title: Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 2 week-old male MeCP2 A140V mutant mouse cerebellum

first: Garilyn

last: Jentarra

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates. The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from whole cerebella of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).

first: Vinodh

last: Narayanan


title: Kc167 Mcm2-7 Localization in HU

status: Public on Nov 27 2014

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

type: Genome binding/occupancy profiling by genome tiling array

summary: Determination of the genome-wide distribution of the Mcm2-7 helicase by chromatin immunoprecipitation in the Drosophila Kc167 cell line at the beginning of S phase.  Kc167 cells were arrested at the G1/S transition with hydroxyurea (HU).  Goal was to evaluate changes in the genome-wide Mcm2-7 distribution throughout the cell cycle, and how this relates to the excess Mcm2-7 loaded onto chromatin in G1.

overall_design: ChIP-Chip of Mcm2-7 in HU compared to input genomic DNA.  Biological Replicates: 2

middle: A

first: David

middle: M

last: MacAlpine


title: Real-time quantitative PCR analysis of the effects of a longitudinal dietary intervention on human adipose tissue

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

summary:
Abdominal subcutaneous adipose tissue was obtained from obese individuals before, after an 8-week low calorie diet and after an ad libitum 26-week weight control phase. Clinical investigations including subcutaneous adipose tissue biopsies were performed at baseline and at the end of each phase.
Main clinical outcome measures were body weight, body composition, energy intake, metabolic biochemistry. Adipose tissue gene expression profiling and lipidomics from the same samples were also assessed.

overall_design: 135 adipose tissue RNA samples were analysed before, after low calorie diet and after weight maintenance phase

first: Emilie

last: Montastier

first: Dominique

last: Langin


title: Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain

status: Public on Nov 21 2014

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Background: Prenatal alcohol exposure (PAE) is associated with alterations in numerous physiological systems, including the stress and immune systems. We have previously shown that PAE increases the course and severity of arthritis in an adjuvant-induced arthritis (AA) model. While the molecular mechanisms underlying these effects are not fully known, changes in neural gene expression are emerging as important factors in the etiology of PAE effects. As the prefrontal cortex (PFC) and hippocampus (HPC) play key roles in neuroimmune function, PAE-induced alterations to their transcriptome may underlie abnormal steady-state functions and responses to immune challenge. The current study examined brains from adult PAE and control females from our recent AA study to determine whether PAE causes long-term alterations in gene expression and whether these mediate the altered severity and course of arthritis in PAE females  Methods: Adult females from PAE, pair-fed [PF], and ad libitum-fed control [C]) groups were injected with either saline or complete Freund’s adjuvant. Animals were terminated at the peak of inflammation or during resolution (days 16 and 39 post-injection, respectively); cohorts of saline-injected PAE, PF and C females were terminated in parallel. Gene expression was analyzed in the PFC and HPC using whole genome mRNA expression microarrays.   Results: Significant changes in gene expression in both the PFC and HPC were found in PAE compared to controls in response to ethanol exposure alone (saline-injected females), including genes involved in neurodevelopment, apoptosis, and energy metabolism. Moreover, in response to inflammation (adjuvant-injected females), PAE animals showed unique expression patterns, while failing to exhibit the activation of genes and regulators involved in the immune response observed in control and pair-fed animals.   Conclusions: These results support the hypothesis that PAE affects neuroimmune function at the level of gene expression, demonstrating long-term effects of PAE on the CNS response under steady-state conditions and following an inflammatory insult.  Key words: prenatal alcohol exposure (PAE), ethanol, inflammation, arthritis, gene expression, rat.

overall_design: 192 samples, including 20 hybridization replicates

first: Katarzyna

last: Stepien

first: Alexandre

last: Lussier

first: Sarah

last: Neumann

first: Paul

last: Pavlidis

middle: S

first: Joanne

last: Weinberg


title: Pig skin includes dendritic cells subsets homologous to human CD1a and CD14 dendritic cells presenting different migrating behaviors and T CELL activation capacities.

status: Public on Dec 19 2014

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Characterization of swine skin DC subpopulations by means of global expression analysis.

overall_design: Three sets of swine skin DC plus peripheral blood B cells and monocytes (1 color hybridizations)

first: Marquet

last: Florian

first: Vu-Manh

last: Thien-Phong

first: Maisonnasse

last: Pauline

first: Elhmouzi-Younes

last: Jamila

first: Urien

last: Céline

first: Bouguyon

last: Edwige

first: Bourge

last: Mickael

first: Simon

last: Gaëlle

first: Bonneau

last: Michel

first: Dalod

last: Marc

first: Schwartz-Cornil

last: Isabelle

first: Bertho

last: Nicolas


title: Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci (tiling)

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

summary: Hox genes are required during the morphogenesis of both vertebrate digits and external genitals.We investigated whether transcription in such distinct contexts involves a shared enhancer-containing landscape. We show that the same regulatory topology is used, yet with some tissue-specific enhancer-promoter interactions, suggesting the hijacking of a regulatory backbone from one context to the other. In addition, comparable organizations are observed at both HoxA and HoxD clusters, which separated through genome duplication in an ancestral invertebrate animal.We propose that this convergent regulatory evolution was triggered by the pre-existence of some chromatin architecture, thus facilitating the subsequent recruitment of the appropriate transcription factors. Such regulatory topologies may have both favored and constrained the evolution of pleiotropic developmental loci in vertebrates.

overall_design: Chromatin ImmoPrecipitation on chip (Tiling array): Distribution of H3K27ac and H3K27me3 in WT genital tubercle (GT) at E13.5 and E15.5  Distribution of H3K27ac WT forelimb autopods are from Montavon et al., 2011.

first: N

first: T

last: Montavon

first: F

last: Darbellay

first: S

last: Gitto

first: D

last: Duboule


title: COLO 320 (Human colorectal cancer cell line) xenograft: Control (Xenograft without rat mesenchymal stem cells (MSCs)) vs Xenograft with rat MSCs

status: Public on Nov 18 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of COLO 320 xenograft tumor cells comparing control COLO 320 xenograft without co-implanted rat MSCs with COLO 320 xenograft with co-implanted rat MSCs. The latter makes co-implanted MSCs visualization possible by using MSCs labeled by GFP under FACS and single cell microscopy.

overall_design: Two-condition experiment, COLO 320 xenograft without rat MSCs [COLO320 MSC(-)] vs. COLO 320 xenograft with rat MSCs [COLO320 MSC(+)]. Biological replicates: 1 control, 1 sample, paired xengraft tumor cells grown and harvested from the same mouse host. One replicate per array.

first: Yoshiaki

last: Arimura

first: Suguru

last: Nakagaki


title: Replication timing in Suz12 knockout ESCs

status: Public on Nov 20 2014

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

type: Genome variation profiling by genome tiling array

summary: We profiled replication timing in Suz12 knockout ESCs and observed no differences relative to wild-type controls.

overall_design: Profile comparison of normal (control) and Suz12 knockout mouse embryonic stem cells.

first: David

last: Gilbert


title: miRNA profiling of Macaca mulatta intact duodenum samples following chronic Delta9 Tetrahydrocannabinol (Δ9-THC) treatment to SIV infected rhesus macaques

status: Public on Nov 19 2014

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: The study describes miRNA expression in intact duodenum following chronic delta 9 tetrahydrocannabinol (Δ9-THC) administration to SIV-infected rhesus macaques. Chronic Δ9-THC administration to uninfected macaques significantly and positively modulated intestinal miRNA expression by increasing the total number of differentially expressed miRNAs from 14 to 60 days post infection (DPI). At 60DPI, ~28% of miRNAs showed decreased expression in VEH/SIV compared to none in the THC/SIV group. Furthermore, compared to the VEH/SIV group, THC selectively upregulated the expression of miR-10a, miR-24, miR-99b, miR-145, miR-149 and miR-187 previously shown to target proinflammatory molecules. NOX4, a potent reactive oxygen species  generator was confirmed as a direct miR-99b target. A significant increase in NOX4+ crypt epithelial cells was detected in VEH/SIV compared to the THC/SIV group. We speculate that miR-99b-mediated NOX4 downregulation may protect the intestinal epithelium from oxidative stress-induced damage.

overall_design: Twelve age and weight matched male Indian rhesus macaques were randomly divided into 4 groups. Group 1 (n=1) received vehicle (1:1:18 of emulphor : alcohol : saline) and no infection. Group 2 (THC only, n=3) animals received twice daily intramuscular injections of Δ9-THC and no infection. Group-3 THC/SIV, (n=4) animals received twice daily injections of vehicle and were infected intravenously with 100TCID50 of SIVmac251. Group-4 (VEH/SIV, n=4) animals received twice daily injections of Δ9-THC similar to group 1 for four weeks prior to SIV infection. Duodenal pinch biopsies were collected before infection and thereafter at 14 and 30 days post infection. All animals were necropsied at 60 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. microRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software. Data was normalized to three endogenous controls (RNU44, RNU48 and snoU6). Delta CT values were calculated by subtracting individual miRNA CT values from an average of all three endogenous controls.  Comparisons were made between preinfection and all three treatment groups at 14, 30 and 60 DPI. To determine the effect of chronic THC treatment during SIV infection, comparisons were also made between VEH/SIV and THC/SIV at all three time points.

