title: Quantification of allele-specific expression patterns in Arabidopsis by tag profiling

status: Public on Mar 28 2014

city: Gent

first: Marnik

last: Vuylsteke

address: Technologypark 927

department: Plant Systems Biology

country: Belgium

institute: VIB

type: Expression profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary: we demonstrate that 3' end tag profiling vi deep sequencing is a powerful approach to mesure allele-specific expression genome-wide.

sample_organism: Arabidopsis thaliana x Arabidopsis lyrata

overall_design: examination of gene expression in A. thaliana, A. lyrata and the F1 hybrid

first: Remco

last: Van Poecke


title: Genome Wide Linkage analysis of large family with coronary artery disease

city: jena

first: kolsoum

last: Inanloo Rahatloo

address: Beutenberg street 11

country: Germany

institute: Fritz Lipman Institute

summary: We used linkage data from CAD family to search for the responsible variant in disease.

overall_design: we used illumina array for linkage analysis of CAD affected family.

first: Elahi

last: Elahe

first: InanlooRahatloo

last: Kolsoum


title: Expression profiles of X-ray responsive miRNA in human cells [miRNA data]

status: Public on Mar 14 2014

city: Chiba

first: Ken-ichi

last: Ishikawa

state: Chiba

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Charged Particle Therapy

country: Japan

institute: National Institute of Radiological Sciences

summary: MicroRNA (miRNA) is a type of non-coding RNA that regulates the expression of its target genes by interacting with the complementary sequence of the target mRNA molecules. Recent evidence has shown that genotoxic stress induces miRNA expression, but the target genes involved and role in cellular responses remain unclear. We examined the role of miRNA in the cellular response to X-ray irradiation by studying the expression profiles of radio-responsive miRNAs and their target genes in cultured human cell lines. We found that expression of miR-574-3p was induced in the lung cancer cell line A549 by X-ray irradiation. Overexpression of miR-574-3p caused delayed growth in A549 cells. A predicted target site was detected in the 3'-untranslated region of the enhancer of the rudimentary homolog (ERH) gene, and transfected cells showed an interaction between the luciferase reporter containing the target sequences and miR-574-3p. Overexpression of miR-574-3p suppressed ERH protein production and delayed cell growth. This delay was confirmed by knockdown of ERH expression. Our study suggests that miR-574-3p may contribute to the regulation of the cell cycle in response to X-ray irradiation via suppression of ERH protein production.

overall_design: miRNA expression were measured at 1 and 3 h after exposure to doses of 0, 2 or 20 Gy. Microarray experiments were performed with duplicate for each experiment.

first: Atsuko

first: Takashi

last: Imai


title: Platelet micro-RNA expression in type 2 diabetes mellitus

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

summary:
Results Platelets in non-diabetic patients demonstrated miRNA expression profiles comparable to previously published data. The miRNA expression profiles of platelets in diabetics were similar. Statistical analysis unveiled only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques, corresponding to signatures with only modest discriminatory performance. Functional annotation of predicted targets for these miRNAs pointed towards an influence of diabetes mellitus on mRNA processing.
Conclusions/interpretation  We did not find any major differences in platelet miRNA profiles between  diabetics and non-diabetics. Minor differences pertained to miRNAs associated with mRNA processing. Thus, previously described differences in plasma miRNAs between diabetic and nondiabetic patients cannot be explained by plain changes in the platelet miRNA profile.

overall_design: Platelet miRNA profiles were assessed in clinically stable diabetic and nondiabetic patients (each n=30). Platelet miRNA was isolated from leucocyte-depleted platelet-rich plasma, and miRNA profiling was performed using LNA micro-array technology (miRBase 18.0, containing 1,917 human miRNAs). Effects of diabetes mellitus were explored by univariate statistical tests for each miRNA, adjusted for potential confounders, and by developing a multivariable signature, which was evaluated by resampling techniques. Platelet phenotype was assessed by light transmission aggregometry and impedance aggregometry.

first: Christian

last: Stratz

last: Nührenberg


title: Deep sequencing-based expression transcriptional profiling of RAW264.7  infected with Brucella 16M

status: Public on Mar 25 2014

city: jilin

first: liu

last: qianhong

state: jilin

address: No.77, Hanlin Road, Economic Development Districe

department: College of Animal Science and Veterinary Medicine

country: China

institute: Jilin Agricultural Science and Technology University

summary: Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated the kinetic transcriptional profile of gene expression in macrophages infected with Brucella melitensis strain 16M. A key aspect of Brucella virulence is their ability to proliferate within professional and nonprofessional phagocytic host cells, thereby successfully bypassing the bactericidal effects of phagocytes. Their virulence and chronic infections are thought to be due to their ability to avoid the killing mechanisms within host cells. Defining the interaction between a host cell and Brucella is crucial to understanding the infectious process. Most researchers have studied the pathogens, but the host plays a very important role during infections. To date, relatively few host factors have been shown important in Brucella infections. However, little is known about the host networks that mediate infection. The objective of the study is to analyze the genes and cellular components related to the innate immunity response to determine the mechanisms through which Brucella avoids the host innate immunity. A total of 3576 and 3962 genes that are differentially expressed between 0 and 4 h and between 0 and 24 h were identified. The identified genes are related to immune processes, signal transduction, inflammation, apoptosis, cell membrane, transcriptional regulation, and intracellular trafficking. Our data have added to the current understanding of different host gene expressions during different infection phases by Brucella spp.

overall_design: The RAW264.7 cells were seeded into 24-well plates at 5-105 cells/well, incubated in 5% CO2 at 37 °C for 24 h, and then infected with Brucella at a multiplicity of infection of 200. To synchronize the infection, the infected plates were centrifuged at 200 ug for 5 min at room temperature and then incubated at 37 °C for 20 minutes. The infected cell monolayers were washed three times with PBS, overlaid with 0.5 ml of DMEM containing 100 mg/ml of ampicillin and 50 mg/ml of kanamycin at 37 °C for 0, 4, and 24 h. At the end of the incubation period, the culture medium was removed and centrifuged at 1500 rpm for 15 min. The cell pellet and adherent cells were resuspended in TRIzol. Total RNA were extracted from the cells at 0, 4 and 24 h post infection.

first: Liu

last: Qianhong


title: Gene Expression analysis of znuA of Moraxella catarrhalis

status: Public on Mar 16 2014

city: Dallas

first: Todd

middle: C.

last: Hoopman

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

country: USA

institute: University of Texas Southwestern Medical Center

summary: Analysis of the gene expression pattern of a znuA mutant constructed in the O35E background.  It's pattern of expression was compared to that of O35E.

overall_design: 3 biological replicates were prepared.  Each replicate was grown in BHI broth and RNA extracted with the Ambion Ribopure bacterial kit.

middle: C

first: Eric

middle: J

last: Hansen

first: Wei

middle: Z

last: Liu


title: Evaluation of global methylation profile in recipient BMMSCs of MRL/lpr mice after cell therapy (MeDip)

status: Public on Mar 20 2014

city: Los Angeles

first: Shiyu

address: 2250 Alcazar Street, CSA103

institute: CCMB

type: Methylation profiling by genome tiling array

summary: Mesenchymal stem cell transplantation (MSCT) has been widely used to treat a variety of human diseases. However, the detailed mechanisms underlying its success are not fully understood. Here we show that MSCT rescues recipient bone marrow mesenchymal stem cell (BMMSC) function in Fas-deficient-MRL/lpr systemic lupus erythematosus (SLE) mice via rescuing their hypomethylated DNA profile. Using the methylation microarray, we found the global hypomethylation pattern in the recipient BMMSCs of MRL/lpr mice could be rescued by MSCT.

overall_design: In the present study, mesenchymal stem cell transplantation (MSCT) was used to treat MRL/lpr mice. One week after the treatment, normal control MSCs from C3H/HeJ mice (C3H), recipient MSCs from untreated MRL/lpr mice (LPR) and recipient MSCs from MSCT-treated MRL/lpr mice (MSC) were used for total DNA extraction and DNA methylation microarray for analysis of global genome methylation patterns.

first: Songtao

last: Shi


title: Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia (mRNA)

status: Public on Mar 13 2014

city: Boston

first: Tsuneya

last: Ikezu

state: MA

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

summary:
The aim of this study was to determine the role that miRNAs have on influencing murine microgial phenotypes under M1(LPS) and M2a (IL-4) stimulating conditions.
This Series includes expression data obtained from mRNA gene expression microarrays; miRNA expression profiles obtained from the same RNA samples were deposited as a separate Series.

overall_design: 9 total samples were analyzed, n=3 for the three stimulating conditions (resting state, LPS and IL-4) for murine primary microglia. This allowed us to perform the following pairwise comparisons: PBS vs. LPS, and PBS vs. IL-4. This was performed for both mRNA and miRNA gene expression profiles.

first: Robert

last: Freilich


title: Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition

status: Public on Mar 31 2014

city: Bellaterra

first: Jordi

last: Corominas Galbany

state: Barcelona

address: UAB Campus

department: Animal genetics

country: Spain

institute: CRAG

summary:
In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particulary involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group).   High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes.  These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases.
The supplementary files contains the five arrays reported in the paper.

overall_design: Backfat from five animals were assayed with high-density oligonucleotide microarray chips (GeneChip® Porcine) from Affymetrix, in order to validate RNA-Seq data.

