area in parents and hybrids.  Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis.  The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period.  At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS.  The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass.  In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis.  In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased.

overall_design: Whole plants in Col, C24, and their F1 hybrids with two replications

first: Ryo

last: Fujimoto


title: Effects of Ars2 or DGCR8 siRNA on microRNA expression

status: Public on Feb 01 2012

city: New York

first: Scott

last: Olejniczak

state: NY

address: 417 E68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Ars2 is a component of the nuclear cap-binding complex that is required for cellular proliferation and contributes to microRNA biogenesis. Arrays were performed to determine the repertoire of microRNAs that change following knock-down of Ars2.  Knock-down of DGCR8 was also performed to determine which microRNAs were expressed and had half-lives short enough to significantly decrease over the duration of the experiment.

overall_design: 9 samples were analyzed including: three biological replicates of control siRNA-transfected HeLa cells, HeLa cells transfected with three independent siRNAs targeting Ars2, or HeLa cells transfected with three independent siRNAs targeting DGCR8.

first: Josh

last: Gruber

first: Gideon

last: Dreyfuss

first: Craig

middle: B

last: Thompson


title: Inhibition of Jak2 in SET2 cell line with INC424 (two time points and 3 dose levels in triplicate)

status: Public on Feb 08 2012

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

summary: SET2 cells were incubated with increasing concentration of INC424/Ruxolitinib for 3-6 h and RNA was purified. Affymetrix Genechip miRNA array 2.0 was used to identify miRNA species showing a differential expression in treated cells compared with control cells.

overall_design: Exponentially growing SET2 cells were cultured in medium supplemented with 10% fetal bovine serum in the presence or the absence (control cells) of 160, 800 e 1,600 nM concentrations of the JAK1 and JAK2 inhibitor INC424/Ruxolitinib for 3 and 6 h. Triplicate cultures were prepared for each drug concentration and culture time. Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA. Total RNA (500ng for samples) was labeled using the FlashTag Biotin HSR kit (Genisphere) and hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's protocols.

first: Alessandro

last: Vannucchi

first: Rossella

last: Manfredini

first: Ruggero

last: Norfo


title: Affymetrix SNP array data for acute T-cell leukemia/lymphoma (ATL)

city: Tokyo

first: Aiko

last: Sato-Otsubo

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

institute: University of Tokyo

summary: SNP array analysis was performed using 168 ATL specimens.

overall_design: To obtain genotypes and intensities for each SNP, Affymetrix 250K SNP arrays were performed for 168 ATL samples.

first: Makoto

last: Yamagishi

first: Kazumi

last: Nakano

first: Ariko

last: Miyake

first: Tadanori

last: Yamochi

first: Yayoi

last: Kagami

first: Akihisa

last: Tsutsumi

first: Yuka

last: Matsuda

first: Satsuki

last: Muto

first: Atae

last: Utsunomiya

first: Kazunari

last: Yamaguchi

first: Kaoru

last: Uchimaru

first: Seishi

last: Ogawa

first: Toshiki

last: Watanabe


title: NCI60 Affy500K Profiling

city: Rochester

first: xiaoyang

last: ruan

state: MN

address: 200 1st Street

department: Health Science Research

institute: Mayo Clinic

summary: Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

overall_design: Runs of homozygosity analysis was done for 63 cell lines by both dChip basic-HMM method and PLINK ROH module

first: Ruan

last: Xiaoyang

first: Reinhold

last: William


title: Differential miRNA expression caused by Dicer knockout in small intestine

status: Public on Jan 07 2012

city: Baltimore

first: Tai-Chung

last: Huang

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: Dicer knockout cause lipid metabolism dysregulation in small intestine. Analyses of transcriptomics and proteomics reveal key enzymes affected by Dicer knockout.

overall_design: Conditional knockout of Dicer in adult mice

first: Huang

last: Tai-Chung

first: Yang

last: Yi

first: Pandey

last: Akhilesh


title: MicroRNA expression data from human breast cancer cell lines after demethylation treatment.