first: M


title: Plasmodium falciparum gene expression measured directly from tissue during human infection

status: Public on Nov 15 2014

city: Boston

first: Daria

last: Van Tyne

address: 243 Charles Street

institute: Harvard Medical School

summary: Abstract of associated publication: Background: During the latter half of the natural 48-hour intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium tissues, away from the spleen and inaccessible to peripheral blood. These late-stage parasites may cause tissue damage and likely contribute to clinical disease, and a more complete understanding of their biology is needed. Because these life cycle stages are not easily sampled due to deep tissue sequestration, measuring in vivo gene expression of parasites in the trophozoite and schizont stages has been a challenge. Methods: We developed a custom nCounter® gene expression platform, and used this platform to measure malaria parasite gene expression profiles in vitro and in vivo. We also used imputation to generate global transcriptional profiles, and assessed differential gene expression between parasites growing in vitro and those recovered from malaria-infected patient tissues collected at autopsy.   Results: We demonstrate, for the first time, global transcriptional expression profiles from in vivo malaria parasites sequestered in human tissues. We found that parasite physiology can be correlated with in vitro data from an existing life cycle data set, and that parasites in sequestered tissues show an expected schizont-like transcriptional profile, which is conserved across tissues from the same patient. Imputation based on 60 landmark genes generated global transcriptional profiles that were highly correlated with genome-wide expression patterns from the same sample measured by microarray. Finally, differential expression revealed a limited set of in vivo upregulated transcripts, which may indicate unique parasite genes involved in human clinical infections. Conclusions: Our study highlights the utility of a custom nCounter® P. falciparum probe set, validation of imputation within Plasmodium species, and documentation of in vivo schizont-stage expression patterns from human tissues.

overall_design: 89 sample total; 12 in vitro ring/schizont dilutions; 4 mock FFPE/Filter paper test samples; 4 in vitro control time points; 17 in vivo patient tissue samples; 52 in vivo patient blood samples

first: Danny

last: Milner Jr


title: Genomic landscape of metastatic colorectal cancer

status: Public on Nov 14 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumor biology. Here we describe the genomic landscape of tumor samples of a homogeneous well-annotated series of patients with metastatic CRC of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal sub-regions are associated with progression free survival PFS (uncorrected single-test p-values < 0.005). These sub-regions are filtered for effect on mRNA expression, using an independent data set from The Cancer Genome Atlas (TCGA) which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1-q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of metastatic CRC reveals a number of DNA copy number aberrations associated with response to drug therapy.

overall_design: aCGH data of colorectal cancers of patients from 2 clinical trials (CAIRO, CAIRO2). 105 patients were treated with capecitabine first line (CAIRO arm A), 111 patients were treated with capecitabine and irinotecan first line (CAIRO arm B), and 133 patients were treated with capecitabine, oxaliplatin and bevacizumab (CAIRO2 arm A).

first: Josien

middle: C

last: Haan

first: Mariette

last: Labots

first: Christian

last: Rausch

first: Miriam

last: Koopman

first: Jolien

last: Tol

first: Leonie

middle: J

last: Mekenkamp

first: Mark

last: van der Wiel

first: Danielle

last: Israeli

first: Hendrik

middle: F

last: van Essen

first: Nicole

last: van Grieken

first: Quirinus

last: Voorham

first: Linda

last: Bosch

first: Xueping

last: Qu

first: Omar

last: Kabbarah

first: Henk

last: Verheul

first: Iris

middle: D

last: Nagtegaal

first: Cornelis

last: Punt

first: Bauke

last: Ylstra

first: Gerrit

last: Meijer


title: Genome-wide location of histone acetyltransferase Sas3 from Saccharomyces cerevisiae

status: Public on Nov 07 2014

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

type: Genome binding/occupancy profiling by array

summary: We have investigated the genome-wide occupancy of Sas3p by ChIP-Chip, using tiled microarrays. Using this technique, it has been described that H3K14 and H3K9 acetylation is enriched at promoter regions and transcriptional start sites of active genes. Considering that Sas3p is a HAT whose main target in vitro is H3K14 we expected to detect Sas3 binding largely to promoter regions of genes. Surprisingly, we found that Sas3p is associated to the coding regions of genes, with a peak enrichment located) within the 5’ half of the ORF, and this enrichment drops substantially toward the 3’ region of the ORF. This result is very similar to that obtained for Yng1 genome-wide occupancy, also a component of the NuA3 complex, suggesting that this complex could be involved in transcriptional elongation, at least, in an initial step of the process.

overall_design: The experiments described in this study compare ChIP with an anti-HA antibody of a SAS3-HA tagged strain (BQS1217) to a control ChIP with an anti-HA antibody of a wild type strain (BY4742). Budding yeast samples were analyzed in exponential growing conditions (YPD). 2 biological replicates were performed.

first: Mercè

last: Pamblanco

first: Vicente

last: Tordera


title: Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA

status: Public on Nov 12 2014

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

summary: The Infinium 450K Methylation array is an established tool for measuring methylation. However, the bisulfite (BS) reaction commonly used with the 450K array cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The oxidative-bisulfite assay disambiguates 5mC and 5hmC. We describe the use of oxBS in conjunction with the 450K array (oxBS-array) to analyse 5hmC/5mC in cerebellum DNA. The methylation level derived by the BS reaction is the combined level of 5mC and 5hmC at a given base, while the oxBS reaction gives the level of 5mC alone. The level of 5hmC is derived by subtracting the oxBS level from the BS level. Here we present an analysis method that distinguishes genuine positive levels of 5hmC at levels as low as 3 %. We preformed four replicates of the same sample of cerebellum and found a high level of reproducibility (average r for BS = 98.3, and average r for oxBS = 96.8). In total, 114,734 probes showed a significant positive measurement for 5hmC. The range at which we were able to distinguish 5hmC occupancy was between 3 % and 42 %. In order to investigate the effects of multiple replicates on 5hmC detection we also simulated fewer replicates and found that decreasing the number of replicates to two reduced the number of positive probes identified by > 50%. We validated our results using qPCR in conjunction with glucosylation of 5hmC sites followed by MspI digestion and we found good concordance with the array estimates (r = 0.94). This experiment provides a map of 5hmC in the cerebellum and a robust dataset for use as a standard in future 5hmC analyses. We also provide a novel method for validating the presence of 5hmC at low levels, and highlight some of the pitfalls associated with measuring 5hmC and 5mC.

overall_design: Eight DNA samples from the same DNA source have been hybridized to a methylation array to detected methylation and hydroxymethylation. Four of the samples have been bisulfite converted, the other four samples have been oxidised and bisulfite converted.

first: Sarah

last: Field

first: Martin

last: Bachman

first: Sabrina

middle: K

last: Stewart

first: Stephan

last: Beck

first: Shankar

last: Balasubramanian


title: The ω subunit of RNA polymerase is essential for thermal acclimation of the Cyanobacterium Synechocystis sp. PCC 6803

status: Public on Nov 11 2014

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

summary: The rpoZ gene encodes the small ω subunit of RNA polymerase (RNAP). A ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m-2s-1; 32 °C; ambient CO2) but was heat sensitive and died at 40 °C. In the control strain , 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40 °C, while in ∆rpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80 % of heat-responsive genes were unique for ΔrpoZ. The RNAP core and the primary σ factor SigA were down-regulated in control strain at 40 °C, but not in ΔrpoZ. In accordance with reduced RNAP content, the total RNA content of mild-heat-stress-treated cells was lower in control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in control strain upon mild heat stress. The amounts of Photosystem II and Rubisco decreased at 40 °C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.

overall_design: Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and RNA polymerase omega subunit inactivation strain, ΔrpoZ, were harvested (A730=1, 40 mL) after treated at 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h.

first: Liisa

last: Gunnelius

first: Kaisa

last: Hakkila

first: Hans

last: Matthijs


title: Identification of H3N2 specific antibodies cross-reacting with H7 strains

city: CHICAGO

first: Patrick

last: Wilson

state: Illinois

address: 924 E 57th street, Knapp building

department: Medicine, Rheumatology

institute: University of Chicago

summary: Binding profile of H3N2 hemagglutinin (HA) reactive antibodies for various H3N2 and H7 HA proteins

sample_organism:
Capra hircus
Influenza A virus

overall_design: The same set of antibodies was printed 24 times on the microarray slide and different HA proteins were probed to assess the reactivity of the antibodies.