last: Galbany

first: Yuliaxis

last: Ramayo

first: Anna

last: Puig

last: Estellé

last: Castelló

first: Estefania

last: Alves

first: Ramona

middle: N

last: Pena

first: Maria

middle: B

last: Devis

first: Josep

middle: M

last: Folch


title: Evaluation of phenotypic plasticity in Rana temporaria tadpole development

status: Public on Mar 18 2014

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

summary: Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria.

platform_organism:
Xenopus laevis
Aquarana catesbeiana
Lithobates pipiens

overall_design: Six animals each originating from four different islands were reared in either constant or reduced water conditions and hepatic mRNA levels of Gosner stage 37 animals evaluated by MAGEX DNA array analysis.

first: Caren

last: Helbing

first: Frank

last: Johansson


title: ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

status: Public on Mar 27 2014

city: Dublin

first: Heather

last: Quinn

address: College green

country: Ireland

institute: Trinity College Dublin

type: Genome binding/occupancy profiling by array

summary: OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently,  OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Analysis of OmpR binding at pH 7 and pH 4.5 in E-minimal medium in both SL1344 and CSH50. Three independent biological replicates at each pH 7 and pH 4.5 was performed. This was done in each strain background. DNA was immunopreciptated using an anti-FLAG anitbody which binds to flag-tagged OmpR in both strains. Two control ‘mock’ experiments were performed under the same culture condtions in each strain background; DNA was immunopreciptated using normal mouse IgG antibody. To analyse the effect of DNA relaxation onOmpR binding SL1344 was maintained in the exponential growth phase in LB broth with and without treatment with the drug novobiocin (25 μg/ml) for 40 min. This was peformed on two independent occasions. In all cases the experimental immunoprecipitated DNA was hybridised against the input DNA.

first: Andrew

middle: D

last: Cameron

first: Charles

last: Dorman


title: Homozygosity mapping in family segregating premature ovarian insufficiency (POI)

city: Madinah AlMunawara

first: Sulman

last: Basit

address: Qurban

department: Center for Genetics and Inherited Diseases

country: Saudi Arabia

institute: Taibah University

summary: Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.
DNA of eight individuals including three affected subjects was used for homozygosity mapping. Genotyping was performed using the Affymetrix Axiom_GW_Hu_SNP array. Briefly, 250 ng genomic DNA was digested with Digestion Master Mix containing 2 µl NE buffer 2 (10X), 0.5 µl BSA (100X; 10 mg/ml) and 1 µl Nsp1. Digested DNA sample was ligated to Nsp1 adaptor using T4 DNA ligase and amplified by 2 µl of TITANIUM Taq DNA polymerase (50X) and 100 µM PCR primer. PCR products were purified on a Clean-Up plate (Clontech Lab, Madison, USA) and eluted by RB buffer. Purified PCR products were fragmented using Fragmentation Reagent (0.05U/µl DNase 1) for 35 minutes at 37°C followed by labeling of fragmented samples with Labeling Master Mix (30 mM GeneChip DNA Labeling Reagent, 30 U/µl Terminal Deoxynucleotidyl Transferase) for 4 hours at 37°C. Labeled samples were hybridized to Axiom_GW_Hu_SNP array by mixing the sample with Hybridization Master Mix, denatured on thermoblock and loaded on to Array. Array was then placed in a hybridization oven (GeneChip Hybridization Oven 640, USA) for 16-18 hours. After hybridization, array was washed and stained on an automated Fluidic Station 450 followed by scanning on GeneChip Scanner 3000 7G using GeneChip Operating Software (GCOS).

first: Sibtain

last: Afzal


title: Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

city: Uppsala

first: Anna-Maja

last: Molin

address: Gerda Nilssons väg 2

department: Department of Animal Breeding and Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences

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

summary: This study used the CanineHD genotyping array to investigate copy number variants in the dog genome in a total of 351 samples from 30 different breeds.

overall_design: In total, 359 samples from 30 different breeds were genotyped on the CanineHD array. Signal intensities from the array were used to assess copy number variants and a supplied clusterfile from Illumina was used as reference file (downloadable at http://supportres.illumina.com/documents/downloads/productfiles/caninehd/caninehd_a.egt). Eight samples did not fulfill the quality criteria for CNV calling and therefore CNV calling was performed on 351 samples.

first: Jonas

last: Berglund

first: Matthew

middle: T

last: Webster

first: Kerstin

last: Lindblad-Toh


title: Expression analysis of Staphylococcus aureus USA300 LAC in response to vehicle and benzbromarone.

status: Public on Mar 19 2014

city: Albuquerque

first: Brian

middle: Marshall

last: Gray

state: NM

address: 1 University of New Mexico

department: Pharmaceutical Sciences

institute: University of New Mexico

summary:
Compilation fo whole genome gene expression changes in Staphylococcus aureus USA300 LAC cultures grown in the presence of vehicle or the anti-gout drug benzbromarone.
The drug was intially screened as effective against the agr quorum sensing system in Staphylococcus aureus AH1677.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: A microarray study using total RNA harvested from three cultures of Staphylococcus aureus USA300 LAC plus vehicle control and three cultures of Staphylococcus aureus USA300 LAC plus 12 uM benzbromarone.

first: Pamela

last: Hall


title: Dissecting the signaling pathways associated with the oncogenic activity of MLK3 P252H mutation

status: Public on Mar 21 2014

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

summary:
MLK3 gene mutations were described to occur in about 20% of microsatellite unstable gastrointestinal cancers and to harbor oncogenic activity. In particular, mutation P252H, located in the kinase domain, was found to have a strong transforming potential, and to promote the growth of highly invasive tumors when subcutaneously injected in nude mice. Nevertheless, the molecular mechanism underlying the oncogenic activity of P252H mutant remained elusive.In this work, we performed Illumina Whole Genome arrays on three biological replicas of human HEK293 cells stably transfected with the wild-type MLK3, the P252H mutation and with the empty vector (Mock) in order to identify the putative signaling pathways associated with P252H
Our results showed that mutant MLK3 exerts its oncogenic effects by deregulating several important colorectal cancer- associated signaling pathways such as WNT, MAPK, NOTCH, TGF-β and P53. A more detailed analysis of the alterations affecting the WNT signaling pathway revealed a down-regulation of molecules involved in the canonical pathway, such as DVL2, LEF1, CCND1 and c-Myc, and an up- regulation of DKK, a well-known negative regulator of canonical WNT signaling, in MLK3 mutant cells. Additionally, FZD6 and FZD10 genes, known to act as negative regulators of the canonical WNT signaling cascade and as positive regulators of the planar cell polarity (PCP) pathway, a non-canonic WNT pathway, were found to be up-regulated in P252H cells.

overall_design: 9 samples, 2 conditions with 3 biological replicates per condition

first: Sergia

last: Velho


title: Global murine pulmonary response to highly and less virulent influenza A (H3N2) virus infections at 12, 48 and 96 h post-infection

city: Singapore

first: Vincent

middle: Tak Kwong

last: Chow

state: Singapore

address: 5 Science Drive 2, BLK MD4 (NUS)

country: Singapore

institute: National University of Singapore (NUS)

summary: Array analysis of total lung RNAs from female BALB/c mice collected at 12, 48 and 96 h post-infection with highly and less virulent influenza A (H3N2) viruses. Viruses (designated as LVI and HVI) were derived from influenza strain virus A/Aichi/2/68 (Aichi68). LVI is Aichi68 propagated in eggs, and HVI is mouse adapted Aichi68.

overall_design: Infection: lung homogenate (mock), LVI and HVI; time of sample collection: 12, 48 and 96 h post-infection; two biological replicates for each group.

first: Fransiskus

middle: X

last: Ivan

first: Gordon

first: T

last: Narasaraju


title: Interaction with Human Bronchial Epithelial Cells in vitro Affects Gene Expression in Moraxella catarrhalis

status: Public on Mar 24 2014

first: Eric

last: Hansen

address: 5323 Harry Hines Boulevard

summary: In this study, DNA microarray technology was used to measure global gene expression in M. catarrhalis cells that had attached to human bronchial epithelial cells in culture.

overall_design: M. catarrhalis ATCC 43617 was allowed to attach (MOI~30) to a monolayer of 16HBE14 human bronchial epithelial cells for 2 hr in OmniTray cell culture plates.  Additional portions of these bacteria were incubated in tissue culture medium in 75-cm2 cell culture flasks in the absence of 16HBE14 cells for 2 hr.  After this incubation period, the medium in the flask with the 16HBE14 monolayer was decanted and replaced with tissue culture medium containing 25 mM sodium azide (to protect RNA). The 16HBE14 monolayer and attached bacteria were released from the plastic by scraping.  After low-speed centrifugation to collect these bronchial cells and attached bacteria, the cell pellet was re-suspended in TE containing 1% saponin (which lyses the human cells).  After a 10-min incubation at 37°C, the bacterial cells were collected by centrifugation.  The bacteria growing in the flask without human cells were treated identically and then harvested by centrifugation.  Total RNA was extracted from both sets of bacterial cells by using the Qiagen RNeasy Midi kit.  DNA microarray analysis, slide scanning, and statistical analysis of the data were performed.  RNA was isolated four times and used in five DNA microarray hybridizations; “dye swap” experiments were performed twice.  Two additional independent experiments were performed to isolate two sets of RNA samples for qRT-PCR analysis to validate DNA microarray data.

