title: Transcriptome-wide microRNA expression of white blood cells before and after intense cardiorespiratory exercise

status: Public on Apr 01 2014

city: Melbourne

first: Francine

last: Marques

state: VIC

address: Level 3, 75 Commercial Rd

country: Australia

institute: Baker IDI Heart and Diabetes

summary: Regular physical exercise reduces cardiovascular disease (CVD) morbidity and mortality through several biological mechanisms. We were interested in white blood cell microRNA expression in response to exercise. Ten healthy adult males (19-39 years old) undertook 30 minutes of continuous treadmill running at 80% of maximal oxygen uptake (VO2max). Blood samples were taken before and immediately after exercise.  Whole-genome microRNAs were then analysed in the extracted RNA.

overall_design: Microarrays (one per sample, with no pooling) were performed on ten healthy adults (19-39 years old) who undertook 30 minutes of continuous treadmill running at 80% of maximal oxygen uptake (VO2max). Blood samples were taken before and immediately after exercise.Whole blood was collected from arm vein, and white blood cells were separated and  preserved in liquid nitrogen and later transferred to a –80C freezer.  After extraction of RNA, cRNA was prepared and arrays performed using the Agilent Human miRNA Microarray Kit Release 16.0 performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

first: Warrick

last: Chilton

middle: Z

first: Jenny

last: West

last: Luke

first: Sharon

last: Olsen

first: Brendan

last: Toohey

first: George

last: Kannourakis

last: O'Brien

first: Fadi

last: Charchar


title: Human Mesenchymal Stem Cells (hMSCs): Fibroblast vs. hMSCs from various origins

status: Public on May 05 2014

city: Seoul

first: Nayoung

last: Suh

address: 88 Olympic-ro 43-gil, Songpagu

department: Department of Medicine

country: South Korea

institute: Asan Medical Center, University of Ulsan College of Medicine

summary: To identify the key microRNAs (miRNAs) of hMSCs required for fate determination, miRNA profiling was performed with hMSCs from three different sources including adipose-derived stem cells (ADSCs), bone-marrow-derived stem cells (BMSCs), and umbilical cord-derived stem cells (UCSCs) versus fibroblasts, a more differentiated mesenchymal cell types.

overall_design: We compared the expression profiles of two different donors per hMSCs to that of fibroblasts. All hMSCs were used for profiling at passage 3-6.

first: Supyong

last: Hwang


title: Moderate hypoxia influence at intermediate altitude in Argentinean Andes

status: Public on Apr 05 2014

city: Cambridge

first: Christina

middle: A

last: Eichstaedt

address: Fitzwilliam Street

department: Biological Anthropology

country: Germany

institute: University of Cambridge

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

summary: This study evaluates genetic and phenotypic variation in the intermediate altitude Calchaquí population living in the Calchaquí Valleys of the Argentinean Andes in the town of Cachi at 2300 m. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to moderate hypoxia at a intermediate altitude.

overall_design: DNA from 24 saliva samples of Calchaquíes living at 2300 m in Cachi in the Province of Salta in Argentina was genotyped.

first: Maru

last: Mormina

first: Toomas

last: Kivisild

first: Tiago

last: Antão

first: Luca

last: Pagani

first: Alexia

last: Cardona


title: Expression analysis of a full Lsr locus knockout on the luxS knockout background of Haemophilus influenzae strain CZ4126/02

status: Public on May 06 2014

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

country: USA

institute: Drexel University College of Medicine

summary: Investigation of whole genome gene expression differences between a full (nine-gene) Lsr locus deletion and a luxS deletion strain (double knock-out) compared to a luxS isogenic mutant strain (each derived from the CZ4126/02 parent strain). Both strains are unable to produce the autoinducer-2 (AI-2) quorum sensing molecule. In addition, the Lsr mutant is unable to import AI-2 nor mediate any potential LsrR-based transcriptional regulation.

overall_design: ΔluxS and ΔlsrΔluxS strains were grown in a chemically defined media (CDM) to two different time-points with or without the addition of 3µM synthetic AI-2. RNA was extracted from these sampling conditions in two separate cultures (biological replicates). Each of these RNA samples was run on two different H. influenzae supragenome arrays (technical replicates). 3-13 probes represent each subcluster(gene) and two replicate probe sets are included on each custom NTHi supragenome chip thus under each sampling condition 8 separate values are obtained per strain and used for WT:Lsr-KO comparisons.

first: Luisa

middle: N

last: Hiller

first: Jennifer

last: Kress-Bennett

first: Rory

last: Eutsey

first: Margaret

middle: E

last: Dahlgren

first: Joshua

last: Earl

first: Byers

last: Barbara

first: Evan

last: Powell

first: Azad

last: Ahmed

first: Ramaz

last: Geguchadze

first: Mike

last: Passineau

first: Christopher

middle: J

last: Post

first: Fen

last: Hu

first: Garth

middle: D

last: Ehrlich


title: Gene expression profiling after Wig-1 knockdown in HCT116 cancer cell line

status: Public on Mar 01 2014

city: Stockholm

first: Cinzia

last: Bersani

address: Cancer Center Karolinska, R8:04

country: Sweden

institute: Karolinska Institutet

summary: Wig-1 is a p53 target gene that encodes an RNA-binding protein involved in regulation of mRNA stability through binding to AU-rich elements (AREs). The aims of this study were to identify novel Wig-1 target mRNAs and to characterize the mechanisms of their regulation. Using a microarray approach, we identified 2447 transcripts with >4-fold differential expression between Wig-1 siRNA and control siRNA treated HCT116 cells. Among the deregulated transcripts we found a number of p53 target genes. We demonstrated that Wig-1increases 14-3-3σ transcription while it binds to an ARE in the FAS 3’UTR and decreases the FAS mRNA stability. Furthermore, we show that Wig-1 depletion favours cell death rather that cell cycle arrest after DNA damage. We propose a role of Wig-1 in directing the p53 stress response towards cell cycle arrest rather than cell death through regulation of 14-3-3σ and FAS mRNA levels.

overall_design: Use HEEBO microarrays to examine the effects of Wig-1 protein knockdown by siRNA silencing in HCT116 cells. 3 microarrays in total.

first: Klas

middle: G

last: Wiman


title: Genome-wide analysis of cold adaptation in indigenous Siberian populations

status: Public on Mar 05 2014

first: Alexia

last: Cardona

department: Archaeology and Anthropology

country: United Kingdom

institute: University of Camrbidge

summary: Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood.  Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels, increased blood pressure, short stature and broad skulls that have been attributed to adaptation to the extreme cold climate. We have genotyped 200 individuals from ten indigenous Siberian populations for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and  long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. We present a list of cold adaption candidate genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

overall_design: 200 blood samples from 200 Siberian individuals that come from ten different indigenous populations were genotypes for 730,525 SNPs across the genome.  Eighteen Vietnamese samples were also genotyped and used as reference samples.

first: Luca

last: Pagani

first: Tiago

last: Antao

first: Daniel

last: Lawson

first: Christina

last: Eichstaedt

first: Bryndis

last: Yngvadottir

first: Ma

middle: T

last: Shwe

first: Joseph

last: Wee

first: Irene

last: Romero

first: Srilakshmi

last: Raj

first: Mait

last: Metspalu

first: Richard

last: Villems

first: Eske

last: Willerslev

first: Chris

last: Tyler-Smith

first: Boris

last: Malyarchuk

first: Miroslava

middle: V

last: Derenko

first: Toomas

last: Kivisild


title: Rad51 binding in meiosis after undergoing S phase with different replication programs.

status: Public on Feb 20 2014

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

type: Genome variation profiling by genome tiling array

summary: ChIP-on-chip analysis of Rad51 binding in cells induced to undergo synchronous meiosis after growth in continuous nitrogen-rich conditions or after nitrogen depletion.

overall_design: Comparison of pat1-114 cells grown in -N and +N conditions as well as pat1-114 cells with altered Cdc45 levels in -N conditions. pat1-114 rec12Δ mutants in -N and +N conditions were also evaluated to confirm that Rad51 binding is dependent on the Rec12 transesterase.

first: Pei-Yun


title: Replication origin mapping of mitotic and meiotic cells in different conditions

summary:
Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase.
Experiments were performed in the following strains and conditions for mitotic cells: cdc25-22 (temperature-sensitive mutation arrests cells at G2/M for synchrony, otherwise wild type), nitrogen-rich conditions; wild type, haploid and diploid, nitrogen-depletion conditions. Experiments were performed in the following strains and conditions for meiotic cells: pat1-114 diploid (temperature-sensitive mutation induces a synchronous meiosis, otherwise wild type), nitrogen-depletion and nitrogen-rich conditions; pat1-114 diploid with altered Cdc45 levels, nitrogen-depletion conditions.

overall_design: Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged.


title: Localization of histone H3 and histone H3 lysine 4 trimethylation at the start of pre-meiotic S phase

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion.

overall_design: Comparison of H3 and H3k4Me3 in diploid pat1-114 cells grown in -N and +N conditions.