first: Carole

last: Henry-Dunand


title: Gene expression in aortic roots of Apoe KO mice with Nod1 stimulation

status: Public on Nov 06 2014

city: Higashi-ku

first: Shunsuke

last: Kanno

state: Fukuoka

address: 3-1-1 Maidashi

institute: Kyushu University

summary: To explore the mechanisms underlying progression of atherosclerosis provoked by Nod1 ligand stimulation, we performed microarray gene expression profiling of aortic roots of 6- and 9-week-old Apoe KO mice with or without oral FK565 administration. A gene ontology analysis of the genes up-regulated in FK565-administrated group at both time points showed that a number of biological process terms were associated with immune response. Among chemokine/cytokine genes, we observed that only 3 genes such as Ccl5, Ccl8 and Cxcl16 elevated more than 2-fold in response to oral administration of FK565 at both time points.

overall_design: An eight chip study using total RNA recovered from aortic roots in Apoe KO mice with or without FK565 administration, at the age of 6 and 9 weeks. Two independent experiments were performed in each group. In FK565-administrated groups, mice were orally administrated FK565 (50 µg) twice a week for 1 or 4 weeks from 5 weeks of age.

first: Hisanori

last: Nishio

first: Tamami

last: Tanaka

first: Toshiro

last: Hara


title: SInsights into molecular features of Venerupis decussata oocytes: a microarray-based study.

status: Public on Nov 05 2014

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: The European clam, Ruditapes decussatus (Linnaeus, 1758), is a bivalve mollusc of the family Veneridae native to the European Atlantic and Mediterranean coastal waters. Its production is exclusively based on natural recruitment, which is subject to high annual fluctuations due to adversely affected by pollution and other environmental factors. In the present study, oocytes from 15 females were collected in Ria de Aveiro (Western coast of Portugal) and microarray analysis was performed in order to investigate gene expression profiles characterizing naturally released oocytes and ovarian oocytes obtained by stripping. Released oocytes were obtained in the context of a study carried out by de Sousa and co-workers (GSE54954: de Sousa et al., 2014, submitted) focusing on expression profiles characterizing oocytes with different quality level. In particular, to compare stripped and spawned oocytes, a total of 10 samples (5 with bad/intermediate hatching rate and 5 with good hatching rate) out of the 25 analyzed in the previous study (GSE54954), and 5 new pools of stripped oocytes, have been analyzed by microarray analyses.

overall_design:
Released oocytes were obtained in the context of a study carried out by de Sousa and co-workers (de Sousa et al., 2014, submitted) focusing on expression profiles characterizing oocytes with different quality level. Spawning of females was induced by thermal stimulation, consisting of exposure to alternate cycles of 29°C (1 hour) and 5°C (30 minutes). As each female began to spawn, it was removed from the spawning tank and transferred to an individual spawning beaker with filtered seawater at the same temperature. Once spawning was completed, the obtained oocytes were gently washed into a clean glass. The remaining oocytes of each female spawning were mixed with a sperm suspension (from 7 males) by gentle agitation, aiming to obtain around 10 spermatozoids by oocyte in a microscopic view. Moreover, to evaluate the quality of the collected oocytes, the D-larval rate (ratio between the number of free swimming larvae at 48h post fertilization and the number of starting eggs) of each eggs batch was registered. Based on that observation, oocytes were divided into two experimental groups: spawned oocytes with low hatching rate (LHR, 5%-21% of D-larval rate) and spawned oocytes with medium hatching rate (MHR, 40%-47% of D-larval rate). In addition, gonads from five females were dissected and oocytes were collected through a practice known as gamete stripping. As the name indicates, this procedure involves removal of gametes from gonad tissue. Briefly, fully ripe gonads were slashed repeatedly with a scalpel and washed with filtered seawater to harvest the gametes. Finally, sex determination and oocytes appearance were achieved through microscopy examination. About 20,000 oocytes for each spawning/stripping were collected and filtered in a 40 µm sieve. The oocytes were transferred into an Eppendorf tube and, after a short spin, the seawater was removed. To remove salts, the pellet of oocytes was re-suspended with a solution of ammonium formate 3%, which was immediately removed after a short spin. Then the oocytes were included in 1.5 ml of Extract-all solution (Eurobio) and preserved in liquid nitrogen until RNA isolation. RNA quality and integrity were controlled on the Agilent Bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use.
Gene expression profiling was performed using an R. decussatus oligo-DNA microarray of 59,951 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal. The fluorescence values were normalized by performing a quantile normalization in R statistical software. Statistical analyses were performed on 31,862 out of 59,951 probes with signal higher than background in at least 5 out of 15 target samples. A log base 2 transformation was applied to all expression values and finally, the parametric Combat algorithm was implemented in R in order to adjust for the known between-experiments batch effect.

first: Marianna

last: Pauletto

first: Bargelloni

last: Luca

first: Joana

last: Teixeira de Sousa


title: High-resolution custom array spanning short arm of chromosome 17

status: Public on Nov 01 2014

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

summary: The goal of this experiment was to determine the size, genomic extent and gene content of rearrangements involving 17p.

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the entire 17p chromosomal region. A 4x44k Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website. We selected 42,000 probes covering Chr17: 29,000-22,100,000 (hg18), which represents an average distribution of 1 probe per 526 bp.

first: Claudia

last: Carvalho

middle: R


title: Genome-wide copy number and allele-specific copy number analysis of choroid plexus tumors (II)

city: Toronto

first: Diana

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Copy number analysis was performed using genotyping microarrays for 20 choroid plexus tumors. Genomic aberrations were investigated by tumor histological classification and the pattern observed in each subgroup was further refined. Allele-specific copy number analysis also allowed us to identify regions of acquired uniparental disomy with neutral copy number values.

overall_design: Twenty choroid plexus tumors (15 choroid plexus carcinomas, 3 choroid plexus papillomas, 2 atypical choroid plexus papillomas) were used in this study. No replicates were included.

first: Adam

last: Shlien

first: Anita

last: Villani

first: Margaret

last: Pienkowska

first: Stephen

last: Mack

first: Vijay

last: Ramaswamy

first: David

last: Shih

first: Ruth

last: Tatevossian

first: Ana

last: Novokmet

first: Sanaa

last: Choufani

first: Rina

last: Dvir

first: Myran

last: Ben-Arush

first: Brent

middle: T

last: Harris

first: Eugene

middle: I

last: Hwang

first: Rishi

last: Lulla

first: Stefan

last: Pfister

first: Maria

last: Achatz

first: Nada

last: Jabado

first: Jonathan

middle: L

last: Finlay

first: Rosanna

last: Weksberg

first: Cynthia

last: Hawkins

first: Michael

last: Taylor

first: Uri

last: Tabori

middle: W

last: Ellison

first: Richard

last: Gilbertson

last: Malkin


title: M. smegmatis response to deletion of Crp1 and overexpression of Crp2

status: Public on Oct 31 2014

city: Dunedin

first: Htin Lin

last: Aung

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Transcriptional profiling of M. smegmatis and  Dcrp1 grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol. Transcriptional profiling of M.smegmatis HLA102 harboring tetracycline inducible vector pMind containing the Crp2 and M. smegmatis harboring pMind grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol

overall_design: Comparing transcriptional response of wild-type compared with the deletion of crp1 gene (Msmeg_0539). Biological replicates: 4 independently grown and harvested. One replicate per array. Comparing transcriptional response of strain HLA102 to conditional expression of Crp2 (Msmeg_6189) compared with the wild-type with empty vector pMind. Biological replicates: 4 independently grown and harvested. One replicate per array.

first: Htin

first: J

last: Robson

first: G

last: Cook


title: Systems analysis reveals down-regulation of a network of prosurvival miRNAs drives the apoptotic response in dilated cardiomyopathy

first: Andrew

last: Emili

address: 160 College St #602

department: Donnelly Centre

institute: University of Toronto

summary:
miRNA expression in early stage mouse model of dilated cardiomyopathy
Apoptosis is a hallmark of multiple etiologies of heart failure, including dilated cardiomyopathy. Since microRNAs are master regulators of cardiac development and key effectors of intracellular signaling, they represent novel candidates for understanding the mechanisms driving the increased dysfunction and loss of cardiomyocytes during cardiovascular disease progression. To determine the role of cardiac miRNAs in the apoptotic response, we used microarray technology to monitor miRNA levels in a validated murine phospholambam mutant model of dilated cardiomyopathy. 24 miRNAs were found significantly differentially expressed, most of which have not been linked to cardiac disease before. We showed that individual silencing of 6 out of 7 significantly down-regulated miRNAs (mir-1, -29c, -30d, -149, -486,  -499)  led to a strong apoptotic phenotype in cell culture , suggesting they repress pro-apoptotic factors. To identify putative miRNA targets most likely relevant to cell death, we computationally integrated transcriptomic, proteomic and functional annotation data. We showed the dependency of prioritized target abundance on miRNA expression using RNA interference and quantitative mass spectrometry. We concluded that down regulation of key pro-survival miRNAs causes up-regulation of apoptotic signaling effectors that contribute to cardiac cell loss, potentially leading to system decompensation and heart failure.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Two different microarray platforms, were used to identify and quantify miRNA expression at early stage dilated cardiomyopathy times.  Total RNA was collected from mouse ventricle tissues in a transgenic model expressing a mutant form of phospholamban which results in dilated cardiomyopathway versus healthly littermates as a control.