status: Public on Jan 24 2012

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
The contribution of aberrant DNA methylation and the downstream effects in tumorogenesis through silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations can be reversed, we investigated the effects of the epigenetic therapy in breast cancer cell lines.
We used microarrays to investigate the global microRNA expression profile after demethylation treatment with 5-aza-2’-deoxycytidine (DAC) in breast cancer cell lines and identified distinct classes of early and late systematic stable or transient effects of the treatment.

overall_design: Three selected breast cell lines including MDA-MB231, SKBR3, BT549, HS578T, MCF7 and HB2 (a breast epithelial cell line as control) were subject for miRNA isolation before treatment, after treatment with DAC and at five point follow-ups (1st, 3rd, 5th, 7th and 10th passages) at “drug holiday” condition and hybridized on Affymetrix microarrays.

first: Frank

last: Staedtler

first: Martin

last: Schumacher

first: Nicole

last: Hartmann


title: miRNA expression profiling of human immune cell subsets (Roche)

status: Public on Jan 31 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

summary: Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs.  mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes.  Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes.  These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network.  miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity.

overall_design: Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry.  Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used.  RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.

first: Florence

last: Allantaz

first: Tobias

last: Bergauer

first: Palanikumar

last: Ravindran

first: Michel

last: Rossier

last: Ebeling

first: Laura

last: Badi

first: Bernhard

last: Reis

first: Hans

last: Bitter

first: Matilde

last: D'Asaro

first: Alberto

last: Chiappe

first: Sriram

last: Sridhar

first: Gonzalo

last: Duran Pacheco

first: Michael

middle: E

last: Burczynski

first: Denis

last: Hochstrasser

first: Jacky

last: Vonderscher

first: Thomas

last: Matthes


title: ChIP-on-chip analysis of H3K27me3 levels in leaves and calli

status: Public on Jan 01 2012

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured with appropriate plant hormones. Recent studies demonstrated that callus resembles the tip of a root meristem, even if it is derived from aerial organs. However, the underlying mechanism that guides differentiated organs to form callus is unknown. Here we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is critical in callus formation. During culture of leaf explants, the H3K27me3 level was decreased first at certain auxin-pathway genes, and then increased at the leaf- but decreased at the root-preferentially expressed genes. In addition, only the root but not the leaf explants of the Polycomb group (PcG) mutants can normally form callus. Our data indicate that PcG and H3K27me3 demethylation pathways act separately in reprogramming of H2K27me3 distributions, and also suggest that this is a general mechanism leading to cell fate transition.

overall_design: We analyzed the genome-wide profiles by the ChIP-on-chip assay to determine genes with altered H3K27me3 modifications between the leaf and the callus

last: Xu

first: Chongsheng

last: He


title: Expression data from human breast cancer cell lines after demethylation treatment

first: Ramin

last: Radpour

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

overall_design: Refer to individual Series


title: miRNA expression profiling of human immune cell subsets (HUG)

first: Donavan

last: Cheng

first: Florence

last: Allantaz

first: Tobias

last: Bergauer

last: Ravindran

last: Rossier

first: Martin


title: Role of microRNAs in Neural Stem Cell-supported Endothelial Morphogenesis

city: Albuquerque

first: Tamara

last: Roitbak

state: NM

address: 2212 Lomas NE

department: Neurosurgery

institute: UNM

summary: We checked whether the inhibition of the FGF, VEGF, and TGF signaling pathways would influence the miRNA profile in ECs, co-cultured with NSPCs.

overall_design: EC/NSPC co-cultures were incubated with FGF/VEGF receptor inhibitor PD 173074 (1μM in DMSO), and the TGF-β receptor inhibitor SB431542 (10μM in DMSO, Millipore)

first: Olga

last: Bragina

first: Jamie

middle: L

last: Padilla

first: Gavin

middle: G

last: Pickett


title: Affymetrix SNP array data for short-segment Hirschsprung trios

status: Public on Mar 18 2012

city: Valencia

first: Joaquín

last: Dopazo

state: Valencia

address: c/ Eduardo Primo Yufera, 3

department: Computational Genomics

institute: Centro de Investigación Príncipe Felipe (CIPF)

summary: Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a functional association study (pathway-based analysis) has been conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung's disease that have been further validated in a larger population of 146 trios. The study revealed a strong association of 10 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes to the disease. A total of 10 new loci among the preselected candidates were found to be significantly associated to HSCR. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases.