first: Wei

last: Wang


title: Identification of latent tuberculosis infection-related microRNAs in human U937 macrophages expressing Mycobacterium tuberculosis Hsp16.3

status: Public on Mar 17 2014

city: Suzhou

first: Chun

last: Zhang

institute: Suzhou Institute of Biomedical Engineering and Technology, Chinise Academy of Sciences

summary:
Latent tuberculosis infection (LTBI) relies on a homeostasis of macrophages and Mycobacterium tuberculosis (Mtb). The small heat shock protein, Mtb Hsp16.3 (also known as latency-associated antigen), plays an important role in Mtb persistence within macrophages. However, the mechanism of LTBI remains elusive. The aim of this study was to delineate LTBI-related miRNA expression in U937 macrophages expressing Mtb Hsp16.3 protein.
This study intends to explore the potential function of miRNAs in the interaction of macrophages with Mtb Hsp16.3 and provide insights for investigating the role of macrophage homeostasis in LTBI.

overall_design: U937 macrophages were infected with an integrase-deficient Lentivirus vector to transiently express Mtb Hsp16.3, and green fluorescent protein (GFP) as a control. We used a microRNA (miRNA) microarray chip containing more than 1000 probes to identify the significant differentially expressed miRNAs in the infected U937 cells, and employed real-time quantitative polymerase chain reaction (qRT-PCR) for validation. Furthermore, we confirmed these candidate LTBI-related miRNAs in peripheral blood mononuclear cells from subjects with LTBI and in healthy control individuals. Functional annotation prediction of miRNA target genes and pathway enrichment analyses were used to explore the putative links between these miRNAs and LTBI.

first: Q

middle: L

last: Meng

first: C


title: BTG1 and BTG2 Regulate B Linege Commitment by Modulation of EBF1 Activity

city: Nijmegen

first: Blanca

last: Scheijen

address: Kapittelweg 29

country: Netherlands

institute: Radboudumc

summary: The human BTG1 and BTG2 genes are targeted by genetic alterations in hematological malignancies. In this study we examined the unique and overlapping functions of Btg1 and Btg2 in mouse B cell development. Mice deficient for Btg1 and Btg2 displayed the strongest phenotype with a decrease in B cell numbers in bone marrow due to impaired B cell commitment and immature B cell differentiation. To determine the underlying mechanism, microarray expression analyis was performed on  early (B220+ CD43+) and late (B220+ CD43-) B cells of WT and Btg1;Btg2 dKO mice.

overall_design: Total RNA obtained from sorted B220+ CD43+ ( Hardy fractions ABC) and B220+ CD43- (Hardy fractions DEF) BM cells of WT and Btg1-/-;Btg2-/- mice. In total 4 samples were analyzed and no replicates were included.

first: Esther

last: Tijchon

first: Liesbeth

last: van Emst

first: Dorette

last: van Ingen Schenau

first: Jørn

last: Havinga

first: Felice

last: Tirone

first: Jean-Pierre

last: Rouault

first: Peter

last: Hoogerbrugge

first: Frank

last: van Leeuwen


title: Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay

status: Public on Mar 26 2014

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

summary:
Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.
manuscript accepted by PLoS ONE

overall_design: 4 datasets: 1) fluorescence data for 3 treatments combined, 2) isotopic data for treatment = LOW, 3) isotopic data for treatment = MEDIUM, 4) isotopic data for treatment = HIGH


title: Gene expression analysis of eight-cell stage rat embryos sired by paternally exposed males to saline or BEP

city: Montreal

first: Jennifer

last: Maselli

state: Quebec

address: 3655 Prom Sir William Osler

institute: McGill University

summary: 8-cell stage rat embryos were sired by males treated with saline or a chemotherapeutic cocktail, BEP, consisting of Bleomycin, Etoposide, and Cisplatin for 9 weeks. Animals were given an additional 9 weeks of recovery, without any treatment, prior to mating.

overall_design: qPCR gene expression profiling for 84 stem cell transcription factors. Total RNA extracted from 25-35 embryos at the eight-cell stage sired by control or BEP-treated males after a 9-wk recovery period (2 females mated per male, n= 4 males/treatment).

first: Barabara

middle: F

last: Hales

first: Bernard

last: Robaire


title: Evaluation of microRNA levels in recipient BMMSCs of MRL/lpr mice after cell therapy (miRNA)

first: Shiyu

last: Liu

summary: Mesenchymal stem cell transplantation (MSCT) has been widely used to treat a variety of human diseases. However, the detailed mechanisms underlying its success are not fully understood. Here we show that MSCT rescues recipient bone marrow mesenchymal stem cell (BMMSC) function in Fas-deficient-MRL/lpr systemic lupus erythematosus (SLE) mice via a miR-29b/Dnmt1/Notch epigenetic cascade. Using the microRNA microarray, we found that MSCT could rescue the high level of miR-29b in the recipient BMMSCs of MRL/lpr mice.

overall_design: In the present study, mesenchymal stem cell transplantation (MSCT) was used to treat MRL/lpr mice. One week after the treatment, normal control MSCs from C3H/HeJ mice (C3H), recipient MSCs from untreated MRL/lpr mice (LPR) and recipient MSCs from MSCT-treated MRL/lpr mice (MSC) were used for total RNA extraction and microRNA microarray for analysis of microRNA expressions.

first: Songtao

last: Shi


title: Evaluation of global methylation profile and microRNA levels in recipient BMMSCs of MRL/lpr mice after cell therapy.

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

overall_design: Refer to individual Series


title: Small nucleolar RNAs as new biomarkers in chronic lymphocytic leukemia

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs are non-coding RNAs involved in the maturation of other RNA molecules. Alterations of sno/scaRNA expression may play a role in cancerogenesis. This study elucidates the patterns of sno/scaRNA expression in highly purified cells from 211 chronic lymphocytic leukemia (CLL) patients (Binet stage A) also in comparison with those of different normal B-cell subsets. CLLs display a sno/scaRNAs expression profile similar to normal memory, naïve and marginal-zone B-cells, with the exception of a few down-regulated transcripts (SNORA31, -6, -62, and -71C). Our analyses also suggest some heterogeneity in the pattern of sno/scaRNAs expression which is apparently unrelated to the major biological (ZAP-70 and CD38), molecular (IGHV mutation) and cytogenetic markers. Moreover, we found that SNORA70F was significantly down-regulated in poor prognostic subgroups and this phenomenon was associated with the down-regulation of its host gene COBLL1. Finally, we generated an independent model based on SNORA74A and SNORD116-18 expression, which appears to distinguish two different prognostic CLL groups. These data extend the view of sno/scaRNAs deregulation in cancer and may contribute to discover novel biomarkers associated with the disease and potentially useful to predict the clinical outcome of early stage CLL patients.

overall_design: This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 211 patients (Binet stage A), 6 normal controls from peripheral blood mononuclear cells (BC), and B-cell sub-populations from tonsils (3 naïve B-cells (N), 2 marginal zone (MZ)-like, 3 switched memory (SM) B-cells and 4 germinal center (GC) ). For gene and miRNA expression profiling experiments CLL cells were enriched by negative selection with the EasySep-Human B cell enrichment kit without CD43 depletion (Stem Cell Technologies) using the fully automated protocol of immunomagnetic cell separation with RoboSepTM (Stem Cell Technologies).

first: Domenica

last: Ronchetti

first: Laura

last: Mosca

first: Giovanna

last: Cutrona

first: Giacomo

last: Tuana

first: Massimo

last: Gentile

first: Sonia

last: Fabris

first: Gabriella

last: Ciceri

first: Serena

last: Matis

first: Carlotta

last: Massucco

first: Monica

last: Colombo

first: Daniele

last: Reverberi

first: Anna

last: Recchia

first: Sabrina

last: Bossio

last: Negrini

first: Pierfrancesco

last: Tassone

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Differential expression of genes in the WT and hupB KO strain of Mycobacterium  tuberculosis H37Rv upon iron limitation

city: Hyderabad

first: Manjula

last: Sritharan

state: Andhra Pradesh

address: Prof. CR Rao Road

department: Animal Sciences

country: India

institute: University of Hyderabad

summary: HupB is a 28 kDa in Mycobacterium tuberculosis that is co-expressed with the siderophores mycobactin and carboxymycobactin upon iron limitation. High levels of all the three components are seen in low iron (LI; 0.02 µg Fe / mL) organisms, with negligible expression in high iron organisms (HI; 8 µg Fe / mL). We generated a hupB knock out mutant of M. tuberculosis (H37Rv ∆ hupB) and studied the differential expression of genes upon iron limitation in the WT H37Rv and the mutant.  The RNA transcripts of the WT H37Rv, grown under high and low iron conditions of growth were isolated and subjected to microarray analysis to identify the iron-regulated genes and second, the differential expression of genes in iron-limited H37Rv ∆ hupB vs iron-limited WT H37Rv was analysed. Microarray analysis was done commercially by Genotypic Technology (Bangalore, India), an authorised service provider for Agilent Technologies. The study revealed the up-regulation of all the mbt genes of the mycobactin biosynthetic machinery in LI - H37Rv and several other reported iron-regulated genes. The salient feature of this study is the failure of LI - H37Rv ∆ hupB to show any up-regulation of the mbt genes as compared to LI - H37Rv.  Among several other genes influenced by HupB, the mutant strain showed low levels of mmpL5 and mmpS5 transcripts, whose expressed products are reported to be associated with siderophore transport and biosynthesis.

overall_design: One-color experiment,Organism: Mycobacterium tuberculosis ,Custom Mycobacterium tuberculosis 8x15k Array designed byGenotypic Technology Private Limited (AMADID: 20181), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: SatyaDeo

last: Pandey


title: Prunus mume bud microarray

city: Kyoto

first: Hisayo

last: Yamane

address: Sakyo-ku

department: Grad. Sch. of Agriculture

institute: Kyoto University

summary: Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next season’s growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. ‘Nanko’ vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release.

overall_design: In this study, we used chilling exposed bud samples (0, 40, 60 days starting at November) and seasonal monthly bud samples (June to March). For the samples in dataset 1 (three different time points during chilling treatment), three technical replicates (60K × 3 per sample) with three biological replicates were averaged, whereas three technical replicates were averaged for the samples in dataset 2 (10 different seasonal time points)

first: Tsuyoshi

last: Habu

first: Ryuta

last: Sasaki

first: Ryutaro

last: Tao


title: The identification of putative circulating miRNA biomarkers of Thioacetamide-induced hepatotoxicity.