first: Ruth

last: Isserlin

first: Daniele

last: Merico

first: Dajana

last: Vuckovic

first: Nicolas

last: Bousette

first: Anthony

middle: O

last: Gramolini

first: Gary

last: Bader


title: Nile tilapia (Oreochromis niloticus)  gene expression profiling in males and females at early embryonic development (2, 5 and 9 days post fertilization )

city: Bet Dagan

first: Orly

last: Eshel

address: The Volcani Center POB 6

department: Institute of Animal Science

country: Israel

institute: ARO

summary: Commercial production of tilapia relies on monosex cultures of males, which so far proved difficult to maintain in large scale production facilities. Thus, a better understanding of the genetic architecture of the complex trait of sex determination in tilapia is needed.We aimed to detect genes that were differentially expressed by gender at early embryonic development. Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively. Pools of all-female and all-male embryos at 2, 5 and 9 days post fertilization were used for custom Agilent eArray.

overall_design: 56 pool samples of Nile tilapia full siblings groups (female or male) at day 2, 5 or 9 post fertilization were subjected to total RNA extraction from whole embryo tissues and hybridized to the custom Agilent array. Each sample was yielded from different cross of artificial fertilization: six dams X five sires. The resulting gender were known based on the sire, sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively.

first: Micha

last: Ron

first: Mark

last: Band

first: Andrey

last: Shirak

first: Joel

last: Weller

first: Eyal

last: Seroussi

first: Ester

last: Feldmesser

first: Tatiana

last: Zak

first: Gideon

last: Hulata


title: microRNA profiling of luminal and TNBC breast cancer cell lines

status: Public on Oct 03 2014

city: Singapore

first: Min

last: FENG

address: 60 Biopolis Street,

department: Cancer Therapeutics & Stratified Oncology

country: Singapore

institute: Genome Institute of Singapore

summary:
two luminal cell lines were added, MCF7 and BT-474
two TNBC cell line were added, MB231 and BT-549

overall_design: microRNA expression profiles were conpared between the luminal group and the TNBC group

first: Feng

last: Min

first: Yu

last: Qiang


title: Expression profiling of control vs. ndr1 overexpression zebrafish blastulas

status: Public on Oct 15 2014

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

institute: University of Warwick

summary: Identification of genes downstream of ndr1 in zebrafish blastulas, and identification of direct targets by reference with Smad2 and Eomesa ChIP-seq data

overall_design: Triplicate control injected samples and triplicate samples of embryos injected with 50pg ndr1 mRNA per embryo.  Total RNA prepared from ~200 sphere stage embryos per sample.

first: Stephen

last: Cutty

first: Derek

last: Stemple

first: Paul

last: Flicek

first: Ashley

middle: E

last: Bruce

first: Fiona

last: Wardle


title: Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction

status: Public on Sep 30 2014

city: Notre Dame

first: David

last: Severson

state: IN

address: 44 Galvin Life Sciences

department: Biological Sciences

institute: University of Notre Dame

summary: Investigation of gene expression level differences in Culex pipiens (SB) and C. quinquefasciatus (JHB) at three time points (8, 16, and 24 hours post-exposure) during the early pupal state in standard (25°C; 16 h light/8 h dark) and diapause-inducing (18°C; 8 h light/16 h dark) conditions.

sample_organism:
Culex pipiens
Culex quinquefasciatus

overall_design: A forty-eight chip study (4 Expr12x135K slides) using cDNA from total RNA collected from two species in the Culex pipiens complex at 3 time-points during the early pupal stage to study gene expression differences between standard (25°C; 16 h light/8 h dark) and diapause-inducing (18°C; 8 h light/16 h dark) conditions, and between Culex pipiens  (diapause) and C. quinquefasciatus (no diapause).  Each chip measures the expression level of 18,692 protein coding genes, with 3 probes per gene and two-fold technical redundancy. Each of the 12-plex slides was used for one of four biological replicates. Probes were designed using the C.quinquefasciatus CpipJ1.2 geneset in VectorBase.

middle: V

last: Hickner

first: Akio

last: Mori

first: Erliang

last: Zeng

first: John

last: Tan


title: miRNA profiles in Primary and Recurrent GBM

status: Public on Sep 28 2014

city: Taipei

first: Shih-Hwa

last: Chiou

address: No. 201, Sec. 2, Shih-Pai Road

country: Taiwan

institute: Vghtpe

summary: Glioblastoma (GBM) bears a dismal prognosis with rapid relapse following complete resection and radiochemotherapy. The involvement of microRNAs in tumor progression has been demonstrated in hepatoma, breast cancer, and prostate cancers. However, the microRNAs involved in modulating the progression and relapse of GBM are still unclear. Initially, we compared the miRNA expression profiles between primary and recurrent GBM tissues from the same patient in twelve independent cases.


title: microRNAs involved in neuropathic pain following a peripheral nerve injury

status: Public on Sep 29 2014

city: New York

first: Esperanza

last: Recio-Pinto

address: 180 Varick Street

department: Anesthesiology

institute: NYU

summary: Peripheral nerve injury alters the expression of hundreds of proteins in dorsal root ganglia (DRG). Targeting some of these proteins has led to successful treatments for acute pain, but not for sustained postoperative neuropathic pain. The latter may require targeting multiple proteins.  Since a single microRNA (miR) can affect the expression of multiple proteins, here, we describe an approach to identify chronic neuropathic pain-relevant miRs. We used two variants of the spared nerve injury (SNI): Sural-SNI and Tibial-SNI and found distinct pain phenotypes between the two. Both models induced strong mechanical allodynia, but only Sural-SNI rats maintained strong mechanical and cold allodynia, as previously reported. In contrast, we found that Tibial-SNI rats recovered from mechanical allodynia and never developed cold allodynia. Since both models involve nerve injury, we increased the probability of identifying differentially regulated miRs that correlated with the quality and magnitude of neuropathic pain and decreased the probability of detecting miRs that are solely involved in neuronal regeneration. We found seven such miRs in L3-L5 DRG. The expression of these miRs increased in Tibial-SNI. These miRs displayed a lower level of expression in Sural-SNI, with four having levels lower than those in sham animals. Bioinformatics analysis of how these miRs could affect the expression of some ion channels supports the view that, following a peripheral nerve injury, the increase of the 7 miRs may contribute to the recovery from neuropathic pain while the decrease of four of them may contribute to the development of chronic neuropathic pain.  The approach used resulted in the identification of a small number of potentially neuropathic pain relevant miRs. Additional studies are required to investigate whether manipulating the expression of the identified miRs in primary sensory neurons can prevent or ameliorate chronic neuropathic pain following peripheral nerve injuries.

overall_design: To identify the miRs that were differentially dysregulated between Tibial-SNI and Sural-SNI, we first performed 12 microarrays in a limited number of samples (in four individual DRGs per group: Sham, Tibial-SNI and Sural-SNI; two L3-DRG and two L4-DRG). Then, miRs identified as having differential expression were corroborated with real time qRT-PCR in RNA isolated from individual DRGs (L3, L4 and L5) derived from 4 rats per group (not presented here, but in the manuscript).

first: Monica

last: Norcini

first: Thomas

last: Blanck

first: Alexandra

last: Sideris


title: Real-time quantitative PCR analysis of human mononuclear cells from bone marrow.

status: Public on Sep 27 2014

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

institute: Istituto Superiore di Sanità

summary: Activation of non-canonical TGF-β1 signaling indicates an autoimmune mechanism for bone marrow fibrosis in primary myelofibrosis

overall_design: Two condition experiment. Biological replicates: 3 control human healty subjects, 3 PMF patients

first: Fiorella

last: Ciaffoni

first: Maria

last: Verrucci

first: Elena

last: Cassella

first: Lilian

last: Varricchio

first: Margherita

last: Massa

first: Giovanni

last: Barosi

first: Anna

last: Migliaccio


title: Comparison of human NK and T cell microRNAs

status: Public on Sep 08 2014

city: Lexington

first: Steven

middle: Ray

last: Presnell

state: KY

address: 800 Rose St.

