title: The role of miR-199 in HIF1a-mediated hypoxia response in epithelial ovarian cancer cells

status: Public on Sep 24 2011

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary:
The high rates of mortality associated with epithelial ovarian cancer (EOC) are a direct consequence of its metastatic nature. Metastasis is dependent on many factors, among which activation of angiogenesis is most significant. Angiogenesis is, in turn, contingent upon the cellular response to hypoxia within the tumor microenvironment. Hypoxia-inducible factor 1 (HIF1) is a transcription factor composed of HIF1alpha and HIF1beta subunits and is the master regulator of the hypoxic response. It is therefore a critical mediator of tumor angiogenesis and metastasis. Regulation of HIF1 is primarily at the level of protein. In normoxia, the HIF1alpha subunit is hydroxylated via an oxygen- and iron-dependent mechanism and targeted for destruction. In hypoxia, low oxygen levels preclude hydroxylation and HIF1alpha is stabilized, allowing for its association with constitutively expressed HIF1beta to form bioactive HIF1.
We have identified a novel mechanism of HIF1alpha regulation in EOC cells that involves microRNAs (miRs), ~22 nucleotide, non-coding RNA molecules that repress translation of target mRNAs by binding their 3’ untranslated regions (UTRs).  Using microarray and qPCR analysis, we found that levels of miR-199a-1, a miR that is predicted in silico to target the HIF1alpha 3’ UTR, were reduced under hypoxia in EOC cells. We further demonstrated that miR-199a-1 directly targets the HIF1alpha 3’ UTR and overexpression of miR-199a-1 suppresses HIF1alpha protein levels and HIF1-driven gene expression. Moreover, cells stably overexpressing miR-199a-1 exhibit marked defects in migratory ability. These data were corroborated by our in vivo findings, which demonstrated that overexpression of miR-199a-1 causes significant reductions in tumor vessel density and tumor burden in nude mice. These findings provide insight into non-canonical, miR- and iron-based mechanisms of HIF1 regulation that may have important implications in the progression of EOC.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: miRNA expression analysis of A2780 epithelial ovarian cancer cells by microarrays

first: Hemant

last: Joshi

first: Xiaoxiao

last: Zhang

first: Sundaram

last: Ramakrishnan


title: Effects of exercise on miRNA expression in human peripheral blood mononuclear cells (PBMCs)

status: Public on Sep 26 2011

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

country: USA

institute: University of California, Irvine

summary: Exercise leads to a rapid change in the profile of gene expression in circulating PBMCs. We hypothesized that miRNA expression in circulating PBMCs would also be affected by brief exercise.

overall_design: 12 healthy men (19-30 yr old) performed 10 2-min bouts of cycle ergometer exercise interspersed with 1-min rest at a constant work equivalent to about 76% of VO2max. A baseline blood sample was taken before and immediately after the exercise.  Neutrophils were isolated using OptiPrep Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol®.  For this study we used Agilent Human miRNA microarrays V2  (total of 24 chips).

first: Frank

last: Zaldivar


title: Viral small RNAs from Drosophila melanogaster flies infected with  FHVdeltaB2 or FHV.

status: Public on Nov 12 2011

city: Riverside

first: JUAN

last: JOVEL

address: 3401 Watkins Drive

department: Plant Pathology

institute: University of California Riverside

type: Non-coding RNA profiling by high throughput sequencing

summary: We focus our analyses on the description of viral small RNAs (FHVdeltaB2 or FHV) and based on genetic and molecular evidende, classify them and discuss their relevance in antiviral defense.

overall_design: Small RNAs from adult Drosophila flies from different genetic backgrounds and infected with FHV-deltaB2 or FHV were sequenced using the illumina platform.

first: Juan

last: Jovel

first: Yanhong

last: Han

first: Shou-Wei

last: Ding


title: Modulation of mRNA in human T-cell development (miRNA)

status: Public on Oct 27 2011

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

summary: miRNA expression of Double Positive, Single Positive CD4+ and CD8+, and unsorted human thymocytes

overall_design: We used microarrays to identify miRNAs involved in T cell maturation

first: M

last: Ghisi

first: A

first: K

last: Basso

first: C

last: Frasson

first: S

last: Mukherjee

first: L

last: Mussolin

first: V

last: Serafin

last: Ruggero

last: Guffanti

first: G

last: De Bellis

last: Gerosa

last: Stellin

first: D

middle: M

last: D'Agostino

last: Bronte

last: Indraccolo

last: Amadori

first: P

last: Zanovello


title: MicroRNA signature during the time course of regeneration of the human airway mucociliary epithelium

status: Public on Jun 07 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
The regeneration of the airway mucociliary epithelium involves several sequential events including migration, proliferation, polarization and final differentiation (i.e ciliogenesis).
The airway mucociliary epithelium is consituted of three main cell types : ciliated cells, secretory cells and basal cells. We used microRNA microrrays to investigate the signature of microRNA during the four step of regeneration of the airway epithelium.

overall_design: Four time points (ALI-D0, ALI-D7, ALI-D14, ALI-D21) of regeneration of the airway epithelium for 3 donors.

first: B

last: Marcet

last: Barbry


title: MicroRNA Profiling of Rhesus Macaque Embryonic Stem Cells

status: Public on Jun 20 2011

city: kunming

first: zhenghua

last: sun

address: jiaochangdong road 32#

country: China

institute: kunming institute of zoology.CAS

summary: We established three new rhesus embryonic stem cells lines and conducted their microRNA profilings by Solexa sequencing. Sequencing of small RNA libraries yielded 12.66 million, 13.12 million and 11.57 million raw reads from IVF1.2, IVF3.2 and IVF3.3, respectively. After filtering, we obtained 10.89 million (IVF1.2), 10.60 million (IVF3.2) and 9.26 million (IVF3.3) clean reads (18-30nt).

overall_design: Examination of 3 different small RNA expression profilings in 3 rhesus embryonic stem cell lines

first: Zhenghua

last: Sun

first: Yanfeng

last: Zhang


title: MiR-192 inhibits nucleotide excision repair by targeting ERCC3 and ERCC4 in HepG2.2.15 cells.

status: Public on Aug 03 2011

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

summary: Deficient DNA repair capacity is associated with genetic lesions accumulation and susceptibility to carcinogenesis. MicroRNAs (miRNAs) are small non-coding RNAs that regulate various cellular pathways including DNA repair. Here we hypothesized that the existence of HBV products may interfere with cellular nucleotide excision repair (NER) through microRNA-mediated gene regulation. We found that NER was impaired in HepG2.2.15 cells, a stable HBV-expressing cell line, compared with its parental cell line HepG2. Altered miRNA expression profile, in particular the significant upregulation of miR-192, was observed in HepG2.2.15 cells. Additionally, ERCC3 and ERCC4, two key factors implicated in NER, were identified as targets of miR-192 and over-expressing miR-192 significantly inhibited cellular NER. These results indicated that persistent HBV infection might trigger NER impairment in part through upregulation of miR-192, which suppressed the levels of ERCC3 and ERCC4. It provides new insight into the effect of chronic HBV infection on NER and genetic instability in cancer.

overall_design: A genome-wide miRNAs microarray was performed to identify differentially expressed miRNAs between HepG2.2.15, a stable HBV-expressing cell line, and its parental cell line HepG2.

