title: Time series of Methanococcus maripaludis MM901, a shift from a H2-excess condition to a H2-limiting condition

first: Sung Ho

last: Yoon

summary: Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 100 different steady-state and time course experiments that were performed in chemostats, or batch cultures, under a spectrum of environmental perturbations that modulated methanogenesis. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to inter-coordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel TFs in the regulation of phosphate-dependent repression of formate dehydorgenase a key enzyme in the methanogenesis pathway.

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

last: Pan

first: John

last: Leigh

first: Nitin

last: Baliga


title: Toxicogenomic Responses to Inorganic and Organic Mercury in Caenorhabditis elegans

status: Public on Sep 09 2013

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary: Humans are exposed to both inorganic and organic mercury.  While the toxicity of mercury is well established, much remains to be resolved about how different mercurials act at the molecular level.  To address this issue, we employed a toxicogenomics approach using the nematode C. elegans.  Using sub-, low- or high-toxic exposures of either HgCl2 or CH3HgCl the effects of these mercurials on steady-state mRNA levels for the entire genome were determined.  A total of 473 and 2,865 genes were differentially expressed in the HgCl2 and CH3HgCl treatments, respectively.  Hierarchical clustering, principal components and pattern analyses indicated that the transcriptional responses of the mercurials were unique.

overall_design: Mixed-stage C. elegans populations were exposed to 0, 2, 7.5 or 20 uM HgCl2 or 0, 0.75, 2, 7.5 uM CH3HgCl for 24 hours.  Three independent experiments were performed for each treatment condition.

first: Matthew

middle: K

last: McElwee

first: Jonathan

middle: H

last: Freedman


title: microRNA profiling of lung adenocarcinomas, induced by cRaf overexpression in lung epithelium (Agilent)

status: Public on Sep 11 2013

city: Trento

first: Valerio

last: Del Vescovo

state: Trentino Alto Adige

address: via delle Regole 101

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
In this study we analyzed the expression of miRNAs in the lungs of SP-C/c-raf transgenic mice. The transgene is under the transcriptional control of the surfactant protein C (SP-C) promoter and consists of the oncogenically activated NH2-terminal deletion mutant c-Raf-1-BxB.
Overall this study aims at identifying miRNAs regulated in precursor lesions of lung cancer.

overall_design: Agilent platform was used to analyze and compare the miRNA expression pattern in RNA extracts derived from two different conditions, i.e. lung of wild type mice and lung of SP-C/c-raf mice expressing the c-Raf-1 transgene. Each gender and condition was tested separately using 6 different individuals from each group: male and female wild type mice (M WT and F WT) and male and female transgenic mice (M c-Raf and F c-Raf).

first: Tatiana

last: Meier


title: Genome-wide transcript profiling for native porcine valvular interstitial cells and those cultured on TCPS and treated with TGF-β1

status: Public on Sep 02 2013

city: Beijing

first: Huan

last: Wang

address: Peking University Health Science Center, No. 38 Xueyuan Road, Haidian District

department: Basic Medical Sciences

country: China

institute: Peking University

summary:
Fibrotic diseases have significant health impact and have been associated with differentiation of the resident fibroblasts into myofibroblasts. In particular, stiffened extracellular matrix and TGF-β1 in fibrotic lesions have been shown to promote pathogenic myofibroblast activation and progression of fibrosis in various tissues. To better understand the roles of mechanical and chemical cues on myofibroblast differentiation and how they may crosstalk, we cultured primary valvular interstitial cells (VICs) isolated from porcine aortic valves and studied how traditional TCPS culture, which presents a non-physiologically stiff environment, and TGF-β1 affect native VIC phenotypes.
We carried out gene expression profiling using porcine genome microarrays from Affymetrix and found that traditional TCPS culture induces major changes in gene expression of native VICs, rendering these cells more activated and similar to cells treated with TGF-β1. We also monitored time-dependent effects induced by TGF-β1 by examining gene expression changes induced by TGF-β1 at 8 hours and 24 hours.

overall_design: Porcine aortic VICs were isolated and cultured with or without TGF-β1 treatment for RNA extraction and hybridization on Affymetrix microarrays. We included 3 biological replicates for each condition. P0 VICs were freshly isolated cells which had not been cultured. P2 VICs were cells that had been passaged 2 times and cultured on plastic plates in low serum media. Some of the P2 VICs were treated with TGF-β1 at 5ng/ml for 8 hours or 24 hours. All the control and TGF-β1-treated conditions were collected at the same time on day 3 of culture.