department: Pathology, Medicine

institute: University of Kentucky

summary: We studied the levels of expression of hundreds of mature miRNA's on an arrray (miRCURY, Exiqon, Cophenhagen, DN) for primary human T cells and NK cells. We found a 4% difference in the level of expression between these two cell types.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: NK and T cells were purified from peripheral blood mononuclear cells by negative selection  from three healthy adult individuals, and total RNA was harvested. Samples reverse transcribed and studied on a microarry (miRCURY, Exiqon)

first: Ahmad

last: Al-Attar

first: Charles

last: Lutz


title: Real-time quantitative PCR analysis of human mononuclear cells from bone marrow

overall_design: Two condition experiment. Biological replicates: 3 control human healty subjects, 6 PMF patients


title: Macrophages from sex-reversed chicken embryos [set1]

status: Public on Jul 31 2014

city: Easter Bush

first: Sunil

last: Nandi

state: Midlothian

address: University of Edinburgh

department: Developmental Biology

institute: The Roslin Institute

summary: To identify markers associated with inherent cellular sex-identity, we analysed cultured macrophages from male and female chick embryos. We found that male and female macrophages respond differently to stimulation by bacterial lipopolysaccharide and that female macrophages constitutively express higher levels of interferon target genes than male macrophages. To determine whether these differences resulted from the actions of gonadal hormones, we induced gonadal sex-reversal to alter the hormonal environment of the developing chick and analysed different tissues and macrophages from male and female embryos.

overall_design: Macrophages were collected from leg-bones of chicken embryos at day 13 of development after administration of either 1mg fadrozole, or 100ul PBS as control, at day 3 of development. Two pools of macrophage cultures were made for each of the following: male control, male fadrozole-treated, female control, female fadrozole-treated. Cells were cultured in either standard medium or in medium containing lipopolysaccharide (LPS) to activate the macrophages. Macrophages were harvested and RNA collected for microarray analysis.

first: Carla

last: Garcia Morales

first: Debiao

last: Zhao

first: Derek

last: McBride

first: Le

last: Yu

first: Jacqueline

last: Smith

first: Dave

last: Burt

first: Helen

middle: M

last: Sang

first: David

middle: A

last: Hume

first: Michael

last: Clinton


title: Macrophages from newly hatched chicks [set2]

summary: To identify markers associated with inherent cellular sex-identity, we analysed macrophages from newly-hatched chicks. We found that male and female macrophages respond differently to stimulation by bacterial lipopolysaccharide and that female macrophages constitutively express higher levels of interferon target genes than male macrophages.

overall_design: Macrophages were collected from leg-bones of chickens between 1 and 3 days after hatch. Three pools of macrophage cells were made for male and female cultures. Cells were cultured in either standard medium or in medium containing lipopolysaccharide (LPS) to activate the macrophages. Macrophages were harvested and RNA collected for microarray analysis.

middle: G

last: Morales


title: Macrophages from male and female chickens

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

overall_design: Refer to individual Series


title: Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae

status: Public on Apr 06 2014

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

institute: ScilifeLab - Karolinska Institutet

summary: Specific histone modifications play important roles in chromatin functions such as activation or repression of gene transcription. These participation must occur as a dynamic process, however, most of histone modification state maps reported to date only provide static pictures linking certain modification with active or silenced states. This study focused on the global histone modification variation that occurs in response to transcriptional reprogramming produced by a physiological perturbation in yeast. We have performed genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after of a saline stress. The most striking change is a quick deacetylation of lysines 9 and 14 of H3 and lysine 8 of H4 associated to repression of genes. Genes that are activated increase the acetylation levels at these same sites, but this acetylation process of activated genes seems minor quantitatively to that of the deacetylation of repressed genes. The observed changes in tri-methylation of lysines 4, 36 and 79 of H3 and also di-methylation of lysine 79 of H3 are much more moderate than those of acetylation. Additionally, we have produced new genome-wide maps for six histone modifications at more than five times higher resolution of previous available data and analyzed for the first time in S. cerevisiae genome wide profiles of two more, acetylation of lysine 8 of H4 and di-methylation of lysine 79 of H3. In this research we have shown that dynamic of acetylation state of histones during activation or repression of transcription is a process much quicker than methylation and therefore the changes produced in the acetylation may affect methylation but the reverse path is not possible.

overall_design: The experiments described in this study compare ChIP with a histone modification antibody to a control ChIP with a core histone antibody. Budding yeast samples were analyzed in exponential growing conditions (YPD) or after 10 minutes of 0.4M NaCl stress.  For each experiment 1 or 2 biological replicates were performed.

first: Lorena

last: Magraner

first: Maria

last: Coloma

first: Vicente

last: Tordera


title: Using tiling arrays to precisely detect DNA targets of THO in yeast

status: Public on Mar 24 2014

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

institute: Ecole Normale Supérieure

summary: Crosslinked DNA from wild type cells or from mutant of the THO complex was analyzed by tiling arrays to precisely detect DNA targets of THO in yeast.

overall_design: DNA coming from SDS-washed DCF pellet and the supernatant SN2k of 2 strains were compared in the study, WT (W303) and mft1 delta (DLY224). The DNA of each condition (Pellet or Supernatant) was labeled either with Cy3 or Cy5 fluorescent dyes and competitively hybridized on 244k agilent arrays. For each strain, the experiment was performed on 2 biological replicates, with dye swap.

first: John

last: Mouaikel

first: Sebastien

last: Causse

first: Yves

last: Daubenton-Carafa

first: Corinne

last: Blugeon

first: Sophie

last: Lemoine

first: Frédéric

last: Devaux

first: Mathieu

last: Rougemaille

first: Xavier

last: Darzac

first: Domenico

last: Libri


title: Agilent custom zebra finch microarray

status: Public on Mar 21 2014

city: Sapporo

first: Kazuhiro

last: Wada

address: Room 910, Building No.5, North 10, West 8, Kita-ku

institute: Hokkaido University

summary: Like human speech, birdsong is a complex vocal behavior that is acquired by sensorimotor learning based on coordination of auditory input and vocal output to mimic memorized tutor song. Here we investigate neural circuits for vocal learning and production in deafened songbirds to elucidate how sensory-input regulate genetic and epigenetic property of vocal development and its associated gene expression dynamics. Compared with audition-intact birds, in deafened zebra finches, the vocal development is delayed but song crystallization is observed at more than three times later, producing individually different but structured vocal patterns. In contrast to the distinct difference of vocal ontogeny between audition (+) and (-), unexpectedly, developmental regulation of gene expression dynamics is strictly conserved with age-locked trend in vocal motor circuit in both intact and deafened birds, indicating sensory-input independent robustness of developmental gene expression dynamics in the motor circuit for sensorimotor learning. This discrepancy between outward vocal phenotype and inward gene expression dynamics provides new insight into neural regulation at closing of the critical period for vocal learning by two different forms: auditory inputs-dependent ‘active’ crystallization and gene expression dynamics-mediated ‘passive’ crystallization.

overall_design: We collected brain samples from intact and early-deafened birds (deafened at day-post hatch 17-23) under silent and dark condition. Song nuclei in vocal motor circuit, HVC and RA tissue samples (juvenile; n = 3, young; n = 3, old; n = 3 of intact and early-deafened birds for HVC and RA) were laser-microdissected from total 24 birds (intact; n = 12, early-deafened; n = 12). Each sample was hybridized to a single array, totaling 36 arrays. Birds were selected per slide such that early-deafened birds were paired with intact birds. To minimize possible interslide bias or batch effects, intact and early-deafened bird samples matching with brain area and age conditions were hybridized side by side on same array glass.

first: Chihiro

last: Mori


title: Gene profile of breast cancer tumors with low and high FAK expression

status: Public on Feb 01 2014

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: The gene expression profiles were identified in breast cancer tumors with different level of FAK

overall_design: three tumors with low FAK expression identified by IHC and 3 tumors with high FAK expression. 2 triple-negative with low and one triple negative with high FAK expression was among these 6 samples

first: Vita

last: Golubovskaya

first: William

last: Cance

first: Song

last: Liu

first: Jeffrey

last: Conroy

first: Baotran

last: Ho


title: Gene profile of colon cancer cells treated with Y15 (FAK inhibitor) and 5-fluorouracil

summary: The gene expression profiles were identified in colon cancer cell lines treated either with Y15 or with 5-FU

overall_design: SW620 and Lovo-1 colon cancer cell lines were treated with 10 microM Y15 for 24 hours or with 5-FU 200 microM for 24 hours and compared treated to untreated

first: Melissa

last: Heffler


title: Effects of exercise on microRNA expression level in human monocytes

status: Public on Feb 15 2014

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

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

overall_design: Twelve healthy men (22-30yr old) performed 10 2-min bouts of cycle ergometer exercise interspersed with 1-min rest at a constant work equivalent to about82% of VO2max. A baseline blood sample was taken before the and immediately after the exercise.  Monocytes were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Monocyte Isolation Kit II, human  #130-091-153 and the autoMACS® Pro Separator). Total RNA was extracted using TRIzol®.  For this study we used Agilent Human miRNA microarrays V2  (total of 24 arrays).

first: Dan

last: Cooper


title: Study of miRNA expression profile in HCV infected human serum samples

status: Public on Nov 01 2013

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: A miRNA microarray was performed from HCV infected patient serum samples of bothe genotype 1b and genotype 3a, which are prevalent in India, with the aim of identifying a set of miRNAs which are uniquely differentially expressed during HCV infection. miR-320c, miR-483-5p, miR-134 and miR-198 were found to be upregulated in the patient samples as compared to the controls and are currenty being validated.