first: Qiong-Hui

last: Xie

first: Ying

last: Chang

first: Ju-sheng

last: Lin


title: Comprehensive analysis of miRNA expression profiles in IDA, IPMA, IPMC and cancer cell line

status: Public on May 30 2011

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary:
This study identified differentially expressed miRNAs exclusively in invasive ductal adenocarcinoma.
The epithelial-mesenchymal transition (EMT) is a critical step for pancreatic cancer cells as an entry of metastatic disease.  Wide variety of cytokines and signaling pathways are involved in this complex process while the entire picture is still cryptic.  Recently,
miRNA was found to regulate cellular function including EMT by targeting multiple mRNAs.  We performed comprehensive analysis of miRNA expression profiles in invasive ductal adenocarcinoma (IDA), intraductal papillary mucinous adenoma (IPMA), intraductal papillary mucinous carcinoma (IPMC) and human pancreatic cancer cell line to elucidate essential miRNAs which regulate invasive growth of pancreatic cancer cells.  Along with higher expression of miR-21 which has been shown to be highly expressed in IDA, reduced expression of miR-126 in IDA and pancreatic cancer cell line was detected.  Re-expression of miR-126 in pancreatic cancer cells resulted in reduced cellular migration, invasion and induction of epithelial marker E-cadherin.  We demonstrated for the first time that the miR-126 plays essential role in the inhibition of invasive growth of pancreatic cancer cells.

overall_design: The expression profile of miRNA in each sample or cell line was evaluated by microarray and cluster analysis was performed.

first: Kennichi

last: Satoh

first: Wataru

last: Fujibuchi


title: Integrative Analysis of microRNA, mRNA and DNA Copy Number Data Reveals Asbestos-Related Changes in Non-Small Cell Lung Cancer

status: Public on Apr 30 2011

city: Helsinki

first: Mohamed

last: Guled

address: Haarmaninkatu 3

department: Department of Pathology

country: Finland

institute: Haartman Institute, University of Helsinki

summary:
Background: Lung cancer has the highest mortality rate of all the cancers in the world and asbestos-related lung cancer is one of the leading occupational cancers. The identification of the asbestos-related molecular changes has been a topic of major research interest over the years. The aim of the current study was to identify novel asbestos-related molecular correlates by integrating miRNA expression profiling with previously obtained microarray data (aCGH and mRNA expression) from the same patient material.
Results: Twelve novel asbestos-related miRNAs (over-expressed: miR-148b, miR-374a, miR-24-1*, Let-7d, Let-7e, miR-199b-5p, miR-331-3p and under-expressed: miR-939, miR-671-5p, miR-605, miR-1224-5p, miR-202) which inversely correlated with target genes (e.g. GADD45A, LTBP1, FOSB, NCALD, CACNA2D2, MTSS1, EPB41L3) were identified. In addition, several known and new lung cancer-associated miRNAs were identified. DNA copy number alterations were also correlated with the deregulation of four miRNAs in lung cancer. The importance of integrated analysis was highlighted by the interesting finding of linking of the over-expression of well known squamous cell carcinoma-associated miR-205 with the down-regulation of the gene DOK4.
Conclusions: Novel deregulated miRNAs and inversely correlating expression of target genes associated with lung cancer etiology and histology were identified. In addition, DNA copy number alterations correlated with the deregulation of some of the miRNAs. The results of the current study could have potential diagnostic implications, but require further investigation.

overall_design:
Methods: The patient material used in the study consisted of 26 tumour and normal lung tissue from highly asbestos-exposed (13 samples) and non-exposed (13 samples) patients. Control lung tissue samples were obtained from 7 patients without cancer as well as from a commercial lung tissue RNA. Data analysis on miRNA expression and integration of miRNA and mRNA data were performed using Chipster (http://chipster.csc.fi/). In addition, miRNA and aCGH data were integrated in a separate analysis.
*** This submission represents the microRNA component of the study

first: Penny

last: Nymark

first: Ioana

last: Borze

first: Ali

last: Faisal

first: Leo

last: Lahti

first: Kaisa

last: Salmenkivi

first: Eeva

last: Kettunen

first: Sisko

last: Anttila

first: Sakari

last: Knuutila


title: Multiple bypass pathways of Hsk1 kinase essential for initiation of DNA replication in fission yeast

status: Public on Aug 26 2011

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

type: Genome binding/occupancy profiling by genome tiling array

summary:
Cdc7/Hsk1 is a conserved kinase required for initiation of DNA replication that potentially regulates timing and locations of replication origin firing. Here, we show that viability of fission yeast hsk1∆ cells can be restored by loss of mrc1, which is required for maintenance of replication fork integrity, by cds1∆, or by a checkpoint-deficient mutant of mrc1. In these mutants, normally inactive origins are activated in the presence of HU and binding of Cdc45 to MCM is stimulated. mrc1∆ bypasses hsk1∆ more efficiently because of its checkpoint-independent inhibitory functions. Unexpectedly, hsk1∆ is viable at 37°C. More DNA is synthesized, and some dormant origins fire in the presence of HU at 37°C. On the other hand, hsk1∆ bypass strains grow poorly at 25°C compared to at higher temperatures. Our results show that Hsk1 functions for DNA replication can be bypassed by different genetic backgrounds as well as under varied physiological conditions, providing additional evidence for plasticity of the replication program in eukaryotes.
BrdU incorporation profiles at early S-phase in mrc1∆, cds1∆ and hsk1-89 mutants.

overall_design: BrdU-incorporated region at early S-phase vs. Input at Metaphase sample

first: S

last: Matsumoto

first: M

last: Hayano

first: Y

first: H

last: Masai


title: Mrc1 marks early-firing origins and coordinates timing and efficiency of initiation in fission yeast

status: Public on Mar 26 2011

summary:
How early- and late-firing origins are selected on eukaryotic chromosomes is largely unknown. Here we show that Mrc1, a conserved factor required for stabilization of stalled replication forks, selectively binds to the early-firing origins in a manner independent of Cdc45 and Hsk1 kinase in fission yeast. In mrc1∆ (and in swi1∆ to some extent), efficiency of firing is stimulated and its timing is advanced selectively at those origins that are normally bound by Mrc1. In contrast, the late or inefficient origins which are not bound by Mrc1 are not activated in mrc1∆. The enhanced firing and precocious Cdc45 loading at Mrc1-bound early-firing origins are not observed in a checkpoint mutant of mrc1, suggesting that non-checkpoint function is involved in maintaining the normal program of early-firing origins. We propose that pre-firing binding of Mrc1 is an important marker of early-firing origins which are precociously activated by the absence this protein.
Mrc1 binding profiles at G1/S boundary or early S-phase in wild type vs hsk1-89 mutant.

overall_design: BrdU-incorporated region, Mcm4-3Flag, Cdc45-3Flag or Mrc1-5Flag ChIPed in early S-phase vs. Input at Metaphase sample


title: microRNA profiles of immune cells and their exosomes

status: Public on Mar 17 2011

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: Microarray analysis of exosomal miRNAs vs the miRNAs of their respective donor cells.