first: Leslie

last: Leinwand

first: Kristi

last: Anseth


title: Effects of hexachlorocyclopentadiene (HCCPD)

status: Public on Sep 01 2013

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary:
Sublethal effects of the flame retardant intermediate hexachlorocyclopentadiene (HCCPD) on the gene expression and protein activity of Daphnia magna
Reference sample is a composite of equal amounts of total RNA (500 ng each) from n=3 culture media controls and n=3 methanol controls

overall_design: Two-condition experiment:  controls (methanol and cell culture) and three sublethal doses of HCCPD (0.138 ug/L, 1.38 ug/L, 13.8 ug/L). Biological replicates:  3 replicates each group.

first: Melanie

last: Douville

first: Magali

last: Houde


title: miRNA expression in Blimp-1-deficient dendritic cells

status: Public on Sep 05 2013

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

country: Germany

institute: Miltenyi Biotec GmbH

summary: Expression of Blimp-1 was specifically deleted in dendritic cells (DCs) by breeding Blimp-1 flox and CD11c-CRE mice. MiRNA expression was evaluated and compared from DCs, CD4+ T cells and total B cells from spleens of control and Blimp-1 KO mice.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Age-matched (6-10 weeks old) female mice from control and Blimp-1 KO mice were sacrificed and spleens were collected. CD11chi/MHCIIhi DCs, CD4+TCRb+ T cells and B220+ B cells were sorted by FACSaria. MiRNA was measured from the total RNA preparation.

first: Sun Jung

last: Kim

first: Betty

last: Diamond


title: Expression analysis from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of 3 different substrates

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

summary:
Abstract: Proteins contribute to a major part of the organic nitrogen in forest soils. This nitrogen is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released nitrogen are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic nitrogen from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates.
Firoz Shah, Francois Rineau, Björn Canbäck, Tomas Johansson and Anders Tunlid (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus (submitted)

overall_design: A one-chip study (data from 9 subarrays collected from a 12-plex Nimblegen microarray (ID: 461228)) using total RNA recovered from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of 3 different substrates (3 replicates of each).

first: Firoz

last: Shah


title: Expression analysis from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of nitrogen (+/-NH4) to substrate followed by incubation for different periods of time

overall_design: A one-chip study (data from 12 subarrays collected from 12-plex Nimblegen microarray (IDs: 527896) using total RNA recovered from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of nitrogen (+/-NH4) to substrate followed by incubation for different periods of time (3 replicates of each).


title: Gene expression analysis of the immortalized human endothelial cell lines HMEC-1 and TIME

city: Turku

first: Johannes

last: Keuschnigg

address: Tykistökatu 6a

country: Finland

institute: University of Turku

summary: The distinction between lymphatic and blood vessels is biologically fundamental. Two immortalized cell lines, which have been widely used as models for endothelial cells of blood vascular origin, are the human microvascular endothelial cell line-1 (HMEC-1) and the telomerase-immortalized microvascular endothelial cell line (TIME). However, analysis of protein expression by flow cytometry revealed expression of lymphatic markers on these cell lines. Furthermore, functional in vitro leukocyte transmigration assays demonstrated deficiencies in several steps of the leukocyte extravasation cascade. Hence we performed this microarray analysis of the gene expression in HMEC-1 and TIME. We then compare the expression profiles to those of published blood- and lymphatic endothelial cells.

overall_design: Analysis of the gene expression profile of the immortalized human endothelial cell lines HMEC-1 and TIME to be compared to published primary blood- and lymphatic endothelial cells (see supplementary file linked below).