title: Replication origin selection organizes meiotic recombination

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

overall_design: Refer to individual Series


title: Kinetic analysis of carolacton-regulated genes

status: Public on Feb 13 2014

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Transcriptional profiling of carolacton-treated Streptococcus mutans biofilm cells in comparison to untreated biofilms in a time series approach.

overall_design: Two-condition times series experiment, carolacton treated vs. untreated for timepoints 5, 20, 40, 60, 80, 100, 120, 160, 200, 240 and 300 minutes post-carolacton addition, 2 technical replicates of each sample (dye swap).

first: Michael

last: Reck

last: Wagner-Döbler


title: microRNA-135b promotes cancer progression acting as a downstream effector of oncogenic pathways in colon cancer (Human cell line)

status: Public on Jan 17 2014

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: MicroRNA deregulation is frequent in human colorectal cancers (CRCs) but little is known to whether it represents a bystander event or actually drives tumor progression in vivo. We show that miR-135b over-expression is triggered in mouse and humans by APC loss, PTEN/PI3K pathway deregulation and by SRC over-expression and promotes tumor transformation and progression. We show that miR-135b up-regulation is common to sporadic and inflammatory bowel disease-associated human CRCs and correlates with tumor stage and poor clinical outcome. Inhibition of miR-135b in CRC mouse models reduces tumor growth controlling genes involved in proliferation, invasion and apoptosis. We identify miR-135b as a key down-steam effector of oncogenic pathways and a potential novel target for CRC patient’s treatment.

overall_design: RNA was extracted using trizol from normal human colon cell lines comparing scrambled with miR-135b oligos transfected cells

first: Nicola

last: Valeri

first: Chiara

last: Braconi

first: Pierluigi

last: Gasparini

first: Claudio

last: Murgia

first: Andrea

last: Lampis

first: Viola

last: Paulus-Hock

first: Jonathan

middle: R

last: Hart

first: Lynn

last: Ueno

first: Sergei

middle: I

last: Grivennikov

first: Francesca

last: Lovat

first: Alessio

last: Paone

first: Khlea

middle: M

last: Sumani

first: Angelo

last: Veronese

first: Muller

last: Fabbri

first: Stefania

last: Carasi

first: Hansjuerg

last: Alder

first: Giovanni

last: Lanza

first: Roberta

last: Gafa’

first: Mary

middle: P

last: Moyer

first: RachelA

last: Ridgway

first: Julia

last: Cordero

first: Gerard

last: Nuovo

first: Wendy

last: Frankel

first: Massimo

last: Rugge

first: Matteo

last: Fassan

first: Joanna

last: Groden

first: Peter

middle: K

last: Vogt

last: Karin

first: Owen

last: Sansom

first: Carlo

last: Croce


title: Overexpression of splicing factor SRSF6 in mouse skin

status: Public on Jan 19 2014

city: Cold Spring Harbor

first: Mads

last: Jensen

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary:
Many biological processes involve post-transcriptional regulation of gene expression by alternative pre-mRNA splicing. Here, we show that an alternative splicing factor SRSF6 affects tissue homeostasis of the skin.
In this dataset, we study effects on gene expression and alternative splicing upon SRSF6 overexpression (+doxycycline) in mouse skin using inducible R26-rtTA+/-, ColA1-TREtight-SRSF6+/- transgenic mice

overall_design: 4 mixed-background strain samples (2 SRSF6-induced skin samples and 2 uninduced skin control samples)

first: Adrian

last: Krainer


title: A Genomic Portrait of the Genetic Architecture and Regulatory Impact of microRNA Expression in Response to Infection

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

institute: Institut Pasteur

summary: Identification of changes in microRNA expression, remodelling of relationships between microRNA and mRNA expression levels, and genetic polymorphisms associated with inter-individual variation in the dendritic cell immune response to Mycobacterium tuberculosis infection.

overall_design: We characterised genome-wide changes in microRNA expression, and of the broader miRNA-mdeiated regulatory system, in response to Mycobacterium tuberculosis (MTB) infection, and assessed the extent to which this response is under genetic control. To do so, we profiled microRNA expression levels in primary dendritic cells from 65 individuals before and after infection with MTB for 18 hours.

first: Matthieu

last: Deschamps

first: Ludovic

last: Tailleux

first: Yohann

last: Nédélec

first: Julien

last: Pothlichet

first: Geanncarlo

last: Lugo-Villarino

first: Valentina

last: Libri

first: Brigitte

last: Gicquel

first: Olivier

last: Neyrolles

first: Guillaume

last: Laval

first: Etienne

last: Patin

first: Luis

middle: B

last: Barreiro

first: Lluis

last: Quintana-Murci


title: Comparative Genomic Analyses among Coffee-Associated strains of Xylella fastidiosa

status: Public on Dec 31 2013

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

summary: With the aid of a biochip, carrying representative sequences from approximately 2200 sequences from the genome of isolate 9a5c from X. fastidiosa (Xf), microarray-based comparisons have been performed with 8 different Xf isolates obtained from coffee plants.

overall_design: DNA from the 9a5c isolate was used as a reference in competitive hybridization experiments against DNA from 8 different Xf isolates obtained from coffee plants. Equimolecular amounts of each DNA have been labelled with either Cy3- or Cy5-dCTP and hybridized with a 9a5c Xf biochip. Statistical validation of fold change variations was performed with the aid of the Significance Analysis of Microarrays (SAM) method Tusher and coworkers, using the software developed by B. Narasimham and available at http://www-stat.stanford.edu/~tibs/SAM/index.html. Spots that showed a Reference/Test ratio <1:2 were considered to be present in greater copy number in the test over the reference strain, as proposed by Smoot and coworkers, while spots that showed an average Reference/Test ratio >5:1 were considered to be missing in the test strain. The application of these criteria in a direct sequence comparison between strains 9a5c and Temecula-1, which have been completely sequenced, provided an estimated error rate below 0.3%


title: The PhtL protein of Pseudomonas syringae pv. phaseolicola NPS3121 affects the expression of both phaseolotoxin cluster (Pht) and Non-Pht encoded genes

status: Public on Dec 28 2013

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

summary: P. syringae pv. phaseolicola, the causal agent of halo blight disease in bean, produces a toxin known as phaseolotoxin, whose synthesis involves the product of some of the genes found within the Pht region. This region, considered a pathogenicity island, comprises 23 genes arranged in five transcriptional units; two single-gene units (argK, phtL) and three arranged as operons (phtA, phtD, phtM), most with unknown function. In P. syringae pv. phaseolicola, maximal expression of most of the genes encoded in the Pht region and the synthesis of phaseolotoxin require the product of the phtL gene, which has been proposed to have a regulatory function. In order to evaluate the role of phtL gene in P. syringae pv. phaseolicola, we performed a comparative transcriptional analysis with the wild type and a phtL- mutant strains using microarrays. The microarray data analysis showed that PhtL regulates the expression not only of genes within the Pht region, but also alters the expression of genomic genes related with the iron-acquisition system, pathogenicity, oxidative stress and virulence. This study suggests the possible relation of the PhtL protein with the iron response genes and with the pathogenicity and or virulence of this bacterium.

overall_design: The microarrays used in this study correspond to an assembled DNA microarray of P. syringae pv. phaseolicola NPS3121 previously reported (GEO accession number GPL7115) (Hernández-Morales et al., 2009). This microarray consist of 1911 probes, with an average length 2.4 Kbp, representing 1X the genome of P. syringae pv. phaseolicola NPS3121, as well as several PCR products corresponding to various known genes,  which were printed as controls. Each microarray experiment was repeated six times (two technical replicates with the same RNA samples and three biological replicates using RNA isolated from a different culture). cDNA synthesis, labeling, hybridization, washing, and chip scanning were performed at the Microarray Core Facility at Cinvestav-Langebio. Hybridized microarray slides were scanned (GenePix 4000, Axon Instruments, Inc) at a 10 um resolution adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. The spot intensities were quantified using Axon GenePrix Pro 6.0 image analysis software. First, an automatic spot finding and quantification option of the software was used. Subsequently, all spots were inspected individually and in some cases, the spot diameters were corrected or the spots were removed from the analysis. The mean of the signals and the median of backgrounds were used for further analysis. Raw data were imported into the R.2.2.1 software. Background signals were subtracted using the Robust Multichip Analysis (RMA) whereas the normalization of the signal intensities within slides was carried out using “print-tip loess” method and the LIMMA package. Normalized data were log2 transformed and then fitted into mixed model ANOVAs using the Mixed procedure. The p-values of the phtL effects were adjusted for by the False Discovery Rate Method “FDR”. Changes in signal intensity of ±1.5-fold or higher/lower between phtL- mutant and wild type were highly significant (FDR, p-value ≤0.05), however we focused only in differential expressed genes that fell within the more traditional criteria, which is the cut-off threshold for up-regulated (≥1.8) and down-regulated genes (≤0.50).