overall_design: To determine the miRNA repertoires of exosomes secreted by immune cells, we isolated exosomes from cell supernatants of the Raji B cell line, the Jurkat-derived J77 T cell line, and primary dendritic cells (DCs) derived from human monocytes. Exosomes were isolated by a series of microfiltration and ultracentrifugation steps

first: María

last: Mittelbrunn

first: Cristina

last: Gutiérrez-Vázquez

first: Carolina

last: Villarroya-Beltri

first: Susana

last: González

first: Fátima

last: Sánchez-Cabo

first: Manuel

last: Ángel González

first: Antonio

last: Bernad

first: Francisco

last: Sánchez-Madrid


title: Tuberculosis patients, latent and uninfected controls; whole blood

status: Public on Nov 23 2010

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

summary: Tuberculosis (TB) still poses a profound burden on global health, owing to significant morbidity and mortality worldwide. Although a fully functional immune system is essential for the control of Mycobacterium tuberculosis infection, the underlying mechanisms and reasons for failure in part of the infected population remain enigmatic. Here, whole-blood microarray gene expression analyses were performed in TB patients and in latently as well as uninfected healthy controls to define biomarkers predictive of susceptibility and resistance. Fc gamma receptor 1B (FCGRIB)was identified as the most differentially expressed gene, and, in combination with four other markers, produced a high degree of accuracy in discriminating TB patients and latently infected donors. We determined differentially expressed genes unique for active disease and identified profiles that correlated with susceptibility and resistance to TB. Elevated expression of innate immune-related genes in active TB and higher expression of particular gene clusters involved in apoptosis and natural killer cell activity in latently infected donors are likely to be the major distinctive factors determining failure or success in controlling M. tuberculosis infection. The gene expression profiles defined in this study provide valuable clues for better understanding of progression from latent infection to active disease and pave the way for defining predictive correlates of protection in TB.

overall_design: Three infection stages. Two-color arrays with independent swap design

first: Dirk

last: Repsilber

first: Gerhard

last: Walzl

first: Hans

last: Mollenkopf

first: Stefan

middle: H

last: Kaufmann


title: DamID for Swi6, Rdp1 and Dcr1 in Schizosaccharomyces pombe

status: Public on Sep 25 2010

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats.  Here we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DamID (DNA adenine methyltransferase identification) we show that Dcr1 and Rdp1 physically associate with some euchromatic genes, non-coding RNA (ncRNA) genes, and retrotransposon long terminal repeats (LTRs), and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model as proposed earlier and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.

overall_design: Methylation levels in strains expressing Dam-Swi6, Dam-Rdp1 and Dam-Dcr1 were compared to those in a Dam only expressing strain. Three biological replicates for each experiment were performed.

middle: J

first: Dimos

last: Gaidatzis

first: Marc

last: Bühler


title: Genome-wide mapping of histone H2A phosphorylation during S-phase in Schizosaccharomyces pombe (fission yeast)

status: Public on Aug 24 2010

city: La Jolla

first: Sophie

last: Rozenzhak

address: 10550 N Torrey Pines Rd MB3

institute: The Scripps Research Institute

summary: Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks. Rad3 and ATR also function during unperturbed growth, although the events triggering their activation and their critical functions are largely unknown. Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (gH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for  DNA repair/checkpoint proteins. Our data showed that gH2A marks a diverse array of genomic features during S-phase, including natural replication fork barriers and a fork breakage site, retrotransposons, heterochromatin in the centromeres and telomeres, and ribosomal RNA (rDNA) repeats.  The enrichment of gH2A at these sites was confirmed by multiple ChiP-qPCR experiments.

overall_design: Phosphorylated Histone H2A was ChIPed with anti-gammaH2A antibody vs. Input(whole cell extract) in S. pombe cells synchronized in S-phase.

first: S

first: P

last: Russell


title: CONVERGENT GENESIS OF AN ADULT NEURAL CREST-LIKE DERMAL STEM CELL FROM DISTINCT DEVELOPMENTAL ORIGINS

status: Public on Sep 03 2010

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

summary: Skin-derived precursors (SKPs) are multipotent dermal stem cells that reside within a hair follicle niche and that share properties with embryonic neural crest precursors.  Here, we have asked whether SKPs and their endogenous dermal precursors originate from the neural crest or whether, like the dermis itself, they originate from multiple developmental origins.  To do this, we used two different mouse Cre lines that allow us to perform lineage tracing: Wnt1-cre, which targets cells deriving from the neural crest, and Myf5-cre, which targets cells of a somite origin.  By crossing these Cre lines to reporter mice, we show that the endogenous follicle-associated dermal precursors in the face derive from the neural crest, and those in the dorsal trunk derive from the somites, as do the SKPs they generate.  In spite of these different developmental origins, SKPs from these two locations are functionally similar, even with regard to their ability to differentiate into Schwann cells, a cell type only thought to be generated from the neural crest.  Analysis of global gene expression using microarrays confirmed that facial and dorsal SKPs exhibit a very high degree of similarity, and that they are also very similar to SKPs derived from ventral dermis, which has a lateral plate origin.  However, these developmentally-distinct SKPs also retain differential expression of a small number of genes that reflect their developmental origins.  Thus, an adult neural crest-like dermal precursor can be generated from a non-neural crest origin, a finding with broad implications for the many neuroendocrine cells in the body.

overall_design: We obtained three independent isolates each of dorsal trunk SKPs, ventral trunk SKPs and facial SKPs and four isolates of MSCs, all generated from adult rats.  RNA samples deriving from these cells were analyzed on the Affymetrix GeneChip Rat Gene 1.0 ST Array.

first: Hiroyuki

last: Jinno

first: Olena

last: Morozova

first: Karen

middle: L

last: Jones

first: Jeffrey

middle: A

last: Biernaskie

first: Maryline

last: Paris

first: Ryoichi

last: Hosokawa

first: Michael

last: Rudnicki

first: Yang

last: Chai

first: Fabio

last: Rossi

first: Marco

last: Marra

middle: D


title: Nutritional programming of the metabolic syndrome is associated with long-lasting changes in nutrient sensing and energy homeostasis in the hypothalamus as revealed by genome-wide DNA microarray analysis

status: Public on Jul 02 2010

city: Nantes

first: Francisco

last: Bolanos

address: CHU-Hôtel Dieu. Place Alexis Ricordeau

institute: INRA-Université de Nantes

summary: Nutrient deficiency during perinatal development is associated with an increased risk to develop obesity, diabetes and hypertension in adulthood. However, the molecular mechanisms underlying the developmental programming of the metabolic syndrome remain largely unknown. Given the essential role of the hypothalamus in the integration of nutritional, endocrine and neuronal cues, here we have analyzed the profile of the hypothalamus transcriptome in 180-day-old rats born to dams fed either a control (200 g/kg) or a low-protein (80 g/kg) diet throughout pregnancy and lactation. From a total of 26,209 examined genes, 688 were up-regulated and 309 down-regulated (P<0.003) by early protein restriction. Based on the hypothesis that variations in gene expression levels often reflect changes in gene’s activity and that transcriptional networks are at the heart of physiological functions, we identified two gene clusters regulating common cellular processes whose expression is coordinately regulated by perinatal protein restriction. The first one is constituted by several genes of the insulin signaling pathway which, additionally, act as gatekeeper genes for regulation of nutrient sensing. The second cluster encompasses a functional network of nuclear receptors and co-regulators of transcription involved in the detection and use of lipid nutrients as fuel which, in addition, link temporal and nutritional cues to metabolism through their tight interaction with the circadian clock. Collectively, these results indicate that the programming of the hypothalamic circuits regulating energy homeostasis is a key step in the development of obesity associated with malnutrition in early life and provide a valuable starting point for the direct and systematic experimental analysis of the role of the hypothalamus in the physiopathological disturbances associated with the programming of the metabolic syndrome.