first: Sirkku

last: Karinen

first: Kaisa

last: Auvinen

first: Heikki

last: Irjala

first: John-Patrick

last: Mpindi

first: Olli

last: Kallioniemi

first: Sampsa

last: Hautaniemi

first: Sirpa

last: Jalkanen

first: Marko

last: Salmi


title: miRNA  profiling of gastric epithelium from Pten mutant mouse

first: Xiao

last: Yang

address: 20 Dongdajie

institute: Beijing Institute of Biotechnology

summary: Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a tumor suppressor that negatively regulates cell survival and proliferation by antagonizing phosphatidylinositol 3-kinase(PI3K)/protein kinase B(PKB/Akt) signaling. Loss of heterozygosity (LOH) of PTEN, reduced expression of PTEN and overexpression of phosphorylated Akt are frequently found in human gastric cancer, and their changes correlate with tumor progression and prognosis. Previous studies have shown that the deregulated miRNAs in human gastric cancer play important roles in gastric cancer cell proliferation, apoptosis and inflammation. However, miRNAs downstream PTEN/Akt signaling is poorly investigated. To clarify whether PTEN is involved in gastric tumorigenesis, we have generated a gastric epithelium specific PTEN knockout mouse which  exhibited gastric tumor formation with enhanced cell proliferation.So the objectives of the microarray experiment were to, a) screen miRNAs which might be regulated by PTEN/Akt signaling by comparing the miRNA expression profiles between PTEN deficient and control gastric epithelia. 2) explore the microRNA mechanism involved in gastric cell proliferation and gastric tumorigenesis.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
miRNA profiling of mouse gastric epithelium,comparing Pten mutant mouse with controls.
4 samples. Experiments in 2 different time point, 20 days and 60 days after birth, 2 Biological replicates. Mutant tissue vs. controls from mixture of 3-4 mouse.

first: Shuilong

last: Guo

first: Yan

last: Teng


title: The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus

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

overall_design: Refer to individual Series


title: Grape berry: control vs late harvest techniques (late harvest, DMR-A, DMR-B)

city: Legnaro

first: Massimiliano

last: Corso

state: Padova

address: Viale dell'Università 16

institute: University of Padova

summary: Transcriptional profiling comparing control berries (sampled at Traditional harvest, TH) with berries sampled after the application of different post-harvest techniques (late-harvest LH; double reasoned maturation-A, DMR-A; double reasoned maturation-B, DMR-B)

overall_design: Comparison of Grape berries subjected to three different post-harvest techniques (LH, DMR-A, DMR-B) versus Grape berries sampled at traditional harvest (TH). Comparisons were as follows: LH berries versus TH berries (2 biological replicates), DMR-A berries versus TH berries (2 biological replicates, only one dye-swapped), DMR-B berries versus TH berries (2 biological replicates, only one dye-swapped).

first: Fiorenza

last: Ziliotto

first: Fabio-Massimo

last: Rizzini

first: Giovanni

last: Teo

last: Cargnello

first: Claudio

last: Bonghi


title: Expression profiling of prostate cell lines by miRNA array

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Prostate cancer (PCa) is the most common malignant carcinoma that develops in men in Western countries. Up to 30% of patients continue to suffer from disease progression following radical prostatectomy. Therefore, better prognostic markers and molecular targets for cancer treatment are needed. MicroRNA (miRNA) has the potential to be used as biomarkers and as a therapeutic target for the treatment of various cancers, including PCa. Here, to determine how miRNA is involved in PCa progression, we investigated the miRNA expression profiles of 3 PCa cell lines, namely PC3, DU145, and LNCaP, and 2 normal prostate cell lines, namely  RWPE-1 and PrSc, using miRNA microarrays.

overall_design: We investigated miRNA genes that were significantly upregulated in PCa cell lines (PC3, DU145, LNCaP) compared with normal cell lines (RWPE-1, PrSc).

first: Naohito

last: Kobayashi

first: Hiroji

last: Uemura

first: Kiyotaka

last: Nagahama

first: Koji

last: Okudela

first: Mitsuko

last: Furuya

first: Yoko

last: Ino

first: Yusuke

last: Ito

first: Hisashi

last: Hirano

first: Yoshiaki

last: Inayama

first: Ichiro

last: Aoki

first: Yoji

last: Nagashima

first: Yoshinobu

last: Kubota

first: Hitoshi

last: Ishiguro


title: Measuring expression from randomly-designed DNA in S. cerevisiae

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

type: Expression profiling by genome tiling array

summary:
Here, we integrated essentially random synthetic DNA sequences into the yeast genome (HO locus) and measured the expression via custom Agilent tiling array.
The purpose of this was to compare the predictions of where transcription would occur output by our computational model to the expression observed in the cell.

overall_design:
The four constructs (A1B1, A1B2, A2B1, A2B2) were integrated into S. cerevisiae, cells were grown and from these both gDNA and mRNA were isolated. G-coupled dyes were used to label samples with Cy3 for mRNA and Cy5 for gDNA.  Samples were sheared/hydrolyzed to an average size of about 250bp, hybridized to the array, and quantified.