last: González-Villanueva

first: Jackeline

middle: L

last: Arvizu-Gómez

first: Alejandro

last: Hernández-Morales

first: Selene

last: Aguilera-Aguirre

first: Ariel

last: Álvarez-Morales


title: microRNA-135b promotes cancer progression acting as a downstream effector of oncogenic pathways in colon cancer (mouse)

first: Luciano

last: Cascione

overall_design: RNA was extracted from fresh frozen tissues from tumours from APC;CpC and AOM/DSS mice and normal matched tissues

first: Nicola

last: Valeri

first: Chiara

last: Braconi

first: Pierluigi

last: Gasparini

first: Claudio

last: Murgia

first: Andrea

last: Lampis

first: Viola

last: Paulus-Hock

first: Jonathan

last: Hart

first: Lynn

last: Ueno

first: Sergei

last: Grivennikov

first: Francesca

last: Lovat

first: Alessio

last: Paone

first: Khlea

last: Sumani

first: Angelo

last: Veronese

first: Muller

last: Fabbri

first: Stefania

last: Carasi

first: Hansjuerg

last: Alder

first: Giovanni

last: Lanza

first: Roberta

last: Gafa’

first: Mary

last: Moyer

first: RachelA

last: Ridgway

first: Julia

last: Cordero

first: Gerard

last: Nuovo

first: Wendy

last: Frankel

first: Massimo

last: Rugge

first: Matteo

last: Fassan

first: Joanna

last: Groden

first: Peter

last: Vogt

first: Michael

last: Karin

first: Owen

last: Sansom

first: Carlo

last: Croce


title: Comprehensive analysis of miRNA expression in T-cell subsets of Rheumatoid arthritis patients and healthy controls reveals defined miRNA signatures of naive and memory Tregs

status: Public on Jan 22 2014

city: Groningen

first: Bart-Jan

last: Kroesen

address: Hanzeplein 1

department: Department of Laboratory Medicine

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

summary: Disturbed expression of microRNAs (miRNAs) in regulatory T-cells (Tregs) leads to development of autoimmunity in experimental mouse models. However, the miRNA expression signature characterizing Tregs of autoimmune diseases, such as rheumatoid arthritis (RA) has not been determined yet. Moreover, the technical limitations prevented the analysis of such minute T-cell population as naive and memory Tregs. In this study we have used a microarray approach to comprehensively analyze miRNA expression signatures of naive Tregs (CD4+CD45RO-CD25++), memory Tregs (CD4+CD45RO+CD25+++), as well as conventional naive (CD4+CD45RO-CD25-) and memory (CD4+CD45RO+CD25-) T-cells (Tconvs) derived from peripheral blood of RA patients, and matched healthy controls. Differential expression of selected miRNAs was validated by TaqMan-based qRT-PCR. We found a positive correlation between increased expression of miR-451 in T-cells of RA patients and disease activity score (DAS28), ESR levels, and serum levels of IL-6. Moreover, we found characteristic, disease and treatment independent, global miRNA expression signatures defining naive Tregs, memory Tregs, naive Tconvs and memory Tconvs. The analysis allowed us to define miRNAs characteristic for a general naive phenotype (e.g. miR-92a), a general memory phenotype (e.g. miR-21, miR-155), and most importantly miRNAs specifically expressed in both naive and memory Tregs, defining as such the Treg phenotype (i.e. miR-146a, miR-3162, miR-1202, miR-1246a, and miR-4281).

overall_design: MicroRNA profiling was performed in four CD4+ T-cell subsets: naive Tconventional (CD3+CD8-CD45RO-CD25-), naive Tregulatory (CD3+CD8-CD45RO-CD25+), memory Tconventional (CD3+CD8-CD45RO+CD25-), and memory Tregulatory (CD3+CD8-CD45RO+CD25+) derived from 2 healthy controls, and 6 rheumatoid arthritis patients (total n=8).

first: Katarzyna

last: Smigielska-Czepiel

first: Anke

last: van den Berg

first: Pytrick

last: Jellema

first: Roelof

last: van der Lei

first: Johan

last: Bijzet

first: Joost

last: Kluiver

first: Anne

last: Boots

first: Elisabeth

last: Brouwer


title: C. tropicalis cells under in vitro biofilm-forming conditions

status: Public on Nov 22 2013

city: Providence

first: Stephen

middle: Knox

last: Jones Jr

state: RI

address: 171 Meeting St.

department: Molecular Microbiology and Imunology

institute: Brown University

summary: Transcriptional profiling of a-type wor1 deleted cells and mixed a-type and alpha-type opaque cells under in vitro biofilm-forming conditions. Specifically, they were grown for two days at room temperature in a 12-well poly-styrene plate containing 1 ml of Lee's + Glucose liquid media. Samples were hybridized against a universal mixed reference sample of a-type cells in white and opaque states grown in Spider liquid media.

overall_design: 2 condition experiment: white wor1-deletion mutant a-type cells, opaque mixed a-type and alpha-type cells; two biological replicates each.

first: S

first: R

last: Bennett


title: Expression data from one-year-old leaves of Populus simonii by high-temperature treatments

status: Public on Oct 12 2013

city: Beijing

first: deqiang

last: zhang

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Technology

country: China

institute: Beijing Forestry University

summary: We take one-year-old plants for high-temperature treatments and controls. We used the Affymetrix Poplar GeneChip to decrypt the gene functions and mechanisms in Populus simonii leaves.

overall_design:
We used microarrays to detail the global program of gene expression during high-temperature treatments.
Populus simonii leaves were taken from high-temperature (42C) treatments and controls (25C) for RNA extraction and hybridization on Affymetrix microarrays. H1 and H2 are from high-temperature treatments, CK1 and CK2 are controls.

first: Deqiang

last: Zhang

first: Qingqing

last: Chen


title: Identification of genes regulated by L-lactate and by DL-lactate in Lactobacillus plantarum

status: Public on Jul 01 2013

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: L. plantarum is known to possess an L-lactate inducible lactate racemase activity (Goffin et al. 2005. J. Bacteriol. 187:6750). In the present study, microarrays were used in order to identify all genes that are up-regulated by L-lactate, but not by a racemic mixture of D- and L-lactate.

overall_design: A mutant of L. plantarum NCIMB8826 deficient for NAD-dependent L-lactate activity (TF101; Ferain et al. 1994. 176:596), and thus producing no L-lactate, was grown in MRS medium at 28°C until mid-exponential phase (OD600nm 0.75). The culture was then divided into 3 sub-cultures. Optically pure sodium L-lactate (200 mM) was added to the first sub-culture (TF101 + L-lac 200 mM). An equimolar mixture of sodium D- and L-lactate (100 mM each) was added to the second sub-culture (TF101 + L/D-lac 200 mM). The third sub-culture was not treated (TF101; reference sample). The three sub-cultures were further incubated at 28°C for 1h30 (a time known to be sufficient for induction of lactate racemase activity by L-lactate). Cells were harvested by centrifugation. Microarray data were used ot identify genes that are specifically induced by L-lactate (comparison of TF101 with TF101 + L-lac 200 mM), but not by DL-lactate (comparison of TF101 with T101 + L/D-lac 200 mM). There are no biological replicates.

first: Eric

last: Viaene

first: Philippe

last: Goffin

last: Kleerebezem

first: Pascal

last: Hols


title: Gestational food-restriction but not nicotine exposure regulates gene expression in the striatum of adolescent rats

status: Public on Sep 06 2013

city: Oxford

first: Nicholas

middle: Edward

last: Ilott

address: South Parks Road

institute: University of Oxford

summary: We used microarrays to determine the effect of prenatal nicotine exposure on gene expression profiles in the striatum of adolescent rats. We found a number of immediate early genes to be differentially expressed due to food-restriction.

overall_design: We compared control (n=8), nicotine exposed (n=7) and a group of animals matched to the food intake of nicotine exposed animals (n=10) to identify gene expression changes associated with prenatal nicotine exposure

first: Philip

last: Asherson


title: Identification of a microRNA expression signature for radiochemosensitivity of colorectal cancer cells, involving miRNAs-320a, -224, -132 and let7g

status: Public on Sep 01 2013

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

institute: University Medical Center Göttingen

summary:
Purpose: Preoperative 5-fluorouracil (5-FU) based radiochemotherapy (RCT) represents the standard treatment for locally advanced rectal cancer. Both, tumor response and progression vary considerably. MicroRNAs represent master regulators of gene expression, and may therefore contribute to this heterogeneity.
Results: Thirty-six miRNAs were identified to significantly correlate with sensitivity of CRC cell lines to RCT (q < 0.05). This list included miR320a as most significantly correlated as well as other miRNAs involved in the MAPK-, TGF- and Wnt-pathway. Importantly, transfection of selected miRNAs (let7g, miR-132, miR-224, miR-320a and miR-429) each induced a shift of sensitivity (p<0.00001). Moreover, high expression of miR-224 was associated with a poor prognosis in rectal cancer patients (p=0.043).

overall_design: Experimental design: Genome-wide microRNA (miRNA) profiling was performed from 12 colorectal cancer (CRC) cell lines. To establish an in vitro signature of radiochemosensitivity, these profiles were correlated to the individual sensitivities of each cell line to 5-FU and radiation. The functional relevance of selected miRNAs was validated by transfecting miRNA-mimics into SW480 cells, followed by treatment with 5-FU and radiation. 12 Samples with 3 replicates each.