overall_design: Five rats fed a control diet, and five rats fed a low-protein diet. All rats are male.

first: Ricardo

last: Orozco-Solís

first: Rhowena

last: Matos

first: Omar

last: Guzmán-Quevedo

first: Sandra

last: Lopes de Souza

first: Audrey

last: Bihouée

first: Rémi

last: Houlgatte

first: Raul

last: Manhães de Castro

last: Bolaños-Jiménez


title: Transcriptome analysis of Geobacter sulfurreducens grown with different nitrogen sources

status: Public on Jun 30 2010

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

type: Expression profiling by genome tiling array

summary: Investigation of comprehensive information about the expression level of RNA transcripts across the entire G.sulfurreducens genome with different nitrogen sources, including NH3, Gln, Asp and N2.

overall_design: A twelve chip study using total RNA recovered from four separate culture conditions of G.Sulfurreducens.  G.Sulfurreducens PCA were harvested at mid-exponential phase. The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures)

first: Karsten

last: Zengler

first: Yu

last: Qiu

first: Jessica

last: De Ingeniis

first: Vasiliy

last: Portnoy

first: Byung-Kwan

last: Cho

first: Derek

last: Lovley

middle: O


title: microRNA expression profiling of human esophageal metaplastic lesions

status: Public on Jan 01 2011

first: Matteo

last: Fassan

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

institute: University of Padova

summary: To test the hypothesis that there is a specific miRNA expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA microarray analysis comparing normal esophageal squamous epithelium with the two different metaplastic lesions occuring within Barrett's mucosa (i.e. gastric metaplasia and intestinal metaplasia). Samples of H. pylori-related gastritis and gastric intestinal metaplasia  were also considered in the definition of esophageal-specific miRNAs.

platform_organism:
Homo sapiens
Mus musculus

overall_design: miRNA microarray analysis was performed in a series of samples obtained from (a) 10 histologically-proven long-segment Barrett's esophagus patients; (b) 10 patients with H. pylori-related chronic atrophic gastritis.  Overall,  10 normal esophageal squamous epithelium samples, 10 esophageal intestinal metaplasia samples, 10 esophageal gastric metaplasia samples, 10 H. pylori -related gastritis samples (no atrophic lesion detected; obtained from the antrum) and 10 gastric intestinal metaplasia samples (obtained from the antrum) were considered.

first: Stefano

last: Volinia

first: Jeff

last: Palatini

first: Carlo

last: Croce

first: Cecilia

last: Fernandez-Cymering

last: Pizzi

first: Mariangela

last: Balistreri

first: Ermanno

last: Ancona

first: Massimo

last: Rugge


title: Comparison between liver transcriptomes of Korean native pig and Yorkshire

status: Public on Dec 31 2010

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

summary: There are clear phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds because of different interests for selection. YS has been artificially selected by industrial interests such as a growth rate and a lean meat production, however, KNP has been maintained as a regional breed by local interests such as a fat content in or between muscle and a disease resistance. A comparison of gene expression profile from a major tissue liver can reflect the overall effects of the artificial selection between the two pig breeds through long history. KNP (n=4) and YS (n=4) pigs were raised under the identical conditions. Global gene expression levels were measured in liver samples from these pigs using Affymetrix porcine genome array containing 23,937 probe sets. The clustering analysis based on the individual transcriptome data showed a clear separation between two breeds in the liver tissue. We collected hepato-transcriptome data including 11,993 genes fully detected from four independent samples either in KNP or in YS. Based on both minimum positive false discovery rate (less than 15%) and fold change (|FC| > 1.5), 160 differentially expressed genes (DEGs) were collected from the liver between the two breeds. The functional analysis of these DEGs indicated clear distinctions in intra- and extra-cellular structure, cell proliferation, membrane trafficking, glycolytic pathway, mitochondrial function, protein metabolism, and immune response. The functional characteristics based on the DEGs were useful indicators to explain the differences between these two breeds developed for the specific purposes each other. The hepatic DGEs indicate that the YS has been lost expressivity of genes not required for the fast growth but maintained expressivity of genes for lean muscle production. The tissue-wise gene expression profiles indicate that the liver could be a major place to make the economic distinction between these two pig breeds.

overall_design: Comparing gene expression profiles to discover differentially expressed genes from liver tissue of two different pig breeds: KNP (n=4) vs. YS (n=4).


title: MicroRNA expression data for human primary and metastatic prostate cancer samples and control normal adjacent benign prostate

status: Public on Jun 24 2010

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

summary: Current knowledge of prostate cancer genomes is largely based on relatively small patient cohorts using single modality analysis platforms. Here we report concordant assessment of DNA copy number, mRNA and microRNA expression and focused exon resequencing in prostate tumors from 218 patients with primary or metastatic prostate cancer with a median of 5 years clinical follow-up, now made available as a public resource. Mutations in known, commonly mutated oncogenes and tumor suppressor genes such as PIK3CA, KRAS, BRAF and TP53 are present but generally rare. However, integrative analysis of mutations with copy number alterations (CNAs) and expression changes reveal alterations in the PI3K, RAS/RAF and androgen receptor (AR) pathways in nearly all metastatic samples and in a higher frequency of primary samples than previously suspected based on single-gene studies. Other new findings include evidence that the nuclear receptor coactivator NCOA2 functions as a driver oncogene in ~20 percent of primaries. Tumors with the androgen-driven TMPRSS2-ERG fusion were significantly associated with a small, previously unrecognized, prostate-specific 3p14 deletion that, through mRNA expression and resequencing analysis, implicates FOXP1, RYBP and SHQ1 as candidate cooperative tumor suppressors. Comparison of transcriptome and DNA copy number data from primary tumors for prognostic impact revealed that CNAs robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. In sum, this integrative genomic analysis of a substantial cohort of tumors clarifies the role of several known cancer pathways in prostate cancer, implicates several new ones, reveals a previously unappreciated role for CNAs in prognosis and provides a blueprint for clinical development of pathway inhibitors.

overall_design: Human prostate samples were profiled on Agilent microRNA V2 arrays per manufacturer's instructions.

middle: S

first: Nikolaus

last: Schultz

first: Haley

last: Hieronymus

first: Charles

last: Sawyers


title: miRNA expression profile of human MALT lymphoma compared to gastritis and gDLBCL

status: Public on Oct 02 2010

city: Zürich

first: Vanessa

middle: Jane

last: Craig

address: Winterthurerstrasse 190

institute: Institute of molecular cancer research

summary: To obtain global miRNA expression signatures of gDLBCL and its precursor lesions, total RNA isolated from 7-8 cases each of Helicobacter-associated reactive gastritis, low grade MALT lymphoma and high grade gDLBCL was hybridized to Agilent miRNA microarrays representing 795 human mature miRNAs. Unsupervised hierarchical clustering analysis revealed a clear segregation of the gDLBCL cases from the low grade MALT lymphomas and the gastritis samples; the segregation of the latter two disease entities was only incomplete (Figure 1A), reflecting the relative biological similarity of gastritis and low grade lymphomas. Statistical analysis of the dataset revealed only 26 differentially expressed miRNAs between these two groups (p<0.05), whereas 57 miRNAs exhibited significant differences in expression between low and high grade lymphomas.