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

country: United Kingdom

institute: MRC Toxicology Unit

summary:
The Thioacetamide-treated rat was first identified as a model of hepatotoxicity by Gupta in 1956 and is now well-established, not least because the histopathogical output closely mimics that seen in humans with chronic liver disease. Acute treatment of rats with Thioacetamide causes pronounced necrosis and inflammation. Animals received intraperitoneal (ip) doses of vehicle-only (0.9% (v/v) saline) (n=3), or 100 mg/kg Thioacetamide (n=3) and were sacrificed after 24 hours. Blood was withdrawn via the descending vena cava and immediately transferred into potassium/EDTA tubes. Following centrifugation (16,100g, 4°C, 5 min) the plasma was collected and stored at -80°C.
miRNA microarray profiling of RNA extracted from the plasma of rats treated with Thioacetamide revealed that a subset of miRNAs were differentially expressed following treatment. These miRNAs appeared to mediate pathways involved in hepatic fibrosis and stellate cell activation, suggesting that they might function as predictive biomarkers following compound-induced hepatotoxicity. The changes correlated well with increases in ALT levels, which are the current gold standard method for determining the extent of liver injury. Furthermore, it is hypothesised that particular aetiologies of liver damage might cause differing expression profiles of miRNAs, thus certain miRNAs could be implemented in a panel-type expression study to distinguish between different types of hepatic injury.

overall_design: Single channel miRNA microarrays were performed on n= 3 samples, 2 treatment groups; control and test. Control animals received vehicle-only (0.9% (v/v) saline) via the ip route. Test animals received 100 mg/kg Thioacetamide dissolved in 0.9% (v/v) saline, via the ip route. 24 h after dosing animals were sacrificed using decapitation under terminal anaesthesia.


title: Analysis of the Zur Regulon of Moraxella catarrhalis

status: Public on Mar 23 2014

city: Dallas

first: Todd

last: Hoopman

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

summary: This series of microarrays explores the genes regulated by the Zur gene of Moraxella catarrhalis.

overall_design: The gene expression profile of O35E Wild-type cells was utilized as the baseline and compared with the gene expression profile of a non-polar mutant of the Zur gene constructed in the O35E background.  There were two biologic replicates and two internal dye swaps performed.

first: Eric

last: Hansen


title: A sputum gene expression signature of six biomarkers identifies asthma inflammatory phenotype and steroid responsiveness

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

summary: This study identifies differentially expression genes in the sputum of people with eosinophilic, neutrophilic and paucigranulocytic asthma. A selection of markers identified using this microarray were further validated using qPCR on a wider sample set.

overall_design: Gene expression profiles were generated from induced sputum samples from 47 asthma patients and were grouped by the inflammatory phenotype assigned using sputum cell counts into neutrophilic asthma (n=12), eosinophilic asthma (n=17) and paucigranulocytic asthma (n=18). RNA was extracted, amplified and hybridised to Illumina Sentrix HumanRef-8 Version 2 Expression BeadChips, and genes that were differentially expressed between asthma inflammatory phenotypes were compared.

first: Katherine

first: Peter

last: Gibson


title: microRNA expression profiles of prostate cancer xenograft model

first: Atsushi

last: Maeno

address: Skyo-ku Shogoin Kawahara-cho 54

department: Urology

institute: Kyoto University Facalty of Medicine

summary: In order to investigate the role of microRNAs in the progression of CRPC, we evaluated expression profiles by microarray analysis of microRNAs derived from xenograft tumor tissues obtained at the CRPC stage in comparison to those at an androgen dependent stage.

overall_design: We evaluated expression profiles of microRNAs derived from the KUCaP2 xenograft tumor tissues at the CRPC stage in comparison to those at the androgen dependent stage (n=4) by microRNA microarray analysis.

first: Takahiro

last: Inoue


title: Diagnostic and prognostic utility of a unique epigenetic prognostic PHYMA signature in prostate cancer

first: Liang

last: Goh

address: College Road

institute: Duke-NUS graduate medical school

summary: Genome wide DNA methylation profiling of normal and Prostate cancer samples. The Illumina GoldenGate Methylation Cancer Panel I with 1,505 CpG sites selected from 807 genes was used to obtain DNA methylation profiles.  Samples included 24 normals and 87 tumors.

overall_design: Bisulphite converted DNA from the 111 samples were hybridised to the Illumina Illumina GoldenGate Methylation array.

middle: K

first: Hong

last: Sim


title: Differential gene expression along with progression of diet-induced atherosclerotic plaque using Microarray

status: Public on Mar 12 2014

city: Bangalore

first: Vrushali

middle: Umakant

last: Deshpande

state: Karnataka

address: No. 258/A, Bommasandra Industrial Area,

department: Molecular Immunology

institute: Thrombosis Research Institute

summary: To understand the changes in gene expression at different stages of diet-induced atherosclerotic development, double knock out Apobtm2Sgy/Ldltm1Her mice were fed with either high-fat or normal chow diet. The microarray was performed using total RNA extracted from ascending aorta of the animals.

overall_design: Double knockout mice fed with rich cholesterol diet and a normal diet were sacrificed after 0, 4, 8, 14 and 20 weeks and RNA was extracted for Microarray analysis

first: Rupak

last: Mukhopadhyay

first: Lakshmi

last: Mundkur


title: Low-density miRNA microarray  of induced mouse myeloid-derived suppressor cell

status: Public on Mar 11 2014

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: Myeloid-derived suppressor cells (MDSCs) are one of the main cell populations that negatively regulate immune responses. However, the mechanism underlying the differentiation and expansion of MDSCs remains unclear. Employing a low-density miRNA microarray and a TaqMan probe-based qRT-PCR assay,  we investigated the miRNAs expression profiles of MDSC. Compared to freshly isolated BM cells, BM-MDSCs had a significantly altered miRNA profile. There were 45 miRNAs that were upregulated and 17 miRNAs that were downregulated more than 2-fold. Among these miRNAs, miR-155 and miR-21 have the highest upregulation after cytokine induction.

overall_design: BM cells were planted into dishes using RPMI1640 medium supplemented with 2 mM L-glutamine, 10mM HEPES, 20µM 2-mercaptoethanol, 150 U/ml streptomycin, 200 U/ml penicillin, 10% FBS and stimulated with combinations of GM-CSF (40ng/ml), and IL-6 (40ng/ml). Cells were cultured at 37°C in 5% CO2-humidified atmosphere for 4 days.Total RNA were isolated,  low-density miRNA microarray was performed

first: Ke

last: Zen

first: Limin

last: Li


title: Real-time quantitative PCR analysis of Hepatic cell lines infected with HCV

status: Public on Mar 07 2014

city: roma

first: antonella

last: minutolo

address: viale del policlinico

summary: huh7.5 hepatic cell lines were infected with HCV. RNA and Protein were extract after 72 hours and The Human Adipogenesis RT² Profiler™ PCR Array was used to compare the gene expression in the two group.

overall_design: qPCR gene expression profiling. HCV infected hepatic cells vs uninfected hepatocyte. Equal amount total RNA from each samples were used

first: Beatrice

last: Conti

first: Antonella

last: Minutolo

first: Marco

last: Corazzari

first: Carmela

last: Viscomi

first: Clara

last: Balsano


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP

first: Eric

last: Hansen

address: 5323 Harry Hines Blvd

department: Microbiology

summary: The goal  of this study was to compare the global trascription profile of a Haemophilus ducreyi hfq deletion mutant to that of the wild type parental strain.

overall_design: This study includes three biological replicates (paired samples of mutant and wild type strains), and all three were subjected to dye swap.

first: Maria

last: Labandeira-Rey


title: Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

institute: University of Colorado Denver

summary: Chromosomal instability is central to the process of carcinogenesis. The detection of somatic chromosomal alterations in small premalignant lesions genome-wide remains challenging since sample heterogeneity dilutes the aberrant cell information. We introduced an analytic metric termed "delta-θ", and applied this metric to a titrated cancer cell model using a pair of cancer cell line and matched lymphoblastoid cell line. We examined heterogeneous clinical specimens including bronchial biopsies and brushings with this metric. Distinctive genomic variation were successfully detected across the whole genome in invasive cancer cases (6/6), carcinoma in situ (3/3), and high grade dysplasia (severe or moderate) (3/11).

overall_design: We modeled titration series (100%, 25%, 12.5%, 6.3%, 3.1%, 1.6% and 0% tumor content) mixing the genomic DNA of the cell line pair. We also investigated 30 malignant/premalignant samples from 18 patients with heavy smoking histories (6 invasive lung cancer, 3 carcinoma in situ,15 dysplasia, 3 hyperplasia and 3 normal histology) using Illumina HumanOmni2.5 and Human 660w SNP microarrays. All of them were paired with matched reference blood DNA and analyzed.