first: Junius

last: Salendo

first: Melanie

last: Spitzner

first: Xin

first: Georg

last: Emons

first: Peter

last: Jo

first: Hendrik

middle: A

last: Wolff

first: Julia

last: Kitz

first: Silke

last: Kaulfuß

first: Tim

last: Beißbarth

first: Matthias

last: Dobbelstein

first: Michael

last: Ghadimi

first: Marian

last: Grade

first: Jochen

last: Gaedcke


title: SOCS2 expression correlates with tumor malignancy, exerts growth promoting effects and is enhanced by androgens in prostate cancer

status: Public on Dec 03 2013

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Deregulation of cytokine- and growth factor signaling due to altered expression of endogenous regulators is well recognized in prostate and other cancers. Suppressor of cytokine signaling 2 (SOCS2) is a key regulator of growth hormone, IGF and prolactin signaling, that have been implicated in carcinogenesis. In this study we elucidate expression pattern and functional significance of SOCS2 in prostate cancer (PCa). Protein expression analysis employing tissue microarrays from two independent patient cohorts revealed significantly enhanced expression in tumor compared to benign tissue as well as association with Gleason score and disease progression. In vitro and in vivo assays uncovered the involvement of SOCS2 in the regulation of cell growth and apoptosis. Functionally, SOCS2 knockdown inhibited prostate cancer cell proliferation and xenograft growth in a CAM assay. Decreased cell growth after SOCS2 downregulation was associated with cell-cycle arrest and apoptosis. In addition, we prove for the first time that SOCS2 expression is significantly elevated upon androgenic stimulation in androgen receptor-positive cell lines, providing a possible mechanistic explanation for high SOCS2 levels in PCa tissue. Consequently, SOCS2 expression correlated with androgen receptor expression in malignant tissue of patients. Taken together, our study linked increased SOCS2 expression in PCa with a pro-proliferative role in vitro and in vivo.

overall_design: Prostate cancer cell lines LNCaP, DUCaP and VCaP cells were cultured in the absence or presence of R1881, an androgen in three independent experiments. Differential gene expression was determined by comparing R1881 treated samples with the corresponding controls (EtOH treated samples).

last: Hoefer

first: Johann

last: Kern

first: Philipp

last: Ofer

first: Iris

middle: E

last: Eder

last: Schäfer

first: Dimo

last: Dietrich

first: Glen

last: Kristiansen

first: Stephan

last: Geley

first: Eberhard

last: Gunsilius

first: Helmut

last: Klocker

first: Zoran

last: Culig

first: Martin

last: Puhr


title: Intrauterine growth restriction is associated with cardiac ultrastructural and gene expression changes related to the energetic metabolism in a rabbit model

status: Public on Oct 30 2013

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

summary: Intrauterine growth restriction (IUGR) affects 7-10% of pregnancies and is associated with cardiovascular remodeling and dysfunction which persists into adulthood. The underlying subcellular remodeling and cardiovascular programming events are still poorly documented. Cardiac muscle is central in the fetal adaptive mechanism to IUGR given its high energetic demands. The energetic homeostasis depends on the correct interaction of several molecular pathways and the adequate arrangement of intracellular energetic units (ICEUs), where mitochondria interact with the contractile machinery and the main cardiac ATPases to enable a quick and efficient energy transfer. We studied subcellular cardiac adaptations to IUGR in an experimental rabbit model. We evaluated the ultrastructure of ICEUs with transmission electron microscopy and observed an altered spatial arrangement in IUGR, with significant increases in cytosolic space between mitochondria and myofilaments. A global decrease of mitochondrial density was also observed. In addition, we conducted a global gene expression profile by advanced bioinformatics tools to assess the expression of genes involved in the cardiomyocyte energetic metabolism, and identified four gene modules with a coordinated over-representation in IUGR: oxygen homeostasis (GO: 0032364), mitochondrial respiratory chain complex I (GO:0005747), oxidative phosphorylation (GO: 0006119) and NADH dehydrogenase activity (GO:0003954). These findings might contribute to changes in energetic homeostasis in IUGR. The potential persistence and role of these changes in long term cardiovascular programming deserves further investigation.

overall_design: In this study, we used gene expression arrays to investigate differences between two experimental groups: IUGR and control. The design includes paired samples.

first: Torre

last: Iratxe

first: González-Tendero

last: Ana

first: García-Cañadilla

last: Patricia

first: Crispi

last: Fátima

first: García-García

last: Francisco

first: Bijnens

last: Bart

first: Iruretagoyena

last: Igor

first: Dopazo

last: Joaquín

first: Amat-Roldán

last: Iván

first: Gratacós

last: Eduard


title: DNA damage responsive microRNAs misexpressed in human cancer regulate chemotherapy sensitivity (lung cancer cell lines)

status: Public on May 31 2013

city: Roterdam

first: Maikel

last: Wouters

address: Dr. Molewaterplein 50

department: Genetics

institute: Erasmus Medical Center

summary:
The DNA damage response (DDR) is a cellular process that protects the genetic information against DNA damage and inhibits malignant transformation.  Tumor cells are characterized by an aberrant DDR, which is exploited by genotoxic chemotherapy. However, cancer cells are able to develop drug resistance, for example by modulation of the DDR.
Although the regulation of the DDR has been extensively studied, not much is known about the role of microRNAs (miRNAs). Here, we describe an approach to specifically identify DDR miRNAs in human primary epithelial cells that also play a role in tumorigenesis and response to cancer therapy in corresponding cancer cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The miRNA expression profile was determined of 12 lung cancer cell lines.

first: Marijn

last: van Jaarsveld

middle: D

first: Antonius

last: Boersma

first: Wilfred

middle: F

last: van IJcken

first: Ron

middle: J

last: Mathijssen

first: Jaap

last: Verweij

first: Jan

last: Hoeijmakers

first: John

last: Martens

first: Steven

last: van Laere

first: Erik

middle: C

last: Wiemer

first: Joris

last: Pothof


title: compare of microRNA expression between IA and MMA

status: Public on Apr 25 2013

city: Changsha

first: Jia

last: Li

state: Hunan province

address: 110, Xiangya Road

institute: State Key Laboratory of Medical genetics

summary: To exploring the difference of microRNA expression between IA and MMA, we have employed microRNA array expression profiling as a discovery platform to identify genes between the IA and MMA. Futher functional analyses were performed based on the data.

overall_design: 3 IA and 3 MMA were used for the microarray.

first: Yugang

last: Jiang

first: Mingming

last: Zhang

first: Hua

last: He

last: Zeng

first: Ranhui

last: Duan


title: Pulsatile exposure to simulated reflux leads to stereotypical changes in gene expression in a 3D model of oesophageal mucosa

status: Public on Mar 22 2013

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary: Oesophageal exposure to duodenogastroesophageal refluxate is implicated in the development of Barrett’s Metaplasia, with increased risk of progression to oesophageal adenocarcinoma. The literature proposes that reflux exposure activates NF-kB, driving the aberrant expression of intestine-specific caudal-related homeobox genes. However, early events in the pathogenesis of Barrett’s Metaplasia from a normal epithelium are poorly understood. To investigate this, our study subjected a 3D model of the normal human oesophageal mucosa to repeated, pulsatile exposure to specific bile components and examined changes in gene expression. Initial 2D experiments with a range of bile salts observed that taurochenodeoxycholate (TCDC) impacted upon NF-kB activation without causing cell death. Informed by this, the 3D human oesophageal model was repeatedly exposed to TCDC in the presence and absence of acid, and the epithelial cells underwent gene expression profiling. We identified ~300 differentially expressed genes following each treatment, with a large and significant overlap between treatments. Enrichment analysis (Broad GSEA, DAVID and Metacore™, GeneGo Inc) identified multiple gene sets related to cell signalling, inflammation, proliferation, differentiation and cell adhesion. Specifically NF-kB activation, Wnt signalling, cell adhesion and targets for the transcription factors PTF1A and HNF4α were highlighted. CDX1/2 transcription factors are believed to play a role in BM development; however, in this study their targets were not enriched, suggesting that CDX1/2 activation may not be the one of the initial events for BM formation. Our findings highlight new areas for investigation in the earliest stages of BM pathogenesis of oesophageal diseases and new potential therapeutic targets.

overall_design: RNA was extracted from oesophageal epithelium grown in a 3D oesophageal mucosa model. The model received pulsatile exposure for 10 mins twice a day for 11 days to pH 7.4 (control, n=6), TCDC (n=6), pH 4 (n=6) or TCDC, pH 4 (n=6). In one experiment, four oesophageal constructs were grown using the epithelial cells from one patient and each construct was exposed to a different insult. The experiment was performed six times using cells from three different patients, repeating each experiment once to produce technical replicates. RNA was then pooled from one technical replicate per patient to produce 8 samples for array analysis.  The three treatments were compared to the control.