overall_design: 7 human gastritis, 8 lowgrade MALT lymphoma and 7 high grade MALT lymphoma samples were used in the microarray analysis

first: Anne

last: Mueller


title: Discovery of microRNAs and other small RNAs in solid human tumors

status: Public on May 20 2010

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

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

overall_design: Refer to individual Series


title: Differential pre-mRNA defects in fission yeast carrying a temperature degron allele of the SMN gene

status: Public on Apr 22 2010

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

institute: CNRS

summary: The SMA disease results from deletions or mutations in the “survival of motor neuron” (SMN1) gene. The SMN protein plays an essential role in the biogenesis of spliceosomal snRNPs but the link between a defect in this process and specific splicing inhibition is not known. Here, we report the construction of a temperature degron (td) allele of the S. pombe SMN protein and show that its depletion at 37°C affects snRNPs stability and splicing. In addition, the function of the tdSMN allele in snRNPs assembly is affected already at 25°C suggesting a deleterious effect of the tag at this temperature. Remarkably, using S. pombe tiling arrays and RT-PCR validation tests, we report that splicing is altered differentially in the tdSMN cells at permissive temperature. Our results suggest that the defects observed in tdSMN fission yeast cells mimic splicing deficits observed in SMN-deficient metazoan cells.

overall_design: Total RNA (triplicate experiment) from the td-SMN strain grown at 25°c vs total RNA from the wild type strain (triplicate experiment)

first: Yannick

last: Campion

first: Henry

last: Neel

first: Thierry

last: Gostan

first: Johann

first: Rémy

last: Bordonné


title: Discovery of microRNAs and other small RNAs in solid human tumors: sequencing

summary: MicroRNAs (miRNAs) are ~22 nucleotide-long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs from 23 breast, bladder, colon, and lung tumor samples using high-throughput sequencing. We identified 49 novel miRNA and miRNA-like small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, normal and tumor tissue samples using two independent platforms, namely microarray and RT-PCR. Some of the novel sequences show a large difference in expression between tumor and tumor-adjacent tissues, between different tumor stages, or between different tumor types. We also report the identification of novel small RNA classes in human: highly expressed small RNA derived from Y-RNA and endogenous siRNA. Finally, we identified dozens of new miRNA sequence variants that demonstrate the existence of miRNA-related SNP or post-transcriptional modifications. Our work extends the current knowledge of the tumor small RNA transcriptome and provides novel candidates for molecular biomarkers and drug targets.

overall_design:
2 samples of pools of different tumor samples:
pool1: breast (5 samples), bladder (5 samples); 2 replicates each
pool2: colon (7 samples), lung (6 samples); 2 replicates each

first: Eti

last: Meiri

first: Asaf

last: Levy

first: Hila

last: Benjamin

first: Miriam

last: Ben-David

first: Lahav

last: Cohen

first: Avital

last: Dov

first: Nir

last: Dromi

first: Noga

last: Yerushalmi

first: Orit

last: Zion

first: Gila

last: Lithwick-Yanai


title: affy_root-dvt-nitrogen_medicago: Genetic determinism of root development in Medicago truncatula

status: Public on Jan 29 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_root-dvt-nitrogen_medicago. The biological question is the study of root development adaptation to external nitrogen availability. One of the typical responses to low N provision consists of an increased root branching which promotes soil exploration. In order to differentiate between genes specifically involved in nitrate response and genes of root development, we had performed experiments on both a wild type and a mutant affected in root architecture, both supplied with two different levels of nitrate. Global gene expression profiling of root cells using microarray analysis will be conducted to identify genes expressed during root branching. First, analysing the differential gene expression between the wild type and the mutant both at low and high level of nitrate, we will identify genes of root development but also genes specifically involved in nitrate response. Then, additional comparisons will concern the modifications of wild type and mutant gene expression between the two levels of nitrate. These genes will be compared to those found to be expressed in the wild type roots under submitted to various nitrogen sources (Ruffel et al., 2008). All together these results will allow us to determine which genes, among the firstly underlined, are specifically involved in root development. The kinetics of expression in different tissues of the most relevant of these genes will be further analysed by qRT-PCR. Three successive experiments in growth chamber were performed on two different genotypes of Medicago truncatula. Each experiment constituted a biological replicate. For each of them, after 4 days of seed cold-treatment followed by 4 days of germination, individual plantlets were transferred onto hydroponic culture tanks containing vigorously aerated nutrient solution. Each tank contained 6 plantlets of J5 and 6 plantlets of the mutant. On one shelf of the growth chamber, nutrient solution in the tanks was supplemented by 1mM of KNO3; on the other shelf, the level of KNO3 in the solution was of 10mM. Nutrient solution was renewed every week. Roots of the two genotypes were harvested separately but at the same time, 10 days after the plantlets transfer onto hydroponic culture tanks.

Keywords: dose response, wt vs mutant comparison

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design:
12 arrays - Medicago.
WT and mutant (tr185) under 1mM or 10mM KNO3. Three biological replicates each genotype/condition.

first: Sandrine

last: Balzergue

first: Virginie

last: Bourion

first: Marie-Laure

last: Martin-Magniette


title: Analysis of deferoxamine treated leaves and roots: Arabidopsis transcriptome in response to deferoxamine

status: Public on Jun 01 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

summary:
au08-04_dfo - analysis of deferoxamine treated leaves and roots - What are the effects of the siderophore deferoxamine on Arabidopsis leaves and roots? - Plants were allowed to grow for 5-6 weeks. The nutrient solution contains 0.25 mM Ca(NO3)2.4H2O, 1mM KH2PO4, 0.5 mM KNO3, 1mM MgSO4.7H2O, 50 µM H3BO3, 19 µM MnCl2.4H2O, 10 µM ZnCl2, 1 µM CuSO4.5H2O, 0.02 µM Na2MoO4.2H2O and 50 µM FeNa-EDTA. Plants were subjected to an 8 h light/16 h dark cycle, at 19°C, with 70% relative humidity. Leaves of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves were harvested 7 and 24 h.p.i.

Keywords: time course,treated vs untreated comparison

overall_design: 8 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

middle: P

last: Renou

first: Alia-

last: Dellagi


title: ChIP-chip of Geobacter sulfurreducens PCA with antibody against RpoN under various conditions.

first: Bernhard

last: Palsson

summary: We applied a ChIP-chip approach to elucidate the σN regulon experimentally under different growth conditions. This technique localizes DNA fragments within σN complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

overall_design: A nine ChIP-chip study using immunoprecipitated DNA (IP-DNA)  from three separate culture conditions.  The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures)

first: Karsten

last: Zengler

first: Yu

last: Qiu

first: Jessica

last: De Ingeniis

first: Vasiliy

last: Portnoy

first: Byung-Kwan

last: Cho

first: Derek

last: Lovley


title: Study of miRNA expression in childhood adrenocortical tumors

status: Public on Apr 01 2010

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

summary: We studied the miRNA expression profile of a series of childhood adrenocortical tumors (ACT) and age-matched normal adrenal samples

overall_design: 25 ACT - 5 normal


title: Effect of human TNF-alpha on schistosomulum stage of Schistosoma mansoni gene expression profile

status: Public on Dec 15 2009

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

summary: Schistosoma mansoni is the major causative agent of schistosomiasis in the Americas. This parasite takes advantage from host signaling molecules such as cytokines and hormones to complete its development inside the host. TNF-α is the most important cytokine involved in the inflammatory response when cercaria, the infective stage, penetrates the human skin and a severe inflammatory response is started. In this work the authors describe the complete sequence of a possible TNF-α receptor in S. mansoni and detect that the  receptor is most highly expressed in cercaria among all life cycle stages. In an attempt to mimic the situation at the site of skin penetration cercariae have been mechanically transformed in vitro into schistosomula and immediately exposed to human TNF-α . Exposure of these early schistosomula to the human hormone caused a large-scale change in the expression of parasite genes. Exposure of adult worms to human TNF-α caused gene expression changes as well, although the set of parasite altered genes was entirely different from that of schistosomula. This work increases the number of known signaling pathways of the parasite, and opens new perspectives into understanding the molecular components of TNF-α response as well as possibly interfering with parasite-host interaction.