first: Jessica

last: Rice

first: Christopher

last: Coldren

first: Robert

middle: S

last: Stearman

first: Michael

middle: G

last: Edwards

first: Bifeng

last: Gao

first: York

middle: E

last: Miller

first: Mark

middle: W

last: Geraci


title: Transcriptional profiling of C. albicans in the presence of mucin versus absence of mucin

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

summary: Candida albicans is the most prevalent fungal pathogen of humans, causing a variety of diseases ranging from superficial mucosal infections to deep-seated systemic infections. Mucus, the gel that coats all wet epithelial surfaces, accommodates Candida albicans as part of the regular microbiome where C. albicans resides asymptomatically in healthy humans. Through a series of in vitro experiments combined with genome-wide transcriptional profiling, we show that mucin biopolymers, the main gel-forming constituents of mucus, induce a new oval-shaped morphology in C. albicans in which a range of genes related to adhesion, filamentation, and biofilm formation are down-regulated. We also show that corresponding phenotypes are suppressed, rendering Candida incapable of forming biofilms on a range of different synthetic surfaces and human epithelial cells. Our data suggests that mucins can manipulate Candida physiology and we hypothesize that they are key regulators for retaining Candida in the host-compatible, commensal state.

overall_design: 3 biological replicates grown in log phase in the presence and absence of mucin for 8 hours. Experiments were performed using RPMI 1640 (Gibco 31800-089) buffered with 165mM MOPS and supplemented with 0.2% NaHCO3 and 2% glucose with and without 0.5% mucin.

middle: J


title: Liver functional genomics in beef cows on grazing systems

city: Montevideo

first: Mariana

last: Carriquiry

address: Ave Garzon 780

department: Department of Animal Sciences and Pastures

country: Uruguay

institute: Facultad de Agronomía, UdelaR

summary: We evaluated liver transcriptome throughout gestation and early lactation of purebred and crossbred beef cows (Angus, Hereford and their F1 crossbreeds, CR), grazing high or low herbage allowances (HA) of native grasslands (4 and 2.5 kg DM/kg BW annual mean; n = 16) using an Agilent 4x44k bovine array.  A total of 4,661 transcripts were affected by days (272 ≥ 2.5-fold difference, FDR ≤ 0.10) and 47 pathways were altered during winter gestation (-165 to -15 days relative to calving, d). Gluconeogenesis and fatty acid oxidation pathways were substantially upregulated, while cell growth, DNA replication and transcription pathways were downregulated (FDR ≤ 0.25). We observed only small changes in the liver transcriptome during the early lactation period (+15 to +60 d). A total of 225 genes were differentially expressed (47 ≥ 2-fold difference, FDR ≤ 0.10) between HA. The majority of those were related to glucose and pyruvate metabolism and were upregulated in high HA, reflecting their better metabolic status. Two genes were upregulated in CR cows, but 148 transcripts (74 ≥ 2-fold change difference, FDR ≤ 0.10) were affected by the HA and cow genotype interaction. The transcriptional changes observed indicates a complex and previously unrecognized adaptive program in beef cow liver. We report novel candidate genes, metabolic pathways, and regulatory mechanisms, which can be used as targets of future studies.

overall_design: Complete randomized block design with two spatial replications and a factorial arrangement of herbage allowance (HA) and cow genotype (CG).  Herbage allowance treatments represented 4 and 2.5 kg DM/kg BW of annual mean (HI and LO, respectively).  Four purebred (PU – Hereford, H and Angus, A) and four crossbred (CR - F1, HA and AH) multiparous pregnant cows (5 to 6 year-old), were evaluated per treatment (HI-CR, HI-PU, LO-CR, and LO-PU) throughout the gestation and lactation period (-165 to +60 days relative to parturition, days). Cows belonged to or were descendants of experimental animals generated as part of a diallel crossbreeding experiment carried out for 10 years at the Experimental Station and were assigned to the same forage allowance (HI or LO) since May 2007 and gestated and lactated one calf every year from 2007 to 2009.

first: Jimena

last: Laporta

first: Hugo

last: Naya

first: Guilherme

last: Rosa


title: Whole Blood Transcriptional Modules generated on Illumina Hu-6 V2 Beadchips

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: This dataset was used to establish whole blood transcriptional modules (n=260) that represent groups of coordinately expressed transcripts that exhibit altered abundance within individual datasets or across multiple datasets.  This modular framework was generated to reduce the dimensionality of whole blood microarray data processed on the Illumina Beadchip platform yielding data-driven transcriptional modules with biologic meaning.

overall_design: This series combines nine independent datasets representing a spectrum of human pathologies expected to result in changes in gene abundance related to changes in expression or cellular composition of whole blood.  These nine datasets are composed of 410 individual whole blood profiles generated from patients with HIV, tuberculosis, sepsis, systemic lupus erythematosus, systemic arthritis, B-cell deficiency and liver transplant.  For each dataset healthy controls are also included. Each dataset’s expression data was preprocessed independently. First, probes were discarded if they were not present in at least ten percent of the dataset’s samples. Then, the sample data for each dataset was normalized using the BeadStudio average normalization algorithm.  Once normalized, the signal was scaled such that all signals less than ten were set to ten. The signal median of all of the dataset’s samples was calculated for each probe. Probes were discarded if no sample had a difference in signal from the median that was greater than or equal to thirty, or if no sample had a fold change relative to the median that was either greater than or equal to 1.5, or less than or equal to 0.67.  Finally, data was transformed to the log2 of the signal divided by the mean.  Each of the preprocessed datasets was clustered in parallel using Euclidean distance and the Hartigan’s K-Means clustering algorithm, a hybrid of hierarchical and K-Means clustering algorithms. The number of clusters (k) was set to thirty, chosen to provide significant power during later module extraction steps.  A higher value could have been chosen for k, but was not in order to minimize possibly arbitrary cluster splitting.   Taking the nine sets of thirty clusters as input, we constructed a weighted co-cluster graph, a probe by probe matrix where the value of each cell (the weight) is set to the number of times probe_i and probe_j are found in the same cluster. In this instance, the values range from zero to nine, inclusive. At this point, the goal is to extract sets of probes that are most frequently clustered together, proceeding from the most stringent requirements to the least.   To accomplish this, we employ the iterative algorithm. To begin, the maximum clique threshold is initialized to the number of input cluster sets, the paraclique threshold is calculated, and a minimum seed size is chosen (we used ten). The outer loop begins by creating an unweighted graph through application of the maximum clique threshold to the weighted co-cluster graph such that a probe pair, or edge, is represented in the unweighted graph if and only if the corresponding weight in the co-cluster graph equals or exceeds this threshold.   We then begin the inner loop. The first step is to isolate the largest set of probes such that all pairs of probes in the set are completely connected in the unweighted graph - that is, there is no pair of probes in the set where the weight from the initial graph is smaller than the maximum clique threshold. In graph theoretic terms, the probes form a maximum clique.  If the size of the probe set is smaller than the minimum seed size, we escape from the inner loop, reduce the threshold by one, and return to the beginning of the outer loop. Otherwise, the probe set is at least as large as the minimum seed size and it becomes the seed for a module. To allow for the inevitable clustering inaccuracies, we then employ the paraclique algorithm revisiting the co-cluster graph and adding to the seed any probe that is found to cluster with at least eighty-five percent of the seed’s members a number of times equal or exceeding the paraclique threshold. This final probe set is a module. It is removed from both graphs and named in accordance with the iterations in which it was found (i.e. a module extracted in the first iteration of the outer loop and the second iteration of the inner loop is designated M1.2). The inner loop then begins again with the reduced graphs.   Those modules with conserved expression across diseases (formed by transcripts that cluster together for all nine datasets) were selected in early rounds whereas modules with greater disease specificity (formed by transcripts that cluster together only in a subset of the nine datasets) were selected in later rounds.


title: Gene expression timecourse in wild-type strain

status: Public on Mar 06 2014

city: Cambridge

first: Joseph

middle: Scott

last: Markson

address: 52 Oxford St, Room 445

department: Molecular and Cellular Biology

institute: Harvard Univ / Howard Hughes Medical Institut

summary: The goal of the experiment was to obtain a replicate of the wild-type LL circadian timecourse published in Vijayan et al, PNAS 106: 22564-22568 (2009), in order to identify reproducible circadian genes in LL.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cultures were grown in a turbidostat as described previously (Vijayan et al, PNAS 2009), except that the culture volume was 3 L instead of 4.5 L.  Cultures were entrained with two consecutive light/dark cycles and released into continuous light at time T = 0.  Cultures were samples every 4 hours from T = 36 h and T = 64 h, inclusive.  Gene expression at each timepoint was compared to the time-averaged gene expression (determined using a pool of equal mass quantities of RNA from all timepoints) using a two-color Agilent microarray.  Timepoint T = 52 h is omitted due to poor data quality.

first: Vikram

last: Vijayan


title: Transcriptomic effects of endocrine disruptors in zebrafish embryos

city: Aachen

first: Viktoria

last: Schiller

state: NRW

address: Forckenbeckstrasse 6

department: UNIFISH

institute: Fraunhofer IME

summary: The identification of endocrine disruptive properties of chemicals certain to enter the aquatic environment relies on toxicity tests with fish, assessing adverse effects on reproduction and sexual development. The demand for quick, reliable endocrine disruption (ED) assays favored the use of fish embryos as alternative test organisms. We investigated the application of a transcriptomics-based assay for estrogenic and anti-androgenic chemicals with zebrafish embryos. Two reference compounds, 17a-ethinylestradiol and flutamide, were tested to evaluate the effects on development and the transcriptome after 48h-exposures. Comparison of the transcriptome response with other estrogenic and anti-androgenic compounds (genistein, bisphenol A, methylparaben, linuron, prochloraz, propanil) showed commonalities and differences in regulated pathways, enabling us to classify the estrogenic and anti-androgenic potencies. This demonstrates that different mechanism of ED can be assessed already in fish embryos.