first: Nicola

middle: H

last: Green

first: Zoe

last: Nicholls

middle: R

first: Jonathan

last: Cooper-Knock

first: Jennifer

last: Wilson

first: Bernard

last: Corfe

first: Sheila

last: MacNeil

last: Bury


title: DNA damage responsive microRNAs misexpressed in human cancer regulate chemotherapy sensitivity (HMEpC & HSAEpC)

first: Maikel

last: Wouters

summary:
The DNA damage response (DDR) is a cellular process that protects the genetic information against DNA damage and inhibits malignant transformation.  Tumor cells are characterized by an aberrant DDR, which is exploited by genotoxic chemotherapy. However, cancer cells are able to develop drug resistance, for example by modulation of the DDR.
Although the regulation of the DDR has been extensively studied, not much is known about the role of microRNAs (miRNAs). We used an approach to specifically identify DDR miRNAs in human primary epithelial cells that also play a role in tumorigenesis and response to cancer therapy in corresponding cancer cells.

overall_design: The miRNA expression profile was determined in 132 samples: 2 primary epithelial cell types, 1 untreated sample, 4 genotoxic treated samples, 3 timepoints, 4 replicates each and 6 zero timepoints for each cell type

first: Marijn

middle: M

last: van Jaarsveld

first: Antonius

last: Boersma

first: Wilfred

last: van IJcken

first: Ron

last: Mathijssen

first: Jaap

last: Verweij

first: Jan

last: Hoeijmakers

last: Martens

last: van Laere


title: C. tropicalis a biofilms of opaque and wor1 overexpressers

status: Public on May 01 2013

first: Richard

last: Bennett

address: 171 Meeting St

department: Molecular Microbiology and Immunology

summary: Transcriptional profiling of C. tropicalis a cells (CAY1503) in opaque state and overexpressing Wor1 in biofilms hybridized against a universal mixed reference sample of a cells in white and opaque states grown in Spider liquid.

overall_design: 2 condition experiment: opaque, tdh3-wor1; 2 biological replicates of each

first: Stephen

middle: K

last: Jones

first: Allison

last: Porman


title: DNA damage responsive microRNAs misexpressed in human cancer regulate chemotherapy sensitivity (lung tumors)

overall_design: The miRNA expression profile was determined of 18 non-small cell lung tumors and 16 normal lung samples.

first: John

first: Steven

first: Erik

last: Wiemer

first: Joris

last: Pothof


title: DNA damage responsive microRNAs misexpressed in human cancer regulate chemotherapy sensitivity

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

overall_design: Refer to individual Series


title: Identification of downregulated microRNA in a gastric cancer cell line co-cultured with M1- or M2-polarized macrophage

status: Public on Sep 05 2013

city: Kumamoto

first: Hidetaka

last: Sugihara

address: 1-1-1 Honjo

country: Japan

institute: Kumamoto university

summary: We showed that co-culture with TAMs triggered Bmi1 expression in gastrointestinal cancer cell lines. miRNAs have been found to target various oncogenes and tumor suppressors. We therefore hypothesized that the regulation of Bmi1 expression in gastrointestinal cancer cells may be mediated by miRNAs using miRNA microarray analysis.

overall_design:
THP-1 cells were seeded in the transwell inserts (3540, Corning) for 6-well plates (1 × 106 cells/well). For preparation of M1-polarized THP-1 macrophages, 320 nM phorbol myristate acetate (PMA) was added to THP-1 cells for 6 h, followed by PMA plus 20 ng/ml interferon (IFN)-γ and 100 ng/ml lipopolysaccharide for the following 18 h. For preparation of M2-polarized THP-1 macrophages, 320 nM PMA was added to THP-1 cells for 6 h, followed by PMA plus 20 ng/ml interleukin (IL)-4/IL-13 for the following 18 h.
After three washes to remove cytokines, M1- or M2-polarized THP-1 macrophages were co-cultured in upper inserts with AGS cells in 6-well plates (1 × 105 cells/well) without direct contact, in each medium without 10% FBS as described above. After 24 h of co-culture, the upper inserts containing macrophages were discarded. AGS cells were collected and analyzed to identify downregulated microRNA in a gastric cancer cell line co-cultured with M1- or M2-polarized macrophage.

first: Takatsugu

last: Ishimoto


title: SNP data from 126 hepatocellular adenomas and carcinomas

status: Public on Dec 18 2013

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary: SNP array data from 127 hepatocellular adenomas and carcinomas were used to detect recurrent copy number alterations.

overall_design: 48 tumors were analyzed with Illumina HumanCNV370-Duo v1.0 chips. 79 tumors were analyzed with Illumina HumanOmniExpress BeadChip.

first: Camilla

last: Pilati

first: Sandrine

last: Imbeaud

first: Jessica

last: Zucman-Rossi


title: ING4 regulates a secretory phenotype in primary fibroblasts with dual effects on cell proliferation and tumor growth

status: Public on Apr 22 2013

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

institute: IIB

summary:
ING proteins play an essential role in the control of a variety of cellular functions whose deregulation is associated with tumor formation and dissemination, such as proliferation, apoptosis, senescence or invasion.  Accordingly, loss of function of ING proteins is a frequent event in many types of human tumors.  In this report, we have studied the function of ING4, a member of the ING family of tumor suppressors, in the context of normal, non-transformed primary fibroblasts.  We show that ING4 negatively regulates cell proliferation in this cell type.  The antiproliferative action of ING4 requires its ability to recognize chromatin marks, it is p53-dependent and it is lost in an ING4 cancer-associated mutant.  Gene expression analysis shows that ING4 regulates the expression and release of soluble factors of the chemokine family.  The secretory phenotype regulated by ING4 in primary fibroblasts displays a selective paracrine effect on proliferation, fostering the division of tumor cells, while inhibiting division in primary fibroblasts.  Consistently, ING4-expressing fibroblasts promoted tumor growth in vivo in co-injection tumorigenesis assays.  Collectively, our results show that ING4 not only can regulate the proliferation of primary non-transformed human fibroblasts, but also orchestrates a secretory phenotype in these cells that promotes tumor cell proliferation in vitro and in vivo.  These findings support a critical role for ING4 expression in normal cells in the non-cell autonomous regulation of tumor growth.
Gene expression analysis shows that ING4 regulates the expression and release of soluble factors of the chemokine family.

overall_design: Two independent retroviral infections were performed in early pasaje IMR-90 fibroblasts with wild-type ING4 wild type and the N214D mutant. All of them were hibridazed by duplicate againts a reference  sample from vector-infected cells

first: Alberto

last: Moreno

first: Irene

last: Soleto

first: Pablo

last: García Sanz

first: Ignacio

last: Palmero


title: Expression analysis of Salmonella enterica serovar Typhimurium strain SL1344 with and without plasmid R27

status: Public on Mar 21 2013

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

summary: Investigation of gene expression level changes in Salmonella Typhiumurium SL1344 (R27) compared to the wild-type SL1344 strain when grown at different growth temperatures and growth phases.

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

overall_design: A 24 microarray study was performed using total RNA recovered from three separate wild-type cultures of SL1344 and three separate cultures of SL1344 (R27) grown to exponential and stationary phase at 25oC and 37oC.  Each microarray measured the expression level of 4,527 genes from Salmonella Typhimurium SL1344 chromosome, 103 genes from plasmid pSLT, 100 genes from plasmid  pRSF, 14 genes from plasmid pCOL1B and 207 genes from plasmid R27. Seven probes were present per transcript, with two-fold technical redundancy.

first: Sonia

last: Paytubi

first: Antonio

last: Juarez


title: Gene expression profile in CD14+ monocytes in patients with SSc or healthy controls (part 3)

status: Public on Mar 12 2013

city: Tokyo

first: Hidekata

last: Yasuoka

address: 35 Shinanomachi, Shinjuku

department: Internal Medicine

institute: Keio University School of Med

summary: To clarify the role of monocyte in the pathogenesis of SSc, we analyzed gene and protein expression in monocyte from SSc and healthy controls in order to identify the molecules which were associated with pathogenesis of SSc.

overall_design: After the screeining using gene and protein expression profiles, functional role of the candidate molecules were further analyzed to clarify the role in the pathogenesis of SSc.

first: Ayako

last: Masuda

first: Takashi

last: Satoh

first: Yukie

last: Yamaguchi

first: Yuka

last: Okazaki

first: Masataka

last: Kuwana


title: Gene expression profile in CD14+ monocytes in patients with SSc or healthy controls (part 2)


title: Gene expression profile in CD14+ monocytes in patients with SSc or healthy controls (part 1)


title: miRNA expression in classical Hodgkin lymphoma diseased nodes

status: Public on Mar 19 2013

city: Brisbane

first: Kimberley

last: Jones

state: QLD

address: 300 Herston Road

country: Australia

institute: Queensland Institute of Medical Research

summary: To determine differential expression of miRNA in classical Hodgkin lymphoma diseased nodes compared to non-malignant lymph nodes, we used agilent microarray release 16 and quantile normalisation using Genespring GX software  to quantify and compare miRNA expression..