overall_design: DNA derived from peripheral blood was hybridized to Affymetrix GeneChip® 500K mapping arrays. In total, 53 trios were analyzed consisting of affected child and their unaffected parents.

first: Raquel

last: Fernandez

first: Marta

last: Bleda

first: Rocío

last: Nunez-Torres

first: Ignacio

last: Medina

first: Berta

last: Luzon-Toro

first: Luz

last: Garcia-Alonso

first: Ana

last: Torroglosa

first: Martina

last: Marba

first: Maria

last: del Valle Enguix-Riego

first: David

last: Montaner

first: Guillermo

last: Antinolo

first: Salud

last: Borrego


title: Persistent Alterations in the imprinted miRNA and snoRNA populations in mouse models of fetal alcohol spectrum disorders (FASD)

status: Public on Dec 14 2011

city: South San Francisco

first: Benjamin

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

summary:
We sought to characterize the persistnet changes in brain miRNAs across multiple mouse models of fetal alcohol exposure
We used miRNA expression arrays to characterize and observe the deregulation of brain specific ncRNAs

overall_design: Whole brain tissue was harvested from day 70 fetal alcohol exposed males and matched controls for RNA extraction and hybridization to affymetrix miRNA 2.0 arrays. We obtained tissue from four models: Trimiester 1,2, and 3, injections and contious preference drinking.

first: Katarzyna

last: Janus

first: Morgan

last: Kleiber

first: Eric

last: Diehl

first: Shiva

last: Singh


title: miRNA profiling during cardiomyocyte-specific differentiation of murine embryonic stem cells based on two different miRNA array platforms

status: Public on Dec 31 2011

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

summary: miRNA plays a critical role in a wide variety of biological processes Profiling miRNA expression during the differentiation of embryonic stem cells will help us to understand the regulation pathway of differentiation, therefore to explain disease mechanisms and to find possible therapeutical targets. In this study miRNA expressions were profiled during cardiomyocyte-specific differentiation of murine embryonic stem cells with high-throughput microarray platforms.

overall_design: Two high throughput platforms (Affymetrix and Febit) were involved in miRNA profiling in order to compare the effect of platform on miRNA profiling result as well as to increase the plausibility of target miRNA identification. Four time points (day 0, day 12, day 19, day 26) which correspond to different stages during cardiac-specific differentiation were chosen for the miRNA profiling study.

first: Silke

last: Schwengberg

first: Bernd

last: Denecke


title: Affymetrix SNP array data of mixtures of tumor and normal DNA

status: Public on Dec 30 2011

city: Boston

first: Qiyuan

last: Li

address: 44 Binney Street

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Single nucleotide polymorphism (SNP) microarrays are commonly applied to tumors to identify genomic regions with copy number alterations (CNA) or loss of heterozygosity (LOH). However, in typical tumor specimens collected in clinical studies, up to 60% of the DNA derives from stromal cells with a normal genome, resulting in attenuated sensitivity to true somatic aberrations in the tumor. Here we describe SNPfilter, a model-based method to decompose SNP array data from heterogeneous tumor specimens into their corresponding normal and tumor profiles. Unlike existing methods, SNPfilter does not require paired normal control data. We assessed the performance of this method using SNP array data representing cancer cell lines with aberrant genomes, B-cell lymphoblastoid cell lines with normal genomes, and defined mixtures of the two. In the pure tumor samples, SNPfilter identified CNA and LOH regions with accuracy similar to existing methods. In the mixture samples containing 40–80% tumor genomic DNA, SNPfilter yielded prediction sensitivity superior to existing methods. Thus, SNPfilter provides a powerful tool for discovery of clinically relevant somatic aberrations in tumor genomes.