overall_design: Agilent one-color experiment, Organism: Homo sapiens , Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]

first: Das

last: Saumitra

first: S

last: Shwetha

first: Chandra

last: Goutham

first: MN

last: Khaja

last: Madhavi

first: B

last: Ravishankar


title: Desai SDQ0803_KNL2_N2_LTemb

status: Public on Oct 30 2013

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_4619
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody SDQ0803 KNL-2 (target is KNL-2); Strain N2

first: Reto

last: Gassmann

first: Arshad

last: Desai


title: MicroRNA expression signatures of CD14-CD45-EpCAM+ cells in human bone marrow for colorectal cancer liver metastasis

status: Public on Nov 11 2013

city: Suita

first: Hiroshi

last: Takeyama

state: Osaka

address: Yamada-oka 2-2

department: Gastroenterological Surgery

institute: Graduate School of Medicine, Osaka University

summary: To further development of our gene expression approach to biodosimetry, we have employed microRNA microarray expression profiling to identify genes with the potential to distinguish liver metastasis related microRNA. Colorectal cancer patients were administered anesthesia and 20 mL BM was taken from the right and left anterior iliac crests before surgery. Mononucleated cells were collected using a standard Ficoll-Hypaque gradient technique. To enrich for EpCAM+ cells, CD14+ cells were removed from the whole bone marrow using auto MACSTM pro (Milteny Biotec, Bergisch Gladbach, Germany) with anti-CD14 immunomagnetic beads (clone; TÜK4, Milteny Biotec). Next, CD45+ cells were removed by treatment with anti-CD45 immunomagnetic beads (clone; 5B1; Milteny Biotec). The residual CD14−CD45− cells were then incubated with FcR blocking reagent (Milteny Biotec), followed by incubation with anti-EpCAM immunomagnetic beads (clone; HEA-125, Milteny Biotec), and the CD14−CD45−EpCAM+ cells were taken up. Total RNA of these cells we analyzed the microRNA levels of  CD14−CD45−EpCAM+ cells obtained from non-metastasis patients (n = 12) and liver metastasis patients (n = 7).  Ten-microRNA consensus signature was identified that distinguished between CD14−CD45−EpCAM+ cells from liver metastasis patients and  CD14−CD45−EpCAM+ cells from non-liver metastasis patients.

overall_design: MicroRNA expression of CD14-CD45-EpCAM+ cells in human bone marrow was measured.  RNA of these cells we analyzed the microRNA levels of  CD14−CD45−EpCAM+ cells obtained from non-metastasis patients (n = 12) and liver metastasis patients (n = 7).

first: Hirofumi

last: Yamamoto

first: Koshi

last: Mimori


title: Desai SDQ0810_KNL2_N2_LTemb

summary:
modENCODE_submission_4620
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody SDQ0810 KNL-2 (target is KNL-2); Strain N2


title: Comparison of miRNA expression profilings between hESCs and hiPSCs

status: Public on Dec 03 2013

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.

overall_design: We extracted total RNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines and hybridized them to Agilent miRNA expression microarrays.

first: M

last: Koyanagi-Aoi

last: Narita


title: Desai SDQ0804_HCP3_N2_LTEMB

summary:
modENCODE_submission_3543
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody SDQ0804 HCP-3 (target is HCP-3); Strain N2


title: Bacteria are the dominant ammonia oxidizers in coastal sediments of the Western English Channel

status: Public on Aug 24 2013

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

summary: The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoA-carrying AOA within these sediments.

sample_organism:
artificial sequences
marine sediment metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: K

last: Tait

first: V

last: Kitidis


title: Chronic academic stress increases a group of microRNAs in peripheral blood

status: Public on Aug 09 2013

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

summary: In this study, we examined alterations in microRNA (miRNA) profiles in peripheral blood from male medical students two months and two days before the National Examination for Medical Practitioners. Blood obtained one month after the examination were used as baseline controls. Several miRNAs were significantly elevated during the pre-examination period in association with significant down-regulation of their target mRNAs two days before the examination. Thus, a distinct group of miRNAs in periheral blood may participate in the integrated response to chronic academic stress in healthy young men

overall_design: Total RNA was prepared from venous blood which was taken from young male medical students. 12 samples from 4 subjects at three time points: two months before, two days before, and one month fater the examination were measured on array platform.

first: Kazuhito

last: Rokutan


title: The metabolic and regulatory networks of carbohydrate utilization of Thermotoga maritima

status: Public on Aug 02 2013

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

type: Expression profiling by genome tiling array

summary: In this study, we combined a subsystem-based comparative genomic approach with experimental validation to reconstruct the metabolic and regulatory networks of carbohydrate utilization in 11 complete genomes from the Thermotogales order.

overall_design: Exression profiling studies were performed using total RNA isolated from mid log phase cultures of T. maritima grown on minimal media with distinct carbon sources.

first: Dmitry

last: Rodionov

first: Vasiliy

last: Portnoy

first: Irina

last: Rodionova

first: Xiaoqing

last: Li

last: Ravcheev

first: Yekaterina

last: Tarasova

first: Olga

last: Zagnitko

first: Karsten

last: Zengler

first: Andrei

last: Osterman


title: Expression data from Andromonoecious poplar flower

status: Public on Jul 30 2013

city: Beijing

first: Yuepeng

last: Song

address: No. 35, Qinghua East Road

country: China

institute: Beijing Forestry University

summary: Exceptionally andromonoecious individuals that flowers appeared to form that structure resembling a carpel attached to the reverse side of stamen cup were detected in strictly dioecious poplar. Andromonoecious poplarswere used to analyze transcript levels accurately.

overall_design: We used microarrays to detail the global programme of gene expression during flower development and identified distinct classes of different-regulated genes between sexes during this process.

first: Deqiang

last: Zhang


title: miRNA analysis of triple-negative breast cancers in association with clinical and molecular phenotypes

status: Public on Sep 30 2013

city: Pomezia(Rome)

first: Emanuele

last: de Rinaldis

address: Via Pontina

institute: IRBM (MERCK)

summary: Background: This study focuses on the analysis of miRNAs expression data in a cohort of 181 well characterised breast cancer samples composed primarily of triple-negative (ER/PR/HER2-negative) tumours with associated genome-wide DNA and mRNA data, extensive patient follow-up and pathological information. Results: We identified 7 miRNAs with a prognostic role in the triple-negative tumours and an additional 8 prognostic miRNAs when the analysis was extended to the set of all ER-negative cases. miRNAs linked to an unfavourable prognosis were associated with a broad spectrum of motility mechanisms involved in the invasion of stromal tissues, such as cell-adhesion, growth factor-mediated signalling pathways, interaction with the extracellular matrix and cytoskeleton remodelling. When we compared different intrinsic molecular subtypes we found 46 miRNAs that were specifically expressed in one or more intrinsic subtypes. Integrated genomic analyses indicated these miRNAs to be largely influenced by DNA genomic aberrations and to exert a silencing effect on their targets through transcriptional down-regulation. Among others, our analyses highlighted the role of miR17-92 and miR-106b-25, two polycistronic miRNA clusters with known oncogenic functions. We showed that their basal-like specific up-regulation is influenced by increased DNA copy number and contributes to the transcriptional phenotype and the activation of oncogenic pathways in basal-like tumours.Conclusions: This is the first study analysing miRNA, mRNA and DNA data in integration with pathological and clinical information, in a large and well-annotated cohort of triple-negative breast cancers. It provides a conceptual framework, as well as integrative methods and system-level results to elucidate the role of miRNAs as biomarkers and modulators of oncogenic processes in these types of tumours.

overall_design: 181 breast tumour samples were analyzed, extracted from 173 patients. For the great majority of patients (165) only one sample was extracted, while for 8 patients two samples were extracted (biological replicates).

first: Brian

last: Burford

first: Patricia

last: Gazinska

first: Anca

last: Mera

first: Zora

last: Modrusan

first: Grazyna

last: Fedorowicz

first: Cheryl

last: Gillett

first: Pierfrancesco

last: Marra

first: Anita

last: Grigoriadis

first: David

last: Dornan

first: Lars

last: Holmberg

first: Sarah

last: Pinder

first: Andrew

last: Tutt


title: Identification of RpoE2 target genes in Sinorhizobium meliloti

status: Public on Jul 22 2013

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: Sinorhizobium meliloti lives as a soil saprophyte, and engages in a nitrogen fixing symbiosis with plant roots.  To succeed in such diverse environments, the bacteria must continually adjust gene expression.  Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase.  The S. meliloti genome encodes 14 of these alternative sigmas, including 11 extracytoplasmic function (ECF) sigmas.  We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti overexpressing the ECF sigma factor, RpoE2.  Our work identifies over 200 genes whose expression is dependent on RpoE2.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: The gene expression profile of Sinorhizobium meliloti strain CL150 carrying the rpoE2 gene on a plasmid, where it was expressed from a melibiose-inducible promoter (the S. meliloti PmelA promoter), was compared to the gene expression profile of CL150 carrying the corresponding empty vector (pCAP11). CL150 is an Rm1021 strain that has been corrected for two point mutations: it is wild type for ecfR1 and pstC.