overall_design: Total RNA was extracted from 8 non-malignant lymph node and 14 classical Hodgkin lymphoma diseased node (6 mixed cellularity and 8 nodular sclerosing) formalin-fixed paraffin-embedded tissue samples

first: Maher

last: Gandhi

first: Colm

last: Keane


title: Gene expression profile in CD14+ monocytes in patients with SSc or healthy controls


title: Candida wildtype cells;control vs. Candida QDR1/QDR2/QDR3 knockout cells;test

status: Public on Mar 01 2013

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: Transcriptional profiling of Candida cells vs putative MFS transporter QDR2 knockout cells

overall_design: One-condition experiment, WT vs. QDR1/QDR2/QDR3 knockout cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.

first: Abdul

last: Shah


title: Comparative transcriptomics of Escherichia coli growing in complex environments

city: Groningen

first: Pilar

last: Puentes-Téllez

address: Nijenborgh 7

department: Microbial Ecology

institute: University of Groningen

summary: Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: An overnight culture of E coli (ancestor culture) was propagated in LB media with three different oxygen regimes during 150 days. One regime involved transfers under constant shaking (200rpm): Treatment A-Replica populations 1 and 2 , second regime consisted in a daily shift between shaking and static (no shaking) conditions: Treatment B-replica populations 3,4 and 5. The third regime involved transfers in constant static conditions: Treatment C-Populations 6 and 7. After 150 days and plating, 3 different colony types were selected by population (populations 6 and 7 only had 2 different morphologies). Morpholigies were marked as a, b, c in each population. cDNA was obtainned  from each morphology after growing separately in LB medium, under they correspondant evolving condition until late logaritmic phase (0,6-0,7 in OD600).  A total of 19 evolved forms were analyzed plus one ancestor.  Each morphology was labeled in a dye-swap design and hybridized to the ancestor into genome-wide multi-strain E. coli (8x15K) microarrays.

first: P

last: Puentes-Tallez

first: Akos

middle: T

last: Kovacs


title: Candida wildtype cells;control vs. Candida QDR2 knock out cells;test

overall_design: One-condition experiment, WT vs. QDR2 knockout cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.


title: Candida wildtype cells;control vs. Candida QDR1 knock out cells;test

summary: Transcriptional profiling of Candida cells vs putative MFS transporter QDR1 knockout cells

overall_design: One-condition experiment, WT vs. QDR1 knockout cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.


title: Candida wildtype cells;control vs. Candida QDR3 knock out cells;test

overall_design: One-condition experiment, WT vs. QDR3 knockout cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.


title: Normal early pregnancy: a transient state of epigenetic change favoring hypomethylation

status: Public on Oct 15 2012

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

summary: The objective of this study was to analyze genome-wide differential methylation patterns in maternal leukocyte DNA in early pregnant and non-pregnant states. This is an age- and body mass index-matched case-control study comparing the methylation patterns of 27,578 cytosine-guanine (CpG) sites in 14,495 genes in maternal leukocyte DNA in early pregnancy (n=14), in the same women postpartum (n=14), and in nulligravid women (n=14) on a BeadChip platform. Transient widespread hypomethylation was found in early pregnancy as compared with the non-pregnant states. Methylation of nine genes was significantly different in early pregnancy compared to both postpartum and nulligravid states (< 10% False Discovery Rate). Early pregnancy may be characterized by widespread hypomethylation compared to non-pregnant states; there is no apparent permanent methylation imprint after a normal-term gestation. Nine potential candidate genes were identified as differentially methylated in early pregnancy and may play a role in the maternal adaptation to pregnancy.

first: Wendy

last: White

first: Brian

last: Brost

first: Carl

last: Rose

first: Iasmina

last: Craici

first: Steven

last: Wagner

first: Stephen

last: Turner

first: Vesna

last: Garovic


title: A nucleolar AAA-NTPase is required for Toxoplasma gondii division

status: Public on Jan 27 2013

city: Tampa

first: Elena

middle: S

last: Suvorova

address: 3720 Spectrum Blvd

institute: University of South Florida

summary:
Toxoplasma gondii cell cycle mutant 11-104A4 reversibly arrests in the G1 phase.  The defect in this mutant was mapped by genetic complementation to a gene encoding a novel AAA-ATPase/CDC48 family member (TgNoAP1).  A change in a tyrosine to a cysteine upstream of an AAA+ domain leads to protein instability and results in cell cycle arrest. This factor  is cell cycle regulated and exclusively expressed in the nucleolus during the G1/S phases.  At high temperature the mutant quickly arrests with a single nucleus and expresses transcripts enriched in the G1 subtranscriptome. This unique CDC48 ortholog operates in a parasite mechanism responsible for G1 progression and is the first G1-specific checkpoint factor described in Toxoplasma.
We describe transcriptome of the temperature sensitive mutant 11-104A4. Transcriptome studies demonstrated that gene expression is reflective of the parasite arrest in G1 phase. mRNAs normally upregulated in S/M phase were largely downregulated in the mutant at the restrictive temperature 40oC.  Genetic complementation with extra copy of the wild type TgNoAP1 rescued growth of the mutant 11-104A4 at 40oC and reversed changes in the transcriptome.

overall_design: RNA samples were isolated in duplicate from mutant 11-104A4 parasites grown for 32h at permissive (34oC) or non-permissive temperatures (40oC). In addition, a duplicate sample of RNA from mutant 11-104A4 complemented with cosmid TOXOV53 encoding wild type copy of TgNoAP1 similarly grown at 40oC was collected. Samples were hybridized to the Toxoplasma gondii Affymetrix microarray (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html). Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies).

first: Michael

middle: W


title: Regulation of cholesterogenic gene expression in Japanese medaka (Oryzias latipes) exposed to 17β-trenbolone

status: Public on Feb 14 2013

city: Tsukuba

first: Katsuyuki

last: Kadota

state: Ibaraki

address: Tokodai 5-13-11

department: Research

institute: Japan pulp & Research Institute, Inc.

summary: The anabolic androgen 17β-trenbolone (TB) can cause masculinization and reduce fecundity of fish. However, the underlying mechanisms of various biological pathways including metabolism, biosynthesis etc. are largely unknown. Here, we evaluated the effects of TB using the medaka DNA microarray representing 36,398 genes. Larval medaka, Oryzias latipes, (within 24 hrs posthatch) were exposed to TB at various concentrations (2, 6, 20, 60, 100, 200 ng/L) for up to 7 days. Dose-response relationships in gene expression levels of the categorized genes were analyzed using the cumulative chisquared method. Microarray analyses of the TB-exposed larvae showed that 117 and 32 genes were determined as up and down-regulated genes, respectively. The most significant GO term for biological process identified within this gene list was lipid metabolic process, which contained 26 genes in up-regulated genes. In this category, “cholesterol biosynthetic process” was highlighted as an important subcategory with 15 genes, including hydroxymethylglutaryl-CoA synthase cytoplasmic, squalene monooxygenase, lanosterol synthase etc. RT-PCR measurements in these genes were consistent with the microarray results in the direction and magnitude of these changes in gene expression. On the other hands, in the category of “sexual differentiation and development”, genes related to hypothalamic-pituitary-gonadal (HPG) axis were not affected by TB treatment except for one gene encoded to cytochrome P450 19A1. Genes related to oogenesis, such as choriogenins and vitellogenins were weakly down regulated at 2-200 ng/L of TB. Our findings demonstrate that genes encoding cholesterol synthesis pathway via the mevalonate pathway were controlled by TB in larval medaka.

overall_design: TB concentrations used were 0 (control), 2, 6, 20, 60, 100 and 200 ng/L for 7 days of exposure. Each TB treatment had 90 larval medaka for each chamber. At day 7 of the exposures, triplicate samples (30 larvae/sample) from each chamber respectively were collected, flash-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.

first: Satomi

last: Mizukami-Murata


title: yeast wt pool

status: Public on Nov 14 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

summary: Contains a collection of wildtype Saccharomyces cerevisiae strains for estimating the biological variation. Wildtypes are obtained from the yeast wildtypes - wt pool background set HybSet, by randomly taking 100 wt vs. refpool (pooled wts) and 100 refpool vs. wt hybridizations

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays.