overall_design: Newly fertilized embryos (<2hpf) were exposed for 48 hours to 0.65mg/l (EC10) and 0.8mg/l (EC20) 17-alpha ethinylestradiol (EE2), 1.2mg/l (EC10) and 1.4mg/l (EC20) flutamide, 8 mg/l (EC10)and 8.5mg/l (EC20) bisphenol A(BPA), 0.8 mg/l (EC10) and 1.1mg/l (EC20) propanil, 19.8mg/l (EC10) and 24.4mg/l (EC20) methylparaben, 1.2 mg/l (EC10) and 1.3mg/l (EC20) linuron as well as to 1.7mg/l (EC10) and 2 mg/l (EC20) prochloraz. Water controls were included in all studies and acetone solvent controls were applied when indicated (AC). For each study, four replicates (a,b,c,d) were performed per condition, each consisting of 24 pooled embryos.

first: Arne

last: Wichmann

first: Ralf

last: Kriehuber

first: Christoph

last: Schäfers

first: Martina

last: Fenske


title: Combinatorial quorum-sensing allows bacteria to resolve their social and physical environment

status: Public on Mar 04 2014

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
Quorum-sensing (QS) is a cell-cell communication system that controls gene expression in many bacterial species, mediated by diffusible signal molecules. While the intracellular regulatory mechanisms of QS are often well-understood, the functional roles of QS remain controversial. In particular, the use of multiple signals by many bacterial species poses a serious challenge to current functional theories. Here we address this challenge by showing that bacteria can use multiple QS signals to infer both their social (density) and physical (mass-transfer) environment.
Analytical and evolutionary simulation models show that the detection of and response to complex social/physical contrasts requires multiple signals with distinct half-lives and combinatorial (non-additive) responses to signal concentrations. We test these predictions using the opportunistic pathogen Pseudomonas aeruginosa, and demonstrate significant differences in signal decay between its two primary signal molecules as well as diverse combinatorial responses to dual signal inputs. QS is associated with the control of secreted factors, and we show that secretome genes are preferentially controlled by synergistic ‘AND-gate’ responses to multiple signal inputs, ensuring the effective expression of secreted factors in high density and low mass-transfer environments. Our results support a novel functional hypothesis for the use of multiple signals and, more generally, show that bacteria are capable of combinatorial communication.

overall_design: The two primary signal molecules of P. aeruginosa are the homoserine lactones N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-C12-HSL) and N-butyryl-homoserine lactone (C4-HSL).  Effects of the different signal molecules was assessed using a double QS synthase mutant of Pseudomonas aeruginosa PAO1 lasI/rhlI grown at 37°C in 25 ml LB broth and 250 ml flasks with shaking at 200 r.p.m. in four treatments, each with a replicate: (a) no addition; (b) 3-oxo- C12-HSL; (c) C4-HSL; and (d) both 3-oxo-C12-HSL and C4-HSL.

first: Daniel

middle: M

last: Cornforth

first: Roman

last: Popat

first: Luke

last: McNally

first: James

last: Gurney

first: Thom

last: Scott-Phillips

first: Stephen

middle: P

last: Diggle

first: Sam

last: Brown

first: Paul

last: Williams


title: Global microRNA expression analysis in mouse skin normal tissues and skin tumors induced by constitutive active YAP mutant.

status: Public on Mar 03 2014

city: Otsu

first: Masaki

last: Mori

state: Shiga

address: Tsukinowa-cho, Seta

department: Molecular Neuroscience Research Center

institute: Shiga University of Medical Science

summary: Global downregulation of microRNAs (miRNAs) is commonly observed in human cancers and can have a causative role in tumorigenesis. The mechanisms responsible for this phenomenon remain poorly understood. Here we show that YAP, the downstream target of the tumor-suppressive Hippo signaling pathway regulates miRNA biogenesis in a cell density-dependent manner. At low cell density, nuclear YAP binds and sequesters p72 (DDX17), a regulatory component of the miRNA processing machinery. At high cell density, Hippo-mediated cytoplasmic retention of YAP facilitates p72 association with Microprocessor and binding to a specific sequence motif in pri-miRNAs. Inactivation of the Hippo pathway or expression of constitutively active YAP causes widespread miRNA suppression in cells and tumors and a corresponding post-transcriptional induction of MYC expression. Thus, the Hippo pathway links contact-inhibition regulation to miRNA biogenesis and may be responsible for the widespread miRNA repression observed in cancer.

overall_design: Two conditions (normal epidermal cells and oncogenic epidermal cells expressing YAP S127A mutant) were analyzed in duplicate.

first: Fernando

middle: D

last: Camargo

first: Richard

middle: I

last: Gregory


title: Global microRNA expression analysis in HaCaT  human keratinocytes transfected with siRNA for YAP or negative control

overall_design: Two conditions (siCtrl and siYAP) were analyzed in duplicate.


title: Global microRNA expression analysis in mouse liver normal tissues and liver tumors induced by deletion of Nf2 (merlin).

overall_design: Two conditions (liver normal tissues and liver tumors) were analyzed in duplicate.


title: Global microRNA expression analysis in HaCaT  human keratinocytes transfected with siRNA(s) for p72, NF2/LATS2, DROSHA/DGCR8, or negative control

overall_design: Four conditions (siCtrl, si p72, siNF2/LATS2 and siDROSHA/DGCR8) were analyzed in duplicate.


title: The 8q24 Enhancer Region including rs6983267 Directly Interacts with Promoter of Oncogenic LncRNA CARLo-5

status: Public on Mar 05 2014

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

summary: The mechanism by which rs6983267 at 8q24.21 increases cancer risk is unclear for the lack of protein?coding genes in the region although the variant is strongly associated with cancer pathogenesis. Here we identify long non-coding RNAs (lncRNAs) near the 8q24 region and show that expression of lncRNA CARLo-5 is significantly correlated with the risk allele of the cancer-associated variant rs6883267. We further report that the 8q24 enhancer region including the variant directly interacts with active regulatory region of the lncRNA CARLo-5 promtoer. Finally, we demonstrate that CARLo-5 has an oncogenic function by regulating cell proliferation and cell-cycle. Our data provide new insight of disease-related variants in a gene desert.

overall_design: Comparison and identification of cell cycle-related genes differentially expressed by CARLo-5 knockdown using Nanostring analysis in HCT116 cells.

first: Hansjuerg

last: Alder


title: Transcriptomic difference caused by fpk1/2 kinase double deletion

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

institute: Kyoto Univ. Sch. of Medicine

summary:
Differential gene expression was determined using yeast cDNA microarray
mRNA were enriched from auxotroph-matched yeast cells; control WT vs fpk1/2∆ cells and transcriptomic difference was examined

overall_design: BY4741 with HIS3 was compared with fpk1::KanMx fpk2::HIS3 cells in the log-phase. mRNA was enriched with mTRAP (Activemotief) from hot-phenol method total RNA fractions and was dual-color labeled with Cy-scribe (Amersham) to seek differentially expressed genes.

first: Reiko

last: Fujinawa

first: Etsuko

last: Kishimoto


title: Global microRNA expression analysis in HaCaT human keratinocytes at low and high cell densities

overall_design: Two conditions (Low density and High density) were analyzed in duplicate.


title: Dysregulation of miRNA in adenocarcinoma of the uterine cervix

status: Public on Mar 01 2014

city: Seongnam-si

first: Hyun

last: Park

address: Bundang-gu, Yatap-dong

department: Obstetrics and Gynecology

country: South Korea

institute: CHA university, CHA Bundang Medical Center

summary: We identified an altered miRNA expression in adenocarcinoma of the uterine cervix compared with normal cervix and futhermore analyzed their association with clinicopthologic characteristics.

overall_design: miRNA expression was measured in four cancerous tissues from the cervical adenocarcinoma and four non-cancerous from the normal uterine cerivx respectively, all of which were obtained from different donors.

first: Hee

last: An


title: Global microRNA expression analysis in HaCaT  human keratinocytes transfected with p72 or control EGFP in addition to siRNAs for NF2 and LATS2.

overall_design: Two conditions (transfection of p72 or control EGFP in addition to siRNAs for NF2 and LATS2) were analyzed in duplicate.


title: Global Gene expression data from Mycobacterium tuberculosis treated with new TB drug named Bedaquiline

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica NV

summary: Sirturo or Bedaquiline has been shown to inhibit the ATP synthase of Mycobacterium tuberculosis. We used microarrays to investigate compound-induced gene expression changes in general as well as effects on the transcription of the different ATP synthase genes and other metabolic pathways.

overall_design: Log phase Mycobacterium tuberculosis were cultivated in Middlebrook 7H9 broth and treated with 1 µM Bedaquiline. We have extracted RNA from five different time-points after treatment: 0 min (T0), 30 min (T30), 60 min (T60), 180 min (T180) and 360 min (T360).