first: Claus

last: Lang

first: Sharon

last: Long


title: Identification of p130Cas/ErbB2-dependent invasive signatures in transformed mammary epithelial cells

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

institute: University of Padova

summary: Understanding transcriptional changes during cancer progression is of crucial importance to develop new and more efficacious diagnostic and therapeutic approaches. It is well known that ErbB2 is overexpressed in about 25% of human invasive breast cancers. We have previously demonstrated that p130Cas overexpression synergizes with ErbB2 in mammary cell transformation and promotes ErbB2-dependent invasion in three-dimensional (3D) cultures of human mammary epithelial cells. Here, by comparing coding and non-coding gene expression profiles, we define the invasive signatures associated with concomitant p130Cas overexpression and ErbB2 activation in 3D cultures of mammary epithelial cells. Specifically, we have found that genes involved in amino acids synthesis (CBS, PHGDH), cell motility, migration (ITPKA, PRDM1), and angiogenesis (HEY1) are upregulated, while genes involved in inflammatory response (SAA1, S100A7) are downregulated. In parallel, we have shown that the expression of specific miRNAs is altered. Among these, miR-200b, miR-222, miR-221, miR-R210, and miR-424 are upregulated, while miR-27a, miR-27b, and miR-23b are downregulated. Overall, this study presents, for the first time, the gene expression changes underlying the invasive behavior following p130Cas overexpression in an ErbB2 transformed mammary cell model.

overall_design: To identify transcriptional changes occurring during invasion we have performed a comparative microarray analysis of non coding RNA (miRNA) between MCF10A.B2 acini over-expressing p130Cas with activation of ErbB2 and control cells.

first: Alessandra

last: Pincini

first: Giusy

last: Tornillo

first: Francesca

last: Orso

first: Emilia

last: Turco

first: Paolo

last: Provero

first: Enzo

last: Medico

first: Paola

last: Defilippi

first: Daniela

last: Taverna

first: Sara

last: Cabodi


title: Expression data from Serinus canaria HVC, RA and Entopallium

status: Public on Aug 22 2013

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

country: Germany

institute: Max Planck Institute for Ornithology

summary:
Within the overall project, we performed a set of microarrays to validate RNAseq data.
In this data set, we compare the expression data of song nuclei to the optical tectrum dissected from adult canaries housed at long day cycles to identify nuclei specific genes.

sample_organism:
Serinus canaria
Taeniopygia guttata

overall_design:
18 total S. canaria samples housed at long day were analyzed, 6 HVC samples, 5 RA samples and 7 Entopallium samples. The differential expression was analyzed using the group-wise exhaustive analysis with False Discovery Rate set to zero and 10-significant probe minimum coverage, HVc/RA compared to entopallium samples. Additionally, 24 total samples of S. canaria housed at short day were analyzed, 6 HVC samples, 6 HVC samples of canaries treated with Testosterone, 6 Entopallium samples and 6 Entopallium samples treated with Testosterone, and  24 total samples of T. guttata, 6 HVC samples, 6 HVC samples of finches treated with Testosterone, 6 Entopallium samples and 6 Entopallium samples treated with Testosterone, the HVC samples were compared to Entopalliun as described before.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

first: C

first: A

last: Bakker

first: M

last: Gahr


title: Dendritic cell subtypes from lymph nodes and blood show contrasted gene expression programs upon Bluetongue Virus infection

status: Public on Jul 09 2013

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: The gene expression in conventional and plasmacytoid dendritic cells (cDC and pDC respectively) during Bluetongue virus (BTV) infection in sheep depends on the lymphoid compartment and suggest that these cell types have a role in the physiopathology

overall_design: We analyzed the gene expression in  lymph node pDC and cDC from 3 control and 3 BTV infected sheep at day 6 post infection, in blood pDC from 2 control and 2 BTV infected sheep at day 6 post infection, and in spleen cDC from 3 control and 2 BTV infected sheep at day 6 post infection.

first: Suzana

last: Ruscanu

first: Luc

last: Jouneau

first: Céline

last: Urien

first: Claudia

last: Bevilacqua

first: Jamila

last: Elhmouzi-Younes

first: Marc

last: Dalod

first: Benoit

last: Loup

first: Marco

last: Moroldo

first: Jérôme

last: Lecardonnel

first: Mickael

last: Bourge

first: Jayne

last: Hope

first: Damien

last: Vitour

first: Stéphan

last: Zientara

first: Gilles

last: Meyer

first: Isabelle

last: Schwartz-Cornil


title: MicroRNA expression profile of platelets in sickle cell disease

status: Public on Jun 20 2013

city: Pittsburgh

first: Shilpa

last: Jain

state: PA

address: 200 Lothrop Street

country: USA

institute: Uinversity of Pittsburgh

summary: Circulating platelets from Sickle cell disease (SCD) patients express distinct gene expression patterns that regulate function. The objective of this study is to identify a role of post-transcriptional regulation of the platelet transcriptional signaling by microRNAs.

overall_design: Comparison of microRNA expression in platelets from SCD patients and control subjects, from 2 cohorts-University of Pittsburgh and National Institutes of Health.

first: Mark

last: Gladwin

first: Naftali

last: Kaminski


title: Identification of differentially expressed miRNAs in HCC cell lines compared with normal livers

status: Public on May 31 2013

city: Tokyo

first: Johji

last: Inazawa

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

institute: Tokyo Medical & Dental University

summary:
To explore functionally crucial tumor-suppressive (TS)-miRNAs in hepatocellular carcinoma (HCC), we performed integrative function- and expression-based screenings of TS-miRNAs in six HCC cell lines.  The screenings identified seven miRNAs, which showed growth-suppressive activities through the overexpression of each miRNA and were endogenously downregulated in HCC cell lines.  Further expression analyses using a large panel of HCC cell lines and primary tumors demonstrated four miRNAs, miR-101, -195, -378 and -497, as candidate TS-miRNAs frequently silenced in HCCs.  Among them, two clustered miRNAs miR-195 and miR-497 showed significant growth-suppressive activity with induction of G1 arrest.  Comprehensive exploration of their targets using Argonute2-immunoprecipitation-deep-sequencing (Ago2-IP-seq) and genome-wide expression profiling after their overexpression, successfully identified a set of cell-cycle regulators, including CCNE1, CDC25A, CCND3, CDK4, and BTRC.  Our results suggest the molecular pathway regulating cell cycle progression to be integrally altered by downregulation of miR-195 and miR-497 expression, leading to aberrant cell proliferation in hepatocarcinogenesis.
Screening of frequently downregulated miRNAs by comparing endgeneous expression status of miRNAs in 6 HCC cell lines with 2 normal livers

overall_design: Expression analysis using total RNAs extracted from standard medium conditioned 6 HCC cell lines, and 2 normal livers derived from patients with  hepatectomy due to metastatic liver tumor

first: Mayuko

last: Furuta


title: Human dendritic cell microRNA profile after NOD2 and / or TLR2 stimulation

status: Public on Jun 01 2013

city: Oxford

first: Oliver

last: Brain

state: Oxfordshire

address: Headley Way

department: TGU

institute: Nuffield Dept of Medicine

summary: microRNA expression in human monocyte-derived DCs following stimulation with NOD2 ligand MDP, TLR2 ligand Pam3CSK4, or both.

overall_design: 4 condition experiment with two timepoints, and 4 biological replicates. Conditions: unstimulated; MDP stimulated; Pam3CSK4 stimulated; MDP + Pam3CSK4 stimulated. Timepoints: 4 hours and 24 hours.

first: Alison

last: Simmons


title: Realtime quantitative PCR array of miRNAs expressed in E15 - E18 mouse male and female fetal lungs

status: Public on May 01 2013

city: Boston

first: Sana

last: Mujahid

state: MA

address: 800 Washington St.

department: Pedatrics

institute: Tufts Medical Center

summary: qPCR profiling of miRNAs in mouse fetal lungs was done. Lungs were dissected and RNA was extracted using miRVANA extraction kit (Applied Biosystems).

overall_design: RNA was isolated from 2 separate lungs (labeled as A or B) for each time point and 2 technical replicates were run for each sample (labeled as 1 or 2).