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Sander

last: van Hooff

first: Philip

last: Lijnzaad

first: Frank

last: Holstege


title: The effect of blood on Fusobacterium nucleatum

status: Public on Sep 01 2012

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

summary: Fusobacterium nucleatum is a Gram-negative oral bacterial species associated with periodontal disease progression. As periodontal disease progresses, it is known F. nucleatum coaggregated with blood is frequently detected in the gingival crevice. However, it is largely unknown whether these interactions between F. nucleatum and blood induce a particular genetic response. We tested the cultures of F. nucleatum ATCC 25586 with or without blood in a semi-defined growth medium by microarray analysis and found 14 genes that were affected after only about 4hr. of adhered blood. Then, we selected 7 genes that changed significantly and tested these genes via real-time RT-PCR to confirm the validity of the microarray results. As a result, one amino sugar-binding protein on the membrane of F. nucleatum was especially expressed high via both microarray and real-time RT-PCR. Based upon these data, it appears that the protein on the F. nucleatum membrane binds and transfers the amino sugar only under blood conditions.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

overall_design: This study aims to determine the effect of blood on the gene expression profiling of F. nucreatum. The study contains 2 separate experiments that both measure the cultures without or with blood. The samples with blood contain 9% and 33% blood.

first: Saori

last: Yoneda


title: Comparison of fire ant adult queens with different supergene genotypes (SB/SB and SB/Sb) and different age classes (1-day-old virgins, 11-day-old virgins and reproductive queens) from 2008 and 2009

status: Public on Nov 07 2012

city: Lausanne

first: Mingkwan

last: Nipitwattanaphon

address: Biophore Building, UNIL-Sorge

department: Department of Ecology and Evolution

institute: University of Lausanne

summary:
In the fire ant Solenopsis invicta, a colony queen number is determined by the founding queen's genotypes at the 13 Mb supergene with the non-recombining variants SB and Sb. Single-queen colonies are always headed by SB/SB queens while multiple-queens colonies are always headed by SB/Sb queens. The two variants of the supergene, SB and Sb are completely linked to the two alleles (B and b) of the gene Gp-9. SB/SB and SB/Sb queens differ in many physiological traits including their maturation rate and odor. To explain why SB/SB and SB/Sb queens have different odors, and why SB/SB virgins mature faster and accumulate more fat, we measured expression of ~6000 genes in virgin queens 1 and 11 days after eclosion and in reproductive queens.
Keywords: fire ants, Solenopsis invicta, Supergene, queen, Gp-9, social form, maturation, fat storage, queen odor, cuticular hydrocarbon, worker discrimination, monogyne, polygyne, transposon, chemical signaling

overall_design: Six-condition experiment: 1-day-old SB/SB virgins, 1-day-old SB/Sb virgins, 11-day-old SB/SB virgins, 11-day-old SB/Sb virgins, SB/SB reproductive queens, SB/Sb reproductive queens. Biological replicates: 8 for 1-day-old SB/SB virgins and 1-day-old SB/Sb virgins that were collected in 2008; 8 for 1-day-old SB/SB virgins, 1-day-old SB/Sb virgins that were collected in 2009; 7 for 11-day-old SB/SB virgins and 11-day-old SB/Sb virgins that were collected in 2008; 8 for 11-day-old SB/SB virgins and 11-day-old SB/Sb virgins that were collected in 2009; 8 for SB/SB and SB/Sb reproductive queens (only collected in 2009). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5. Samples from 2008 were hybridized on the microarrays batch I and samples from 2009 were hybridized on the microarrays batch J.

first: John

last: Wang

first: Michiel

middle: B

last: Dijkstra

first: Laurent

last: Keller


title: Transcriptional profiling of quinidine drug resistance genes in Candida albicans

first: Rajendra

last: Prasad

overall_design: Refer to individual Series


title: Gene expression analysis of uveal melanoma tumor tissue

status: Public on Jul 31 2012

city: Saint Louis

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

summary: Previous studies have demonstrated two distinct classes of primary uveal melanoma tumors based on gene expression profiling.  This study compares the gene expression profiles of primary uveal melanomas collected from fresh frozen samples to those collected by fine needle aspiration biopsy.  Two matched metastatic samples were included to identify changes in gene expression profile with metastatic progression.

overall_design: Total RNA was obtained from tumor samples that were collected at the time of treatment.


title: Screening genes associated with rheumatoid arthritis and ankylosing spondylitis

status: Public on Jul 23 2012

city: Jinan

first: Xiaotian

last: Chang

address: Jingshi road 18877

institute: Shandong Acedemy of medicinal sciences

summary:
Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9 to rheumatoid arthrities (RA) and ankylosing spondylitis (AS).
We previously found that encoding genes of PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6 and DNAH9 could be associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). We used illumina customer designed microarray to verify the above finding with an increased numbers of samples. Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6, DNAH9 to RA and AS. A case-control study was performed with 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls. Tag single nucleotide polymorphisms (tag SNPs) across the above genes were determined by searching the HapMap database. The tag SNPs were selected on the basis of linkage disequilibrium patterns observed in the Han Chinese in Beijing (CHB) samples that were genotyped as a part of the International HapMap Project. Only SNPs with a minor allele frequency of greater than 5% with a pair-wise r2 ≥ 0.8 in the HapMap were considered. SNPs that were in exons and untranslated regions (UTR), as well as promoters and introns within 500 bp of exons were also selected. Candidate SNPs were submitted to Illumina for a design score. The Illumina Assay Design Tool filtered out SNPs that were not suitable for the Illumina platform. Finally, 382 SNPs with a design score of “1” were selected.

overall_design:
382 SNPs within PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9  encoding genes were selected. Genotyping was performed using Illumina VeraCode microarray in a case-control study including 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls
We performed genotyping using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina). Peripheral blood samples were collected from patients with RA (n=266, 183 female) and AS (n=51, 10 female). RA patients had a mean age of 51.7 years, while AS patients had a mean age of 35.9 years. A total of 163 (60 female) healthy individuals with a mean age of 48.0 years were blood donors. Blood samples were put into Monovette tubes containing 3.8% sodium citrate. The genotyping was conducted with the BeadXpress Reader using the Illumina VeraCode GoldenGate Assay kit. 500 ng of sample DNA were used per assay. Genotype clustering and calling were performed using BeadStudio software (Genomestudio V2010.2 Genotyping module V1.6) (Illumina). This work was completed at the Beijing Institute of Genomics.


title: Effect of germline ablation in the nematode P. pacificus

status: Public on Apr 18 2012

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of germline-ablated P. pacificus worms versus un-ablated wild-type controls. Food source E. coli OP50 for both conditions. The goal was to identify genes that regulate the enhanced longevity observed in germline-deficient animals.

overall_design:
One-condition experiments.
Germline ablated P. pacificus versus un-ablated wild-type P. pacificus.
Developmental stage = Young adults.
Food source = E. coli OP50 for both conditions.
3 biological replicates for each condition, including 2 dye-swaps.

first: Robbie

last: Rae

first: Ralf

last: Sommer


title: Genome-wide gene expression profiles of clear cell renal cell carcinoma; Identification of molecular targets for treatment of renal cell carcinoma

status: Public on Jul 16 2012

city: Tokushima

first: Toyomasa

last: Katagiri

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: The University of Tokushima

summary: In order to clarify the molecular mechanism involved in renal carcinogenesis, and identify molecular targets for diagnosis and treatment, we analyzed genome-wide gene expression profiles of 15 surgical specimens of clear cell renal cell carcinoma (RCC), compared to normal renal cortex, using a combination of laser microbeam microdissection (LMM) with a cDNA microarray representing 27,648 genes.

overall_design:
Tissue samples of surgically-resected clear cell renal cell carcinoma (ccRCC) and their corresponding clinical information were obtained from patients with written informed consent. The total of 15 cancer patients (6 women and 9 men; median age, 66; range, 36-75 years) that had been confirmed histologically as ccRCC were selected for this study. Two to three pieces of cancer tissue had been taken from each patient at the time of radical nephrectomy.  Normal tissue had been obtained from the distant region from cancer area in the resected kidney tissue. These samples were immediately embedded in TissueTek OCT compound (Sakura, Tokyo, Japan), frozen, and stored at -80°C.  The frozen tissues were sliced into 8-μm sections using a cryostat (Sakura) and then stained with H&E for histological examination. We used LMM technology to collect pure populations of ccRCC cells as well as non-cancerous renal cortex.  A mixture of normal renal cortex cells in kidney tissues from 11 patients was prepared as a universal control.
Experiments were performed using 6 sets of slides (slide set 1-6 corresponding to ID_REF 1-27648).

first: Yusuke

last: Nakamura


title: Regulation of ykrL (htpX) by Rok and YkrK, a novel type of regulator in Bacillus subtilis

status: Public on Apr 04 2012

first: Bogumila

last: Marciniak

department: Department of Genetics

institute: Rijksuniversiteit Groningen

summary: Expression of ykrL of Bacillus subtilis, encoding a close homologue of the Escherichia coli membrane protein quality control protease HtpX, was shown to be upregulated under membrane protein overproduction stress. Using DNA affinity chromatography, two proteins were found to bind to the promoter region of ykrL: Rok, known as a repressor of competence and genes for extracytoplasmic functions, and YkrK, a novel type of regulator encoded by the gene adjacent to ykrL, but divergently transcribed. Electrophoretic mobility shift assays showed Rok and YkrK binding to the ykrL promoter region as well as YkrK binding to the ykrK promoter region. Comparative bioinformatic analysis of the ykrL promoter regions in related Bacillus species revealed a consensus motif, which was demonstrated to be the binding site of YkrK. Deletion of rok and ykrK in a PykrL-gfp reporter strain showed that both proteins are repressors of ykrL expression. In addition, conditions which activated PykrL (membrane protein overproduction, dissipation of the membrane potential, salt- and phenol stress) point to the involvement of YkrL in membrane protein quality control.

overall_design: Samples for transcriptome analyses were induced at the exponential-growth phase (OD600 = 0.8) with 0.1% subtilin (subtilin containing supernatant of subtilin producing B. subtilis strain ATCC 6633). Cells were harvested 30 min after induction. Three independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment. One of each strain was collected in double volume for technical replicates.