overall_design:
Breast cancer cell lines HCC38 and HCC1143 and paired B lymphoblastoid cell lines HCC38-BL and HCC1143-BL were purchased from ATCC.
Genomic DNA was isolated from cell lines using Qiagen DNA miniprep kit. To mimic tumor containing normal cells, DNA from HCC38 and HCC1143 cells was mixed with DNA from autologous B lymphoblastoid cells HCC38-BL and HCC1143-BL, respectively, in ratios (w/w) 100:0, 80:20, 60:40, 40:60, and 20:80.  Genomic DNA digested with NspI was amplified and hybridized to Affymetrix GeneChip Human Mapping 250K NspI arrays using recommended procedures (Affymetrix, Inc.).

first: Ruiyang

last: Tian

first: Zhigang

last: Wang

first: Zoltan

last: Szallasi


title: Mapping origins of replication in Arabidopsis thaliana: H4K5ac ChIP vs. unmodified H3 ChIP

status: Public on Nov 06 2011

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. Here we have profiled origins in Arabidopsis thaliana by high-throughput sequencing of purified nascent DNA strands. We have identified 1543 replication origins, which were uniformly distributed across the Arabidopsis genome and enriched in binding signals of two replication initiation proteins, CDC6 and ORC1. We have also analyzed novel epigenome maps of various histone modifications and found links between origins and epigenetic signatures, which differ from or have not been reported for other eukaryotic systems. Arabidopsis origins tend to be embedded in G+C-rich regions within the 5’ half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated H3 and H4, and depleted of H3K4me1 and H3K9me2. Our data establish the basis for the understanding of the epigenetic specification of origins of replication in Arabidopsis and have implications for the mechanisms of origin specification in other eukaryotes.

overall_design:
H4K5ac ChIP vs. unmodified H3 ChIP.
Our study utilizes the following datasets in addition to the data we generated:
H3K4me1: GSM343141
H3K4me2: GSM343143
H3K4me3: GSM343144
H3K9me2: GSM310840
H2AZ:    GSM307373

first: Xiaoyu

last: Zhang


title: Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species annotation

status: Public on Dec 01 2011

city: San Francisco

first: Marcus

last: Breese

address: 1550 Fourth St, 382

institute: UCSF

summary: While the heart is the first organ to form during development, the earliest molecular mechanisms surrounding specification and differentiation are not clear. In vertebrates, the first marker of cardiac specification is the expression of the homeobox transcription factor Nkx2-5 and its paralogs. While some downstream targets of Nkx2-5 have been discovered, they alone are not sufficient to completely rescue Nkx2-5 knock-downs, suggesting that other targets of Nkx2-5 regulation remain unknown. In order to identify early targets of Nkx2-5, Xenopus laevis embryos were injected with synthetic Nkx2-5 mRNA and changes in gene expression measured using Affymetrix GeneChips. To interpret the data, X. laevis genomic annotation was augmented using cross-species information from the CrossGene database followed by gene ontology enrichment, network analysis, spatial expression, and Nkx2-5 binding site predictions. This allowed us to compile a list of 99 UniGene clusters representing likely early targets of Nkx2-5.

overall_design:
Nkx2-5+GFP or GFP mRNA was injected into 8 cell Xenopus embryos. Total RNA was collected at St. 11.5.

comparison of gene expression profiles for treated vs, control

first: Matthew

middle: W

last: Grow

first: Howard

last: Edenberg


title: Gene expression profile for X.laevis embryo head vs.tail

summary: This dataset was used to as a filter to annotate the results from another experiment (GSE29791). We used these results to find genes that were enriched in the head regions. In this way, we could eliminate more ubiquitously expressed genes.

overall_design:
St. 18 embryos were bisected and RNA was collected from head and tail fragments. 3 individual heads and 3 tails were run, as well as 1 pool of heads and 1 pool of tails

comparison of gene expression profiles for tissues


title: The RING-containing protein, JMJ24 mono-ubiquitinates RDR2 to coordinate histone methylation and DNA methylation in Arabidopsis.