overall_design: A 4 x 44k microarray platform was designed with the same probe set described by our group in a previous publication (PMID: 17517391). 230 ng of RNA from schistosomula treated with TNF and its control were used for the hybridization. RNA amplification and labeling kit (Agilent Technologies) were used according to manufacturer´s instructions. Each sample was separately labeled with either Cy3 or Cy5 and 825 ng cRNA from each amplification were used for hybridization a control sample was combined with a treated sample and hybridized. Washing and scanning procedures were according to the manufacturer´s instructions using GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Data was extracted using Feature Extraction software (Agilent Technologies). Low intensity data points were filtered out according to Feature Extraction software criteria, which essentially determine those points that are significantly below the average background signal of the array.  Total intensity data from each experiment were normalized by Quantiles Normalization Method, excluding positive and negative external controls. Significance Analysis of Microarray (SAM) was used as to find differentially expressed genes. z-score transformation of normalized data was performed and SAM two class tests were applied; genes were considered as significantly differentially expressed at q-value ≤ 0.05. Hierarchical clustering of selected genes was generated using Spotfire Decision Site software (TIBCO Software Inc., Palo Alto, CA, USA). For a gene that was represented in the array by multiple probes, we picked a single representative probe by selecting the probe with the highest absolute value of the Log2 ratio between intensities of TNF-α Treated/Control.

middle: C

first: Mariana

last: Carvalho

first: Thiago

last: Venancio

first: Patricia

last: Miyasato

first: Toshie

last: Kawano

first: Ricardo

last: DeMarco

first: Sergio

last: Verjovski-Almeida


title: Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly

status: Public on Feb 16 2010

first: Stephan

last: Emmerth

institute: FMI

type: Non-coding RNA profiling by genome tiling array

summary: RNAseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNAseIII enzyme Dcr1 and are required for heterochromatin formation. In this study, we have analyzed the subcellular localization of Dcr1 and found that it accumulates in the nucleus and is enriched at the nuclear periphery. Nuclear accumulation of Dcr1 depends on a short motif which constrains nuclear export promoted by the double-stranded RNA binding domain of Dcr1. Absence of this motif renders Dcr1 mainly cytoplasmic and is accompanied by remarkable changes in gene expression and failure to assemble heterochromatin. Our findings suggest that dicer proteins are shuttling proteins and that the steady-state subcellular levels can be shifted towards either compartment. This has implications for the mechanism of RNAi-mediated heterochromatin assembly and the spatial organization of RNA silencing pathways in general.

overall_design: 25 chips representing 6 different strains. Every condition is represented by at least two replicates

first: Heiko

last: Schober

first: Dimos

last: Gaidatzis

first: Kirsten

last: Jacobeit

first: Marc

last: Bühler


title: Effect of human TNF-alpha on adult Schistosoma mansoni gene expression profile

overall_design: A platform previously designed by our group (PMID: 17517391) was used. 300 ng of RNA from adult schistosomes treated with TNF and its control were used for the hybridization. RNA amplification and labeling kit (Agilent Technologies) were used according to manufacturer´s instructions. Each sample was separately labeled with either Cy3 or Cy5. 825 ng cRNA from each amplification were used for hybridization; self-self experiments were performed. Washing and scanning procedures were according to the manufacturer´s instructions using GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Data was extracted using Feature Extraction software (Agilent Technologies). We calculated a virtual Log2 ratio between intensities of TNF-α Treated/Control, for each gene. With these ratios, we used two different approaches for SAM statistical analyses. SAM one-class approach was used to identify genes with sustained changes in their expression levels along the entire time period of observation (1 and 24 h); SAM two-class approach was used to identify genes with transient changes in their expression levels. In both cases, genes were considered differentially expressed at q-value ≤ 0.05. Hierarchical clustering of selected genes was generated using Spotfire Decision Site software (TIBCO Software Inc., Palo Alto, CA, USA). For a gene that was represented in the array by multiple probes, we picked a single representative probe by selecting the probe with the highest absolute value of the Log2 ratio between intensities of TNF-α Treated/Control.


title: A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts [miRNA]

status: Public on Dec 05 2012

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

institute: Princeton University

summary:
Background: Although quiescence—reversible cell-cycle arrest—is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts.
Results: Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further.
Conclusions: microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts.

overall_design: microRNAs in human neonatal dermal fibroblasts in 3 cell cycle conditions (proliferating, 4 days serum starved, 7 days contact inhibited) were analyzed by one color microarray. 3 separate fibroblast cell lines from different human donors were analyzed for each condition, with two separate labeling and hybridization samples for each cell line. In total, 18 samples were hybridized to the microRNA microarray.

first: Matthew

middle: Y

last: Remillard

first: Aster

last: Legesse-Miller

first: Elizabeth

last: Johnson

first: Johanna

last: Lemons

first: Talia

middle: R

last: Chapman

first: Joshua

last: Forman

first: Mina

last: Kojima

last: Silberman

first: Hilary

last: Coller


title: microRNA expression data from pediatric primary intracranial germ cell tumor

status: Public on Feb 26 2010

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

summary: Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented the first miRNA profile of pediatric primary intracranial GCTs.

overall_design: 12 central nervous system GCT cases with different histological subtypes are subjected to miRNA expression analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma , immature teratoma , mixed GCTs of NGMGCTs category,  yolk sac tumor, immature teratoma, and embryonal carcinoma.

first: Yu-Hsuan

first: Hsei-Wei

last: Wang


title: MicroRNA expression profiling of male breast cancer

status: Public on Jul 22 2009

city: Padova

first: Matteo

last: Fassan

summary: To test the hypothesis that there is a specific miRNA expression signature which characterizes male breast cancers, we performed miRNA microarray analysis in a series of male breast cancers and compared them to cases of male gynecomastia and female breast cancers

overall_design: miRNA microarray analysis was performed in a series of 23 male breast cancers, 5 cases of gynecomastia and 10 female ductal breast carcinomas

first: Raffaele

last: Baffa

first: Juan

last: Palazzo

last: Lloyd

first: Marco

last: Crosariol

first: Chang-Gong

last: Liu

first: Stefano

last: Volinia

first: Hannes

last: Alder

first: Massimo

last: Rugge

first: Carlo

last: Croce

first: Anne

last: Rosenberg


title: miRNA profiling of normal mature B cells

status: Public on Jun 26 2009

first: Katia

last: Basso

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary:
miRNA profiling has been performed on normal mature B cells at different stages of differentiation (naive, germinal center and memory).  The main goal is to identify miRNA signatures associated with differentiation stages of normal B cells.