first: Bogumiła

first: Hein

last: Trip

first: Fabrizia

last: Fusetti

first: Oscar

middle: P

last: Kuipers


title: Single cell fitness of B. subtilis correlates with the ability to adapt to various stresses.

status: Public on Jul 01 2012

first: Imke

last: de Jong

department: GBB, Molecular Genetics

summary: How cells dynamically respond to fluctuating environmental conditions depends on the architecture and noise of the underlying genetic circuits. Most work characterizing stress pathways in the model bacterium Bacillus subtilis has been performed on bulk cultures using ensemble assays. However, investigating the single cell response to stress is important since noise might generate significant phenotypic heterogeneity. Here, we study a single stress response (glucose starvation) to allow comparison of both population- and single cell data. Using a top-down approach, we investigate the transcriptional dynamics of various stress-related genes of B. subtilis in response to glucose starvation. Our data reveal that most stress-induced pathways respond highly heterogeneously to glucose starvation. Bacteria are commonly thought to exhibit phenotypic heterogeneity to increase their survival under changing environments by always having a subpopulation pre-adapted to adverse conditions. Interestingly, growth experiments with cultures that were either pre-adapted for glucose starvation or non-starved cells showed that non-starved cells demonstrate a significant growth advantage when challenged with a new stress. This suggests that once cells engage in a certain stress pathway they are only optimised for this specific condition. Hence it is important for the population to always maintain a 'naïve' subpopulation in case of fluctuating environments. Our data indicate the presence of performance-based selection, by which only cells with a sufficiently high-energy status or cellular fitness are able to diversify.

overall_design: The transcriptome of glucose-starved and non-starved B. subtilis 168 trp+ cultures was compared using 3 biological replicates.

first: Jan-Willem

last: Veening


title: Gene expression in leaves of grapevine plants under abiotic stress conditions: heat and water

status: Public on Mar 28 2012

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

summary:
Experimental research on the effects of abiotic stress over grapevine has mainly focused on water shortage. The adaptation of plants to stress is a complex response triggered by cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues.
The variety Aragonês, used in wine production, was subjected to controlled individual abiotic stresses, WS and HS. Physiological effects were confirmed by measuring photosynthesis light curves at ambient CO2 and stepwise increasing irradiances.

overall_design: To assess physiological effects of stress treatments, light responses (A/I) curves were measured on the third fully expanded leaf from four plants per treatment and in the control, immediately after heat stress, and when Ψw was -0.9 MPa in water stress.

first: Jorg

last: Becker

first: Luisa

last: Carvalho

first: Sara

last: Amâncio

first: José

last: Zapater


title: Barley Germination and Seedling Growth Time Course

status: Public on Apr 01 2011

city: St. Louis,

first: Yong-qiang

last: An

address: 975 N. Warson Road,

department: UD Department of Agriculture

country: USA

institute: USDA-ARS-Plant Genetics Research Unit, Donald Danforth Plant Science Center

summary: Analysis of barley grains/seedlings representing six well characterized and distinct germination stages over the course of seed germination and seedling growth.

overall_design: Three biological replications, six developmental stages.

first: Lin

last: Li


title: Analysis the Ability of Producing Secondary Metabolites of Streptomyces bingchenggensis By The Genome Sequence and GeneChip DNA microarrays

status: Public on Sep 20 2011

city: Haerbin

first: zhang

last: bo

state: Heilongjiang

address: Mucai street 59#

department: Life Sciences

institute: Northeast Agricultural University

summary: Streptomyces bingchenggensis is a soil bacterium that produces a family of macrolide antibiotics, milbemycins, which is commercially important in crop protection, human and veterinary medicine. After the complete genome sequence, and annotation, for further development of our gene expression approach to biosynthesis, we have employed whole genome microarray expression profiling as a discovery platform to obtain improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how gene clusters for secondary metabolism are modulated. In the result, we confirmed the expression mil and nan gene cluster, furthermore, pks3, pks5 and nrps7, nrps8 also showed significant gene expression, but no obvious products detected. In Streptomyces bingchenggensis, there are also corresponding genes belonging to Defense mechanisms, which is much more than other Streptomyces, for the resistance of own metabolites and dealing with complex environmental factors.

first: Bo

last: Zhang

first: Yi-Jun

last: Yan

first: Wensheng

last: xiang

first: Xiangjing

last: wang

first: An

last: Jing


title: Lineage relationship in human dendritic cells - cDNA arrays

status: Public on Dec 01 2011

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

institute: The Florey Institute of Neuroscience and Mental Health

summary: The lineage relationships and fate of human blood and tissue dendritic cells (DC) has significance for a number of diseases including HIV where both blood and tissue DC may be infected. We used gene expression profiling of monocyte and DC sub-populations sorted directly from blood and skin and compared this to monocyte derived DC (MDDC) and MUTZ3 Langerhans cells (LCs) to define the lineage relationships. Hierarchical clustering analysis showed that plasmacytoid DCs formed the most discrete cluster. The ex vivo derived myeloid cells formed two separate clusters of cells derived from blood, and skin. Separate and specific DC populations could be determined within the sub-clusters. During overnight culture CD14+ dermal DCs (DDC) converted to CD1a+ expressing cells in situ consistent with origin of the CD1a+ DDC from a local precursor rather than from circulating blood DC or monocyte precursors. The in vitro derived MDDC and MUTZ3 populations grouped within the skin DC cluster and MDDCs clustered most closely to CD14+ DDC consistent with the proposed similarity between these two cell types. We identified differential expression of novel genes in particular DC subsets including genes related to DC surface receptors (including C-type lectin receptors, toll-like receptors and galectins).

overall_design: Total RNA was extracted and hybridised to 62 cDNA arrays. Dendritic cells and monocytes from human blood and skin using magnetic bead and flow cytometry based cell sorting both before and after culture for 24 hours

first: Andrew

middle: N

last: Harman

first: Chris

first: Kerrie

last: Sandgren

first: Sarah

last: Mercier

first: Najla

last: Nasr

first: Sharon

last: Lewin

first: Anthony

middle: L

last: Cunningham

first: Paul

middle: U

last: Cameron


title: Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

status: Public on Mar 24 2011

city: Corvallis

first: Robert

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control

overall_design: Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

first: J

last: Chen

first: C

last: Huang

first: L

last: Truong

last: La Du

first: S

last: Tilton

first: K

last: Waters

last: Lin

first: R

first: Q

last: Dong


title: Malawi Duplication 20091207

status: Public on Dec 09 2009

city: Portland

first: Suzy

last: Renn

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary: Metriaclima estherae, Protomelas similis, Rhamphochromis "chilingali", and Astatotilapia tweddlei genomic DNA hybridized with Astatotilapia burtoni genomic DNA

sample_organism:
Haplochromis burtoni
Protomelas similis
Maylandia estherae
Rhamphochromis sp. 'chilingali'
Haplochromis tweddlei

overall_design: 2 Metriaclima estherae vs Astatotilapia burtoni, 2 Protomelas similis vs Astatotilapia burtoni, 2 Rhamphochromis "chilingali" vs Astatotilapia burtoni, and 2 Astatotilapia tweddlei vs Astatotilapia burtoni hybs, all in balanced dye swaps

first: Renn

last: Suzy


title: Hybrid Mouse diversity Panel Liver Expression Profile

status: Public on Dec 07 2009

city: los angeles

first: brian

last: bennett

state: CA

address: Gonda

institute: UCLA-lusis lab

summary: Novel, systems-based approach to mouse genetics.

overall_design: Expression Profiles from 99 strains of inbred and recombinant inbred mice.  Most assayed in triplicate. Two of 288 chips were excluded from the final analysis due to low QC scores.

first: Brian

last: Bennett

first: Anatole

last: Ghazalpour


title: Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice [MeDIP array].

status: Public on Dec 16 2011

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

type: Methylation profiling by genome tiling array

summary: Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis.

overall_design: 29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10) and phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28). Blood was withdrawn for PK analysis and target (liver) and non-target (kidney) tissues removed, split into several sections, frozen in liquid nitrogen and stored at −80°C for subsequent analyses. Total RNA from liver and kidney was purified and processed for Affymetrix gene expression profiling while genomic DNA was prepared for promoter array based methylome analysis using the Methylated DNA immunoprecipitation (MeDIP) procedure. Remaining tissue material was used for chromatin immunoprecipitation (ChIP) to analyze histone modifications at individual promoters. Plasma samples were also collected to evaluate phenobarbital exposure in individual animals by LC-MS.

first: Harri

last: Lempiäinen

first: Arne

last: Müller

first: Sarah

last: Brasa

first: Soon-Siong

last: Teo

first: Tim-Christoph

last: Roloff

first: Laurent

last: Morawiec

first: Natasa

last: Zamurovic

first: Axel

last: Vicart

first: Enrico

last: Funhoff

first: Philippe

last: Couttet

first: Dirk

last: Schübeler

first: Olivier

last: Grenet

first: Jennifer

last: Marlowe

first: Rémi

last: Terranova