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: JMJ24 is  a RING motif containing Jumonji protein, whose E3 ligase activity is essential for communication between histone methylation and DNA methylation.In Arabidopsis JMJ24 is higly expressed in mature pollen. JMJ24 interacted with RDR2 and a single C4HC3 RING motif enabled JMJ24 to mono-ubiquitinate RDR2 for stabilization. RDR2 acted downsteam of JMJ24 for DNA methylation and local silencing. Here we performed tiling-array-based transcriptome profiling using mature pollen collected from WT and jmj24-1 and  found that hundreds of loci encoding transposon elements, noncoding RNAs and protein-coding genes are regulated by JMJ24.

overall_design: WT vs. jmj24-1

last: Xu

first: Shulin

last: Deng

first: In-cheol

last: Jang

first: Nam-Hai

last: Chua*


title: Gene Expression Profiling in Spontaneous Corneal Degeneration in Mice

status: Public on Aug 29 2011

city: Suzhou

first: Yiqiang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: When recruiting Balb/c mice for projects concerning corneas, we found that some mice presented corneal abnormality mimicking human corneal degenerations. The mice were unilaterally or bilaterally affected. The corneas of unilaterally affected mice were collected and pooled respectively into Normal and Degenerative samples. RNA was prepared and subjected to dual-labeling microarray analysis using the Capital Bio work station.

overall_design: Spontaneously degenerative corneas vs nomal corneas from same unilaterally affected mice. Dye swap was applied to reduce systemic error.

first: Lingling

last: Yang

first: Changkai

last: Jia

first: Chunxia


title: Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms

status: Public on Sep 12 2011

first: Aiko

last: Sato-Otsubo

summary: In this study, to obtain a complete registry of genetic lesions in MDS and to identify novel therapeutic targets, we performed SNP array analysis and whole exome analysis for novel mutations using high-throughput sequencing technologies. In whole exome analysis, paired CD3-positive T cells were used as a normal control. By comparing sequences in tumors and paired T cells, 268 non-synonymous somatic mutations were confirmed with an overall true positive rate of 53.9 %, including 206 missense, 25 nonsense, and 10 splice site mutations, and 27 frameshift-causing insertions/deletions (indels). The mutations of the known gene targets, however, accounted for only 12.3 % of all detected mutations (N = 33), and the remaining 235 mutations involved previously unreported genes. Combined with the genomic copy number profile obtained by SNP array karyotyping, this array of somatic mutations provided a landscape of myelodysplasia genomes.

overall_design: Copy number analysis of Affymetrix 250K SNP arrays was performed for 29 MDS or related neoplasms and paired 29 germline samples.

first: Kenichi

last: Yoshida

first: Masashi

last: Sanada

first: Yuichi

last: Shiraishi

first: Daniel

last: Nowak

first: Yasunobu

last: Nagata

first: Yusuke

last: Sato

first: Ayana

last: Kon

first: Ryoichiro

last: Kawahata

first: Naoshi

last: Obara

first: Mamiko

last: Sakata-Yanagimoto

first: Ken

last: Ishiyama

first: Hikaru

last: Mori

first: Florian

last: Nolte

first: Wolf-Karsten

last: Hofmann

first: Shuichi

last: Miyawaki

first: Lee-Yung

last: Shih

first: Shigeru

last: Chiba

first: Seishi

last: Ogawa


title: MicroRNA profiling in subventricular zone after stroke: miR-124a regulates proliferation of neural progenitor cells through Notch signaling pathway

status: Public on Nov 29 2011

city: Detroit

first: Xian Shuang

last: Liu

state: MI

address: 2799 West Grand BLVD

institute: Henry Ford Hospital

summary: Expression data of miRNAs from adult neural progenitor cells in subventricular zone after stroke.

overall_design: Genome-wide profilings of miRNAs were measured in cultured non-ischemic (N=3) and ischemic SVZ (N=3) neural progenitor cells using miRNA microarray.

first: X

first: Z

last: Zhang


title: Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species.

first: Marcus

last: Breese

first: Matthew

last: Grow

first: Howard

last: Edenberg


title: MicroRNA Expression Data From Sham or BDL CD1 Mouse Liver

status: Public on Aug 10 2011

first: Robert

middle: Christian

last: Huebert

address: 200 1st Street SW

department: Gastroenterology and Hepatology

summary: Endothelial cells from normal or cirrhotic CD1 mice were screened for changes in microRNA expression using an Affymetrix array.