first: Luc

last: Vranckx

first: Ilse

last: Van den Wyngaert

first: Hinrich

last: Göhlmann

first: Anil

last: Koul


title: Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene expression analyses

status: Public on Mar 02 2014

city: La Jolla

first: John

last: Chang

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: T lymphocytes responding to microbial infection give rise to effector cells that mediate acute host defense and memory cells that provide long-lived immunity, but the fundamental question of when and how these cells arise remains unresolved.  Here we combine single-cell gene expression analyses with machine-learning approaches to trace the transcriptional roadmap of individual CD8+ T lymphocytes throughout the course of an immune response in vivo.  Gene expression signatures predictive of eventual fates could be discerned as early as the first T lymphocyte division and may be influenced by asymmetric partitioning of the interleukin-2 receptor during mitosis.  These findings underscore the importance of single-cell analyses in understanding fate determination and provide new insights into the specification of divergent lymphocyte fates early during an immune response to microbial infection.

overall_design: The goal of the study was to profile the gene expression in single CD8+ T cells responding in vivo to a microbial infection over multiple timepoints.  5 x 103 CD8+ CD45.1+ T cells transgenic for the OT-1 T cell receptor (which recognizes Listeria monocytogenes expressing ovalbumin (Lm-ova)) were adoptively transferred into congenic wild-type CD45.2 C57/B6J recipients, followed by infection intravenously one day later with 5 x 103 colony-forming units (CFU) of Lm-OVA.  Splenocytes were isolated from recipient mice at 5, 7, or 45 days post-infection.  To isolate cells at 3 days post-infection, 2 x 104 OT-1 CD8+ T cells were adoptively transferred.  To isolate cells that had undergone their first division, 2 x 106 OT-1 CD8+ T cells were first labeled with carboxyfluorescein diacetate succinimidyl ester (CFSE) prior to adoptive transfer and recipient mice were sacrificed at 48 hours post-infection.  Unactivated naïve OT-1 CD45.1+ CD8+ T cells were also included. Cells were stained with fluorochrome-labeled antibodies against CD8, CD44, CD4, CD11b, CD11c, and F4/80, and sorted on a MoFlo (Beckman Coulter) or FACS Aria II (BD Biosciences) flow cytometer.      The Ct value for each gene analyzed in each individual cell at each time point is reported in the Matrix non-normalized.  The 94 ABI TaqMan Assay IDs are listed on the left (A2-A96), along with the accession number (B2-B96) and corresponding gene name (C2-C96) of each gene studied. The Il2 gene expression assay was duplicated. Each heading (D1-BCV)) represents a single cell from each of 13 timepoints or T cell subset that were profiled.  The timepoints/T cell subsets and number of each cells profiled from each timepoint/T cell subset were: unactivated naïve (149 cells), distal daughter (48), proximal daughter (83), division 1 (144), day 3 post-infection (143), day 5 post-infection memory precursor (Tmp) (90), day 5 post-infection short-lived effector (Tsle) (79), day 5 post-infection (154), day 7 post-infection memory precursor Tmp (62), day 7 post-infection short-lived effector Tsle (89), day 7 post-infection (134), central memory Tcm (138), and effector memory Tem (136).

first: Janilyn

last: Arsenio

first: Boyko

last: Kakaradov

first: Patrick

last: Metz

first: Stephanie

middle: H

first: Gene

last: Yeo

middle: T


title: Multiple means to the same end: The genetic basis of acquired stress resistance in yeast

city: Madison

first: David

middle: B

last: Berry

state: WI

address: 3456 Genetics Biotech. Building

department: Laboratory of Genetics

institute: University of Wisconsin: Madison

type: Expression profiling by genome tiling array

summary:
A series of experiments comparing the gene expression response before and after 30 min 0.7M NaCl exposure in WT and mutant yeast strains. Mutant strains were identified as having a defect in acquiring
resistance to H2O2 following mild NaCl pretreatment. The mutants in this study were taken from the Yeast Knock-Out Collection, mat a.

overall_design: Unstressed cells vs cells exposed to 0.7M NaCl for 30 min; 5 replicates for WT, 3 replicates for hog1∆, msn2∆, mck1∆, pde2∆, rim101∆, and 2 replicates for the remaining mutants.

first: Audrey

last: Gasch

first: James

last: Hose

first: Suraiya

last: Haroon

first: Qiaoning

last: Guan

first: Marinella

last: Gebbia

first: Lawrence

last: Heisler

first: Corey

last: Nislow

first: Guri

last: Giaever


title: Expression data from peripheral blood mononuclear cells of subjects supplemented with vitamin C [qPCR array analysis]

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

institute: IRBM

summary:
A role of vitamin C(ascorbic acid) as an antioxidant molecule has been recognized, largely based on in vitro studies. However, more recently, the concept of “antioxidant molecule” has been reconsidered and its biological function is no longer considered to be simply due to its ability to act as “electron donors”, rather, it appears to act by modulating signaling and gene expression.
In order to gain a better understanding of the effects of vitamin C supplementation on gene expression in both physiological and pro-inflammatory conditions, we performed  a pilot explorative intervention study based on the utilization of  microarray and qPCR technologies, designed on a “in vivo-ex vivo” structure

overall_design: Five healthy subjects (three males and 2 females, aged 25-40) were recruited for a short term (five days) intervention  study. Subjects were asked to assume one tablet of Redoxon®  (Bayer), a day (containing 1 gr of ascorbate), for 5 days.  A baseline blood withdrawal was performed in fasting condition,  just before the first vitamin C tablet. Tablets were provided to the volunteers, every morning at the same hour for the following 4 days of the study. The last tablet was supplemented about 1,5  hour before the second and last blood withdrawal, performed again in fasting condition. Plasma and peripheral blood mononuclear cells (PBMNC) were obtained . PBMNC from each subject were splitted in three aliquots: one was stored in lysis buffer at -80°C and utilized to isolate RNA for the Affymetrix gene array analysis. The other two aliquots were resuspended in RPMI 1640 w/o phenol red containing 10% of autologous plasma: one was incubated with 10 ug/ml lipopolysaccharides (LPS) for 5 hours at 37°C. At the end of the incubation time, the medium was collected and stored at -80°C for the assessment of cytokine release in response to the inflammatory stimuli. RNA was extracted from the pelleted cells for gene expression analysis, using the Human NFkB Signaling 96 StellARray™ qPCR array (Lonza). The results obtained with PBMNC isolated after vitamin C supplementation (supplemented PBMNC) were compared to those obtained with PBMNC isolated before the supplementation (baseline PBMNC), for each subject.

first: R

last: Canali

first: G


title: Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity [NIAC-NTR]

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

institute: Sir William Dunn School of Pathology

summary:
TGF-b1-stimulation induces an epithelial dedifferentiation-process, throughout which epithelial cell sheets disintegrate and gradually switch into fibroblastic-appearing cells (EMT-like transition). The purpose of these profiles was to identify differentially expressed genes that are regulated transcriptionally. Standard microarry-based gene expression profiles measure steady-state RNA but do not provide insight into underlying regulatory principles. NIAC-NTR-based gene expression profiling (Kenzelmann et al., PNAS, 2007) essentially enables the dissection of transcriptionally versus non-transcriptionally regulated genes within respective analysed time-frames. Briefly, NIAC-NTR relies on incorporation of 4sU (thio-uridine) into nascent RNA, which can subsequently be specifically isolated by custom-made columns. Total- and enriched (4sU-labeled) are then further processed for microarray gene expression profiling by standard procedures. This dataset complements previously released data of NIAC-NTR-based gene expression profiling of cells treated with TGF-b1 and 4sU for 2hrs [GSE23833].
The present data and files represent the outcome of NIAC-NTR-based gene expression profiling of cells treated with TGF-b1 for 24hrs and incubation with 4sU for the last 2hrs (22hrs-24hrs of TGF-b1-stimulation).
NIAC-NTR: Non Invasive Application and Capture of Newly Transcribed RNA

overall_design: NMuMG cells were seeded 24hrs prior to treatment. Cells were stimulated with 5ng/ml TGF-b1 for a total of 24hrs. After 22hrs of stimulation 200µM 4sU thio-uridine was added to the cultures and further incubated for another 2hrs. Total RNA was extracted using RNeasy Mini Kits (Qiagen). 4sU-labeled RNA was further extracted from total RNA using mercury-based custom-made columns.  The experiments were performed as independent biological triplicate. Details about isolation of 4sU-labeled RNA can be found in Kenzelmann et al. PNAS, 2007.

first: Daniel

last: Mathow

first: Prashant

last: Srivastava

first: Norbert

last: Gretz

first: Hermann-Josef

last: Gröne


title: Transcriptomic comparison between brain regions of behaviorally distinct wild and domesticated zebrafish (Danio rerio) populations

city: Moscow

first: Maia

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

summary: Zebrafish populations recently collected from the wild differ from domesticated populations in anxiety-related behaviors. We measured anxiety-related behaviors in wild and domesticated zebrafish populations and performed a multi-brain region transcriptional comparison using microarrays to try to understand the genetic changes that accompany behavioral adaptation to domestication.

overall_design: We performed a microarray analysis comparing the midbrain and telencephalon brain regions of male and female adult zebrafish from four populations varying in domestication history (Wild: Nadia (N) and Pargana (P), and Domesticated: Scientific Hatchery (S) and Transgenic Mosaic 1 (T)). We collected 16 samples per brain region (4 samples per zebrafish population, with 1 telencephalon sample missing for the S population). We attempted to maintain equal sex ratios within each zebrafish population, but this was not always possible due to sex biases within some populations.

first: Robert

last: Drew

first: Matt

middle: L

last: Settles

first: Barrie

last: Robison


title: Hippo signaling regulates Microprocessor and links cell density-dependent  miRNA biogenesis to cancer

first: Masaki

last: Mori

country: Japan

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

summary: The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening.  We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown.  RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally.  However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism.  This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato.