first: Heber

last: Nielsen


title: Microarray-based gene expression profiling of peripheral blood mononuclear cells in dairy cows with experimental hypocalcaemia and milk fever

status: Public on Jun 16 2013

city: Morioka

first: Kouya

last: Sasaki

state: Iwate

department: United Graduate School of Veterinary Sciences

institute: Gifu University

summary: Peripheral blood mononuclear cells (PBMC) from cows with experimentally induced hypocalcaemia or spontaneous milk fever were subject of an oligo-microarray analysis following quantitative real-time reverse transcription PCR (q-PCR). In experimental hypocalcaemia induced by 10 % Na2EDTA infusion (n = 4), the microarray revealed that 32 genes were significantly up- or down-regulated compared to control treatment by 11 % CaEDTA infusion (n = 4). In milk fever cases (n = 8), the microarray demonstrated that 98 genes were expressed differentially higher or lower compared to healthy parturient cows (n = 5). From both data, five genes were selected to be strongly related to both experimental hypocalcaemia and milk fever. Additionally, another gene was judged to be specific for milk fever independent of hypocalcaemia. The mRNA expressions of these six genes in milk fever cases were verified by q-PCR, which were significantly higher or lower than those in healthy parturient cows.

overall_design: In the experimental hypocalcemia study, four healthy nonpregnant, non-lactating ovariectomised Holstein cows were used. The experiment was performed according to a 2 × 2 crossover design with 2 weeks intervals. Cows were infused with either Na2EDTA (hypocalcaemic treatment) or CaEDTA (control treatment) solution during a period of 4 h. The animals were monitored for clinical signs of hypocalcaemia (dry nose, staggering, astasia, reduced ruminal activity, increased heart rate, increased respiratory frequency, sweating, and ear cold). Infusion of EDTA solution was temporarily suspended when hypocalcaemia induced astasia was represent. If affected cow stood again, EDTA infusion was resumed. PBMC samples were collected before the start of infusion (0 h; pre-treatment) and at 4 and 24 h after the start of infusion 24h and utilized for gene expression analysis of PBMC. In the spontaneous milk fever study, a total of 13 Holstein dairy cows, which were 8 parturient cows diagnosed with milk fever within 2 days postpartum and 5 clinically healthy parturient cows within 2 days after parturition (Group H), were used. All spontaneous milk fever cases showed hypocalcaemia (< 1.8 mmol/l) in the blood samples obtained before the first treatment, and were treated by an intravenous infusion of a 20 % Ca borogluconate solution (500 ml). The milk fever cases were divided into two categories according to the reponse of the cows to the first Ca treatment: an immediate response in which the cow could stand within 1 day after a single Ca treatment (Group A, n = 4) and a requirement further treatment over 1 day after a single Ca treatment (Group B, n = 4). PBMC samples were collected vein just before the first Ca treatment in groups A and B and within 2 days postpartum in group H and utilized for gene expression analysis of PBMC.

first: Keiichiro

last: Kizaki

first: Kazuyoshi

last: Hashizume

first: Norio

last: Yamagishi


title: Topoisomerase I cleavage complexes preferentially down-regulate ubiquitin- and RNA degradation-related transcripts in relationship to gene length, exon-intron junctions and p53-dependent up-regulation of miR-142-3p [miRNA]

status: Public on Apr 17 2013

city: Fairfax

first: Michael

last: Ryan

state: VA

address: 11781 Lee Jackson Hwy, Ste 320

institute: In Silico Solutions

summary: DNA topoisomerase I (Top1) is required for transcription as it relaxes positive and negative supercoils by forming transient Top1 cleavage complexes (Top1cc) up- and down-stream of transcription complexes. However, Top1cc can also be trapped by endogenous DNA lesions and by camptothecin (CPT) and its anticancer derivatives, which results in transcription blocks. Here, we undertook a genome-wide analysis of the effects of CPT on gene expression at exon resolution.

overall_design: We tested the impact of Top1 inhibition on miRNA expression at the genome-wide level in human colon carcinoma HCT116. The miRNA of cells treated with camptothecin (CPT) for were measured at several timepoints with Agilent Human miRNA Microarray  V3 (8x15K).

first: Stéphanie

last: Solier

first: Mike

middle: C

first: Sudhir

last: Varma

first: Kurt

last: Kohn

first: Hongfang

last: Liu

first: Barry

last: Zeeberg

first: Yves

last: Pommier


title: Topoisomerase I cleavage complexes preferentially down-regulate ubiquitin- and RNA degradation-related transcripts in relationship to gene length, exon-intron junctions and p53-dependent up-regulation of miR-142-3p

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

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

overall_design: Refer to individual Series


title: Over-expression of miR-18b is associated with the grade of malignancy of hepatocallular carcinoma

status: Public on Apr 10 2013

city: Tokushima city

first: toshihito

last: tanahashi

address: Kuramoto-cho 3-18-15

institute: Tokushima University

summary:
Aberrant expression of microRNA (miRNA) is closely associated with carcinogenesis. The malignancy of the hepatocellular carcinoma (HCC) is prescribed in the degree of histological differentiation. Poorly differentiated HCC is generally more malignant prognosis than well differentiated HCC. We analyzed the miRNA expression profiles in 110 HCC (60 moderately differentiated, 30 poorly differentiated, and 20 well differentiated HCC) by using microarray in order to establish the novel biomarker for the degree of histological differentiation and forecasting relapse of HCC. The expression level of 12 miRNAs was significantly different according to the degree of histological differentiation. The expression level of miR-18b in poorly differentiated HCC was significantly higher than that in well differentiated HCC. Based on the target search algorithm and argonaute 2 (Ago2) immunoprecipitation study for target binding assay, miR-18b can control the expression of trinucleotide repeat containing 6B (TNRC6B) as a target. Over expression of miR-18b and down regulation of TNRC6B accelerated the activity of cell proliferation and lost ability of cell adhesion in two hepatoma cell lines. Low expression of miR-18b is significantly decreased the relapse free rate after surgical
resection. In conclusion, expression pattern of miR-18b is a marker of an important determinant in the control of cell proliferation and adhesion and also prediction of clinical course. From a clinical point of view, our study emphasizes miR-18b as a diagnostic and prognostic marker for HCC progression.

overall_design: In order to establish the novel biomarker for the degree of histological differentiation and forecasting relapse of HCC with HCV positive, we analyzed the miRNA expression profiles in 110 surgically resected hepatocellular carcinoma (60 moderately differentiated, 30 poorly differentiated, and 20 well differentiated HCC).


title: Effects of exercise on miRNA expression level in human NK Cells

status: Public on Apr 02 2013

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

institute: University of California, Irvine

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

overall_design: Eleven healthy men (20-29 yr old) performed 10 2-min bouts of cycle ergometer exercise interspersed with 1-min rest at a constant work equivalent to about 77% of VO2max. A baseline blood sample was taken before the and immediately after the exercise.  NK cells were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Kit #130-092-657 and the autoMACS® Pro Separator). Total RNA was extracted using TRIzol®.  For this study we used Agilent Human miRNA microarrays V2  (total of 22 chips).

first: Dan

last: Cooper


title: MicroRNA signature of young and replicative senescent human umbilical vein endothelial cells (HUVECs)

status: Public on Apr 05 2013

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

summary: MicroRNAs regulate various cellular processes. While several genes associated with replicative senescence have been described in endothelial cells, miRNAs that regulate these genes remain largely unknown. The present study was designed to identify miRNAs associated with replicative senescence and their target genes in HUVECs. We have employed Agilent Human MicroRNAs microarray platform  to evaluate the expressions of 866 human miRNAs and 89 human viral miRNAs, based on Sanger miRNA database release 12.0

overall_design: miRNA expression profiles were established for young and replicative senescent HUVECs

first: Hui-Lan

last: Jong

first: Mohd

last: Mustafa

first: Paul

last: Vanhoutte

first: Sazaly

last: AbuBakar


title: MiRNA profiling in lung epithelial cells during infection with influenza A virus of H5N1 strain

status: Public on Mar 01 2013

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: This study aims at elucidating how H5N1 influenza infection perturbs the host's miRNA regulatory pathways that may lead to adverse pathological events, such as cytokine storm, using the miRNA microarray approach.

overall_design: The cell line - NCI-H292, was infected with various preparations of H5N1 influenza viruses was analysed for miRNA expression profiles subsequently. The miRNA expression profiles were measured at 3, 6, 18, and 24 hours post infection, respectively.

first: W

middle: Y

middle: K

last: Chan


title: MiRNA profiling in lung epithelial cells during infection with influenza A virus of H1N1 strain

summary: This study aims at elucidating how H1N1 influenza infection perturbs the host's miRNA regulatory pathways that may lead to adverse pathological events, such as cytokine storm, using the miRNA microarray approach.

overall_design: The cell line - NCI-H292, was infected with various preparations of H1N1 influenza viruses was analysed for miRNA expression profiles subsequently. The miRNA expression profiles were measured at 3, 6, 18, and 24 hours post infection, respectively.


title: The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)

status: Public on Feb 05 2013

city: Piscataway

first: Michael

middle: P

last: Verzi

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary:
We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi
This metadata file describes the gene expression componant of that data

overall_design: Intestinal epithelia were collected from mouse jejunum using EDTA-based chelation and RNA was made using trizol. RNA was checked for quality and then processed for affymetrix arrays, 430 2.0.

first: Ramesh

last: Shivdasani

first: X

middle: S

first: Hyunjin

last: Shin