Keywords: miRNA, normal mature B cells

overall_design: Cells were isolated by magnetic cell sorting from tonsil tissues obtained from pediatric donors. Each phenotype is represented by 6 samples, each isolated from a different donor. The experiment does not include technical replicates.

first: Riccardo

last: Dalla-Favera


title: Specific acetylase-deacetylase balance controls stress adaptation by modulating global histone H3K14 acetylation.

status: Public on Aug 01 2009

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

summary:
Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation.
The data in this series showed Gcn5 occupancy and H3K14 acetylation levels in wild type, gcn5- and gcn5-/clr3- cells under KCl stress condition.
Related expression data are GSE5227 and GSE13817
Keywords: Chip-chip

overall_design:
This data include: 1 Genome wide analysis study of Gcn5 occupancy in S. pombe in rich media, so called ChIP on chip using Affymetrix tiling arrays with a 20 bp resolution. 2. Under 1M KCl treatment,  H3K14 acetylation levels in wild type cells and cells lacking  the  Gcn5 histone acetyltransferase and cells lacking both Gcn5 and class II HDAC Clr3. To control for nucleosome density we also determined H3 binding.
ChIP on chip data using input (whole cell lysate) as control, at least two biological replicates were used.

first: Anna

last: Johnsson

first: Mickaël

last: Durand-Dubief

first: Yongtao

last: Xue-Franzén

first: Karl

last: Ekwall


title: miRNA expression profiling in high-risk neuroblastoma

status: Public on Jun 27 2009

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

institute: "San Martino" Hospital

summary: In the present study we evaluated the miRNA expression profile of 31 high risk, stage 4 neuroblastoma patients.

overall_design: We compared miRNA expression profiles of 14 long-survivors (alive with an overall survival time > 36 months) and 17 short-survivors (dead of disease within 36 months from diagnosis. Deaths due to toxicity were censored).

first: Paola

last: Scaruffi

first: Sara

last: Stigliani

first: Simona

last: Coco


title: Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types

status: Public on Dec 07 2009

city: Petach Tikva

first: Roy

last: Navon

address: 94 Em Hamoshavot Road

institute: Agilent Technologies

summary:
The data collected in this study consisted of 32 paired samples of cancerous and normal origins from 14 different patients and 8 different cancer types. Each pair of samples was taken from different parts of the same tissue in the same patient - one collected and extracted from the tumor and one collected and extracted from adjacent normal tissue. One pair from each of the breast, lymphoma and prostate tissues, 2 pairs from liver and lung tissues and 3 pairs from colon, ovary and testes tissues. 2 of the ovary and testes pairs were technical replicates. We use commercial adjacent tissue tumor-normal total RNA samples purchased from Ambion/ABI. The samples were hybridized to Agilent's miRNA microarray version 2.0.

Keywords: miRNA

overall_design:
For each microarray analysis, 100ng total RNAs were labeled with Cy3 per Agilent miRNA Micorarray Systems Protocol v1.5. The labeled RNA samples were hybridized onto Agilent miRNA microarray containing 799 miRNAs(Agilent Human miRNA Microarray kit, V2) for 21 hours at 55C. The arrays were then washed at room temperature and scanned to produce the hybridization signals (Agilent miRNA Micorarray Systems Protocol v1.5). The arrays were scanned with extended dynamic range at 5 and 100% PMT using the Agilent scanner (model G2565AA
Technical replicate: Sample 7, Sample 29
Technical replicate: Sample 8, Sample 30
Technical replicate: Sample 19, Sample 31
Technical replicate: Sample 20, Sample 32

first: Hui

last: Wang

first: Israel

last: Steinfeld

first: Anya

last: Tsalenko

first: Amir

last: Ben-Dor

first: Zohar

last: Yakhini


title: Establishing the program of origin firing during S phase in fission yeast

status: Public on Mar 06 2009

first: Pei-Yun

middle: Jenny

last: Wu

address: 1230 York Avenue

institute: Rockefeller University

summary:
Our data have revealed a correlation between the timing of ORC and MCM binding to origins and the timing of replication. We hypothesized that origins bind ORC during M with varying affinities, and that delays in ORC binding and pre-RC formation at late-firing origins result in low efficiencies due to these origins subsequently competing less effectively for limiting replication factors. We investigated if equalizing ORC binding results in changes in origin efficiencies. Because the increase in ORC binding occurs during M, we surmised that extending M might result in origins accumulating ORC more equally, leading to more equal distribution of pre-RC and pre-IC assembly among origins. As a consequence, early origins might become less efficient and late origins more efficient.
To extend M in cells, we used the drug MBC (Carbendazim), which prevents microtubule polymerization and disrupts the mitotic spindle. Cells were then allowed to undergo S phase in the presence of BrdU, and labeled fragments were isolated by immunoprecipitation of genomic DNA and hybridized to Affymetrix tiling arrays. These results were compared to the replication profile of synchronized cells treated with HU but not with MBC, providing a control for normal origin efficiencies across the genome. This method allows the relative efficiency of origin usage genome-wide to be determined based on signal intensities from array hybridizations.

Keywords: comparison between cells treated with a drug and normal cells

overall_design: Fission yeast cells were labeled with BrdU during S phase in normal conditions as well as following MBC treatment. Genomic DNA was isolated, BrdU was immunoprecipitated, and labeled DNA was amplified and hybridized to Affymetrix arrays.  Samples from S phase were normalized to a non-replicating control ("0").  Three replicates of normal replication ("90") were performed, in addition to three replicates of replication following MBC treatment ("MBC").

first: Paul

last: Nurse


title: Analysis of the microRNA that involved the tuberculosis or latent TB infection I

status: Public on May 07 2009

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

department: Microbiology and Immunology

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

summary: To get to know the different levels of the microRNA among the pulmonary tuberculosis patients, latent-infected individuals and the complete healthy people, we have employed the Agilent miRNA microarray (version 2.0)  as a discovery platform to identify microRNA with the potential to diagnose the TB patients and the latent infected persons. Each group have 4 volunteers. The Peripheral Blood Mononuclear Cells (PBMCs) of each group were made up of equally mixed volumes. The results showed that several microRNAs were found up- or low regulated in PBMCs of TB patients versus latent-infected individuals and similarly for latent-infected individuals versus complete healthy ones.

overall_design: Each group have 4 volunteers. The PBMCs of each group were made up of equally mixed volumes after being purified.

first: Liqun

last: Zhang


title: Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

status: Public on Jul 31 2009

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

summary:
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to “genomic shock”, whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development.

NOTE: sff files unavailable for Samples AaL and F1L.

sample_organism: Arabidopsis arenosa x Arabidopsis thaliana

platform_organism:
Arabidopsis thaliana
Arabidopsis arenosa
Arabidopsis suecica

overall_design: 10 samples examined: Arabidopsis thaliana leaf, flower, Arabidopsis arenosa leaf and flower, F1 synthetic allopolyploid leaf and flower, F7 synthetic allopolyploid leaf and flower, Arabidopsis suecica leaf and flower. To determine small RNA profiles in Arabidopsis allotetraploids and their progenitors, we made 10 small RNA libraries from rosette leaves (L) and flower buds (F) in five lines, A. thaliana, A. arenosa, Allo(F1), Allo733(F7), and A. suecica. To examine expression of small RNAs among related species and their hybrids, we employed miRNA microarrays and compared small RNA levels.

first: Jie

last: Lu

first: Lu

last: Tian

first: Vanitharani

last: Ramachandran

first: Kristin

last: Kasschau

first: Elisabeth

last: Chapman

first: James

last: Carrington

first: Xuemei

last: Chen

first: Xiu-Jie

first: Zengjian


title: Control of Virulence Gene Expression in Citrobacter rodentium by Trascription Factor RegA

status: Public on Sep 22 2008

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

summary:
Identification of the targets of RegA with and without bicarbonate stimulation by comparing RegA knockout to multicopy RegA transgenics.