overall_design: For a preliminary screening, we monitored global gene expression in tomato fruits from untransformed control (Ailsa Craig [AC] cultivar) and three transgenic lines with Solyc07g052960 knockdown by RNAi (lines T-7, T-22 and T-23) at the ripening (pink coloring) stage using microarray without biological replication.

last: Fujisawa

first: Toshitsugu

last: Nakano

first: Yoko

last: Shima


title: Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica

city: Sophia Antipolis

first: Gourgues

last: Mathieu

address: 400 routes des Chappes, BP167

department: UMR Institut Sophia Agrobiotech

country: France

institute: University of Nice Sophia Antipolis

summary:
Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease.The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/Phytophthora parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy.The present project aims at analyzing the compatible interaction between A. thaliana roots and Phytophthora parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom designed Phytophthora parasitica biochip will enable analyzing of Phytophthora parasitica gene expression during the same stages.
The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The New phytologist 187: 449–460.  The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010.  New Phytol 185: 248–257.

overall_design: A series of 14 hybridizations corresponding to two biological replicates each corresponding to RNA extractions of the following biological conditions were used: 1-Vegetative mycelium (recovered from two samples of 4 day-old cultures in liquid V8 medium at 24°C), 2- Motile zoospores (recovered from 8 independent cultures), 3-Appressoria differentiated on onion epidermis (epidermis from 20 onion bulbs inoculated with zoospores collected from 8 independent Petri dishes); appressoria collected 3 hours after inoculation (24 °C), 5- Infection of A. thaliana roots by Phytophthora parasitica zoospores (samples recovered at 2.5, 6, 10.5 and 30 hours post inoculation; 5 inoculated plants for each sample).

first: Mathieu

last: Gourgues

first: Agnès

last: Attard


title: Expression data from BCG-immunized monkey PBMCs stimulated with lipid antigen

city: Kyoto

first: Daisuke

last: Morita

address: 53 Shogoin Kawara-cho, Sakyo-ku

department: Institute for virus research

institute: Kyoto-university

summary:
The role of CD1-restricted, lipid-specific T cells in vivo remains to be elucidated.
We used microarrays to detail the global program of gene expression accompanied by the activation of CD1-restricted, lipid-specific T cells.

overall_design: Monkeys were immunized with BCG bacteria to evoke CD1-restricted, mycolyl glycolipid-specific T cell responses at high frequency. The PBMCs were stimulated in the presense or absense of mycolyl glycolipid antigen, followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Ayumi

last: Miyamoto

first: Hiroshi

last: Ichise

first: Yuki

last: Hattori

first: Takashi

last: Nakamura

first: Tatsuhiko

last: Igarashi

first: Hideyoshi

last: Harashima

first: Masahiko

last: Sugita


title: Genome-wide gene expression analysis of HCT116 cells subjected to stable gelsolin overexpression

city: Singapore

first: Jingli

last: Zhuo

address: MD 6, 14 Medical Drive

institute: National University of Singapore

summary: Analysis of gene expression levels altered by stable gelsolin overexpression. Results provide important information of the modulation of various genes by gelsolin.

overall_design: Total RNA obtained from stable gelsolin-overexpressing HCT116 clones  (C1, C2, C3, C8) as well as emtpy vector control HCT116 cell lines (V4, V5)

first: Ee

last: Tan

first: Jayapal

last: Manikandan

first: Celestial

last: Yap


title: A chronological expression profile of gene activity during embryonic mouse brain development

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

summary: The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning we conducted detailed transcriptional profiling during embryonic development of the mouse brain. 2400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected, as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Analysis of left-right asymmetry of expression revealed 35 genes as putatively asymmetric from a combined data set. Our data constitutes a valuable new resource for neuroscience and neuro-development, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

overall_design: Whole genome transcriptional profiling carried out on 24 samples during 3 stages of embryonic development of the mouse brain was carried out with matching left-right asymmetry on four biological replicates at each stage.

first: Paraskevi

last: Goggolidou

first: Shamit

last: Soneji

first: Nicola

last: Powles-Glover

first: Debbie

last: Williams

first: Ioannis

last: Ragoussis

first: Dominic

last: Norris


title: MicroRNA expression data from human high-density lipoproteins.

status: Public on Feb 27 2014

city: Nashville

first: Kasey

middle: C

last: Vickers

state: TN

address: 2220 Pierce Ave   358 PRB

country: USA

institute: Vanderbilt Univ. School of Medicine

summary:
We quantified differential microRNA (miRNA) expression on human HDL before and after incubation with human coronary artery endothelial cells.
These data were used to determine which miRNAs are altered on HDL (taken up or effluxed to) by human coronary artery endothelial cells.

overall_design: Each group had a n=4 and HDL-miRNA levels post incubations were compared to pre incubations with cells.

first: Fatiha

last: Tabet


title: aCGH profiles of parental and oxaliplatin resistant colorectal cancer and ovarian cancer cell lines

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Oxaliplatin resistance was induced in 2 colorectal cancer cell lines (LoVo-92, wt-p53 and LoVo-Li, functionally inactive p53) and one ovarian cancer cell line (A2780, wt-p53). Resistance was induced by weekly exposure to oxaliplatin for 4 hrs or 72 hrs with increasing concentrations for a period of 7 months

overall_design: Genomic DNA of oxaliplatin and cisplatin resistant colorectal cancer and ovarian cancer cell lines as well as the parental cell lines were labeled and subsequently hybridized against pooled reference DNA of healthy volunteers of the opposite gender using across array hybridization. Extracted raw-data were normalised and smoothend using the R-script NOWAVE resulting in normalised log2 ratio profiles of resistant cell line versus parental cell line and parental cell line versus reference DNA.

first: Paul

last: Noordhuis

first: Adrie

last: Laan

first: Nienke

last: Losekoot

first: Kasper

last: van de Born

last: Eijk

first: Bauke

last: IJlstra

first: Godefridus

last: Peters


title: Genome-wide detection by array CGH of copy number variations among diverse horse breeds

status: Public on Feb 26 2014

city: Hohhot

first: Wei

last: Wang

address: Inner Mongolia Hohhot City Saihan District Zhao Wuda road 306

country: China

institute: College of Life Sciences Chinese Inner Mongolia Agricultural University

type: Genome variation profiling by genome tiling array

summary: Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horses’ adaption to the plateau’s environment.

overall_design: Comparison Mongolia horse , Abaga horse, Hequ horse, Kazakh horse, Debao pony, Thoroughbred with Thoroughbred

first: Shenyuan

first: Chenglin

last: Hou

first: Kaifeng

last: Wu

first: Yanping

last: Xing

first: Junwei

last: Cao

first: Chunxia

last: Liu

first: Dong

last: Zhang

first: Li

first: Yanru

first: Huanming

last: Zhou


title: MicroRNA expression data from human coronary artery endothelial cells treated with HDL components

first: Kasey

last: Vickers

summary:
We quantified differential microRNA (miRNA) expression in human coronary artery cells treated with native HDL, reconstituted HDL, lipid-free apolipoprotein A-I, small unilamellar vesicles, or PBS control.
These data were used to determine whichmiRNAs are regulated by native HDL compared to components of HDL and categorize data based on shared sets of miRNAs and distinct sets of miRNAs regulated by each component.

overall_design: Each group had a n=5 and gene expression changes for each condition were compared to control PBS-treat HCAECs

first: Fatiha

last: Tabet


title: Single cell transcriptome analysis of Arabidopsis roots inoculated by Plasmodiophora brassicae indicates a role for brassinosteroids in clubroot formation.

status: Public on Feb 23 2014

city: Dresden

first: Astrid

last: Schuller

address: Zellescher Weg 20B

country: Germany

institute: TU-Dresden

summary: The clubroot disease caused by the obligate biotrophic protist Plasmodiophora brassicae on host plants of the Brassicaceae family is characterized by enhanced cell division and cell expansion. Since a typical root section of an infected plant always includes different stages of the pathogen as well as uninfected cells, we were interested to investigate specific developmental stages of the pathogen and their effect on host transcriptional changes. We extended previous microarray studies on whole roots by using Laser Microdissection and Pressure Catapulting (LMPC) to isolate individual cells harboring defined developmental stages of the pathogen. In addition, we compared the central cylinder of infected to contol plants. We were especially interested to elucidate the stage-specific hormonal network. The upregulation of genes involved in auxin and cytokinin metabolism and signaling was confirmed. In addition, we found evidence that brassinosteroid (BR) synthesis and signal perception was in many cases upregulated in enlarged cells and the central cylinder. This was confirmed by qPCR and mutant analysis of the BR receptor mutant bri1-6, which exhibited less severe gall formation than the respective wild type. Our results identify novel hormone pathways involved in clubroot development. Using this method of single cell preparation combined with transcriptome analysis has been very useful to elucidate the regulation of gall growth by this obligate biotropic pathogen in a cell- and stage-specific manner.

overall_design: Transcription profiling was performed in isolated Arabidopsis thaliana root cells harboring different developmental stages of Plasmodiophora brassicae at two time points after inoculation (dai) (14 and 21 dai), as well as in infected central cylinder tissue from roots at 14 dai (days after inoculation). Control samples were taken from uninfected roots. Host cells were dissected from paraffin embedded roots using Laser Microdissection and Pressure Catapulting (LMPC). 8 samples have been analyzed.

first: Julia

last: Kehr

first: Jutta

last: Ludwig-Müller