overall_design: Total RNA (including microRNA) was extracted from whole liver tissue of CD1 mice, and microRNA expression was assessed using an Affymetrix array.  N=1 for each condition (cirrhosis induced by bile duct ligation, control).


title: Expression data from low nitrate culture in root in maize

status: Public on Sep 01 2011

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

institute: Chinese Academy of Agricultural Sciences

summary:
Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation.
Root is the organ that plants transport nitrate. we used the microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize.

overall_design: MicroRNAs (miRNAs) are small, endogenous RNAs that are regulators of gene expression in plants and animals. And, miRNAs have been known for years to be important for phosphate, sulphate and copper deprivation responses in plants. In Arabidopsis, small RNA deep sequencing associated with nitrate response had been analyzed. However, information about the way by which miRNA are regulated by abiotic stresses in general and by low nitrate in particular is unavailable for maize. In this study, we used GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in roots in maize.

first: Yongmei

last: Bi

first: Shihuang

first: Steven

last: Rothstein

first: Zhenhua

last: Xue

first: Sihui

last: Zhong

first: Xinhai

last: Li

first: Wenxue


title: Expression profiles of embryo-defective Arabidopsis thaliana mutants increased size exclusion limit1 (ise1) and ise2

status: Public on Nov 09 2011

city: Berkeley

first: Patricia

last: Zambryski

address: 281 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS).  Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function.

overall_design: Three biological replicates each of either ise1 or ise2 mutant seeds vs. sister wild-type controls

first: Tessa

last: Burch-Smith

first: Jacob

middle: O

last: Brunkard


title: Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant (miRNA)

status: Public on Oct 05 2011

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: The t(10;11) p (13;q14) translocation, giving rise to CALM-AF10, is a recurring chromosomal translocation observed in several types of acute leukemias as well as in lymphoma. We have previously demonstrated that the expression of the human CALM/AF10 fusion gene in murine bone marrow stem and progenitor cells results in an aggressive acute myeloid leukemia in vivo. In this study, we have screened the various domains essential for CALM-AF10 function and leukemogenicity. Our study identifies a mutant of CALM-AF10 that greatly enhances the clonogenic potential of hematopoietic progenitors while retaining key characteristics of disease induced by the full length CALM-AF10 fusion.

overall_design: Global micro-RNA expression of bone marrow cells transduced with various constructs were compared. We used the empty vector, MIG, as a control and baseline. Four samples are tested with three biological replicates each.

first: Aniruddha

last: Deshpande

first: Arefeh

last: Rouhi

first: Yihui

last: Lin

first: Christiane

last: Stadler

first: Philipp

last: Greif

first: Natalia

last: Arseni

first: Sabrina

last: Opatz

first: Leticia

last: Quintanilla-Fend

first: Wolfgang

last: Hiddemann

first: Guoliang

last: Xu

first: Scott

last: Armstrong

first: Stefan

middle: K

last: Bohlander

first: Christian

last: Buske


title: Direct target gene analyses for TCP20 using a glucocorticoid inducible TCP20 (TCP20-GR)

status: Public on Aug 09 2011

city: Wageningen

first: Selahattin

last: Danisman

address: Droevendaalsesteeg 1

department: Business Unit Bioscience

country: Netherlands

institute: Plant Research International

summary: TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PCF1) transcription factors control developmental processes in plants. We identified direct target genes of the Arabidopsis class I TCP20 protein in leaf development based on a glucocorticoid receptor induction assay and genome-wide expression studies. For this, we tagged TCP20 with a glucucorticoid receptor (GR) domain and transformed the resulting TCP20-GR construct into tcp20 knockout plants. Induction of these and wild type controls was done with Dexamethasone and Cycloheximide. Plants were harvested 8 h after induction, uninduced plants were taken as control.

overall_design: In sum, 8 samples, each pools of 30 seedlings. Wild type and TCP20-GR plants at induction times t=0 and t=8, in two biological replicates.

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