RegA is an AraC like transcription factor identified in a mutational screen for virulence genes in Citrobacter rodentium, an attaching and effacing pathogen that causes transmissible colonic hyperplasia in mice.

This experiment compares the RegA null strain with a multicopy plasmid rescue of this null strain in the presence and absence of bicarbonate with the aim of identifying pathogenesis related genes related to the early and late stages of attachment and effacement.

Keywords: genetic modification, transcription factor, induction

overall_design:
A strain of Citrobacter rodentium with a knockout of RegA was compared to the same strain rescued with a multicopy plasmid containing the wildtype RegA gene.
These strains were analyzed with and without bicarbonate in an unconnected two factor design with dye balanced biological replicates.

first: Emily

last: Hart

first: Ji

last: Yang

first: Marija

last: Tauschek

first: Michelle

last: Kelly

first: Gad

last: Frankel

first: Elizabeth

last: Hartland

first: Roy

middle: M

last: Robins-Browne


title: piRNA libraries from Drosophila melanogaster ovaries

status: Public on Mar 08 2007

city: Cold Spring Harbor

first: Julius

last: Brennecke

address: 1 Bungtown Road

institute: Cold Spring Harbor Labs

summary:
Drosophila Piwi-family proteins have been implicated in transposon
control. Here, we examine piwi-interacting RNAs (piRNAs) associated with
each Drosophila Piwi protein and find that Piwi and Aubergine bind RNAs
that are predominantly antisense to transposons, whereas Ago3 complexes
contain predominantly sense piRNAs. As in mammals, the majority of
Drosophila piRNAs are derived from discrete genomic loci. These loci
comprise mainly defective transposon sequences, and some have
previously been identified as master regulators of transposon activity. Our
data suggest that heterochromatic piRNA loci interact with potentially
active, euchromatic transposons to form an adaptive system for
transposon control. Complementary relationships between sense and
antisense piRNA populations suggest an amplification loop wherein each
piRNA-directed cleavage event generates the 5’ end of a new piRNA. Thus,
sense piRNAs, formed following cleavage of transposon mRNAs, may
enhance production of antisense piRNAs, complementary to active
elements, by directing cleavage of transcripts from master control loci.
Keywords: small RNA libraries from Drosophila ovaries

overall_design:
small RNAs (23-29nt) were isolated from total ovarian RNA or from immunopreciptated Piwi/Aubergine/Ago3 complexes. cDNA libraries were constructed after Pfeffer et al. 2005 (Nat. Methods) and sequenced at 454 Life Sciences.
The used strain is OregonR. Only sequences matching the Release5 genome assembly (www.fruitfly.org) are considered.

first: Alexei

last: Aravin

first: Alexander

last: Stark

first: Ravi

last: Sachidanandam

first: Monica

last: Dus

first: Gregory

last: Hannon


title: Small RNAs from dcl3 and rdr6 mutants of Physcomitrella

status: Public on Dec 19 2008

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: Endogenous 24nt short interfering RNAs (siRNAs) derived mostly from intergenic and repetitive genomic regions constitute a major class of endogenous small RNAs in Arabidopsis thaliana.  Accumulation of A. thaliana 24nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants.  However, the absence of a conspicuous 24nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21nt microRNAs (miRNAs) and 21-22nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation.  Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci which consistently produced a mixture of 21-24nt siRNAs with a peak at 23nts.  These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5mC) DNA modification.  Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22-24nt siRNAs, but not 21nt siRNAs, at Pp23SR loci.  The 21nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6.  Transcriptome-wide, Ppdcl3 mutants specifically failed to accumulate 23 and 24nt small RNAs from repetitive regions.  We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants.  Our results also suggest that Pp DCL3 produces siRNAs of heterogenous size, unlike its A. thaliana homolog which generates exclusively 24nt siRNAs.

overall_design:
Small RNAs from Wild-type (two technical replicates), rdr6-19 (two technical replicates), dcl3-5 (one sample), and dcl3-10 (one sample) were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.
linker 1: CTGTAGGCACCATCAAT (GPL7174 AND GSM313212, GSM313213)
linker 2: CACTCGGGCACCAAGGA (GPL7175 AND GSM313214, GSM313215)
linker 3: TTTAACCGCGAATTCCAG (GPL7176 AND GSM313216, GSM313217)

Raw data:
Two FASTQ files represent the raw data underlying the processed sample data in GSE12468.
080616_s_7_seq_GAK-2.fastq corresponds to GSM313212, GSM313214, and GSM313216.
080616_s_8_seq_GAK-3.fastq corresponds to GSM313213, GSM313215, and GSM313217.
Experimentally, samples GSM313212, GSM313214, and GSM313216 (i.e., all three genotypes) were sequenced in the same run (hence the same FASTQ file).  The sequencing run was a mixture of three different libraries with different linker sequences (as indicated above). These 'barcoded' samples were computationally extracted based on the linker sequences.  This is also true for samples GSM313213, GSM313215, and GSM313217.
Raw data were filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  See Cho et al. for details.

first: Sung-Hyun

last: Cho

first: Charles

last: Addo-Quaye

first: Ceyda

last: Coruh

first: Asif

last: Arif

first: Wolfgang

last: Frank

first: Zhaorong

last: MA


title: Gene expression data from postnatal cerebellum, prefrontal cortex and liver: comparison on tissue differences (miRNA)

status: Public on Jan 04 2013

city: Shanghai

first: Ning

last: Fu

address: 320# Yue-Yang Road

department: Shanghai Institute for Biological Sciences

institute: Chinese Academy of Sciences

summary:
To understand the roles of molecules in functional differentiation among adult human tissues, we performed a systematic survey of mRNA, protein, and protein phosphorylation as well as miRNA expression, in three tissues: cerebellum, prefrontal cortex and liver. We found that tissues were clearly distinct from one another at all levels. Furthermore, our results showed that miRNA differently expressed between tissues have significant, but modest effect on expression of mRNA and somewhat stronger effect on expression of proteins among the tissues.

Notably, miRNA preferentially targeted gene regulators, transcription factors and kinases, in all three tissues studied. Following this path, we found that miRNA effect was further amplified through expression changes of target transcription factors and kinases, leading to further changes in their targets’ expression and phosphorylation levels. Importantly, miRNA regulation leads to reduced, rather than increased gene expression variation among individuals between two brain regions. These observations uncover the complexity of miRNA regulatory interactions and are compatible with suggested role of miRNA in gene expression canalization.

overall_design: Adult human post-mortem tissue samples: cerebellum, prefrontal cortex and liver, were collected. Each tissue contains three individuals totalling 9 samples in this datasets. RNA extracted from these dissected tissue was hybridized to Agilent Human miRNA Microarray.

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich

first: Rong

last: Zeng