The GFF files include features of the region tageted for tiling array analysis in gff format (https://genome.ucsc.edu/FAQ/FAQformat.html#format3).  These include the locations of genomic features (ORFs, transcripts) as well as the locations of the inserts, and the KanMX selectable marker.

microarray_normalized_log+.wig and microarray_normalized_log-.wig include the tiling array data across each of the four inserts in wig format (https://genome.ucsc.edu/goldenPath/help/wiggle.html) for the top and bottom DNA strands, respectively.  This data are provided on a log scale and were normalized as follows:

First, we normalized the data using spacial detrending of the microarray slide. Next, we normalized the tiling array data using a background model (HUBER et al. 2006) which relates, for each probe (k), the signal intensity (yk) to the background signal (Bk) plus the amount of nucleic acid in the sample (xk) times the proportionality factor (ak), or yk=Bk+xk*ak. Here, we want to determine the amount of nucleic acid in the sample (xk). We modified this normalization protocol to take advantage of the fact that the target sequences of many probes were absent from some samples (e.g. the A1B1probe target sequences are absent from the A2B2 strain). Here, we estimated separate mRNA and gDNA background signals (Bk) for each probe by taking the median signal intensity of the probe in strains lacking the target DNA sequences. We estimated the proportionality factor for each probe (ak), corresponding to how probe intensity changes with the amount of nucleic acid, by comparing the background-normalized gDNA signal at each probe to the actual amount of gDNA present in the sample, where the target DNA was present in the sample. We estimated the amount of mRNA at each probe using this model, and scaled the amounts to the median intensity across the kanMX gene to make mRNA levels comparable across constructs. All files reference the sequences contained within the accompanying ".seq.txt" files.

Note: the coordinates in these files do not correspond to genomic coordinates as the construct was integrated into the genome (thereby altering the length of the chromosome).  However, positions  1..5001 in these files corresponds to positions 42000..47000 of chromosome 4 in the yeast genome (May, 2008 genome version) and positions 12341..20888 correspond to positions 47800..56347 of chromosome 4.

first: Harm

last: van Bakel

first: Kyle

last: Tsui

first: Joyce

last: Li

first: Quaid

middle: D

last: Morris

first: Corey

last: Nislow

first: Jack

middle: F

last: Greenblatt

first: Timothy

middle: R

last: Hughes


title: Transcription repressor HANABA TARANU (HAN) controls flower development via integrating multiple hormone actions, floral organ specification and GATA3 family auto-regulation

first: Xiaolan

last: Zhang

address: No.2 Yuanmingyuan Xi Lu Haidian District

department: Vegetable Science

institute: China Agricultural University

summary: Plant inflorescence meristems and floral meristems possess specific boundary domains that result in floral organ separation, and in proper numbers of floral organs. HANABA TARANU (HAN) encodes a boundary-expressing GATA type zinc finger transcription factor that regulates shoot apical meristem organization, cell division and flower development in Arabidopsis, but the underlying mechanism remains unclear. Through time-course whole genome oligonucleotide microarray analyses following transient overexpression of HAN, we find that HAN represses hundreds of genes, especially genes involved in hormone responses and floral organ regulation. Transient overexpression of HAN also causes the repression of HAN itself and three other HAN family genes: HANL2 (HAN-LIKE2), GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM-INVOLVED) and GNL (GNC LIKE), forming a negative regulatory feedback loop.  Double- and triple-mutant strains of han with hanl2, gnc and gnl show synergistic effects on sepal fusion, petal number, and silique length, and embryo development, as well as carpelloid stamens.  Transcripts of HANL2, GNC and GNL have similar accumulation patterns, specifically in petals, stamens, carpels and inflorescence meristems, which are partially overlapping with the expression pattern of HAN, suggesting that HAN and HAN family genes share redundant functions during flower development.  We further show by yeast two hybrid assays that HAN can homodimerize as well as heterodimerize with other HAN family proteins. Chromatin-immunoprecipitation analyses indicate that HAN directly binds to its own promoter and the promoter of GNC in vivo. These findings, together with the fact that constitutive overexpression of HAN has an even stronger phenotype than a loss of function mutation, support the hypothesis that HAN may function as a key repressor that regulates floral development via intricate regulatory networks involving genes in the GATA3 family, hormone actions and floral organ specification.

overall_design: Time course induction experiment. Arabidopsis inflorescences containing flower buds from stages 1-9 were collected for microarray experiment 0h, 4h, 12h and 72h after 10µM Dex treatment. RNA samples from mock- and Dex-treated plants at each time point were co-hybridized, and labeling dyes were swapped between replicates to reduce dye-related bias. Four biological replicates were used for the microarray hybridization.

first: Elliot

middle: M

last: Meyerowitz


title: Transcriptional Response to Nitrogen Limitation in Pelagibacter ubique

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

summary: Nitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result marine microorganisms have evolved specialized systems for responding to nitrogen stress. The highly abundant alphaproteobacterium Candidatus Pelagibacter ubique lacks the canonical GlnB, GlnD, and NtrB/NtrC genes for regulating nitrogen assimilation. A survey of 127 Alphaproteobacteria genomes found these genes to be highly represented in free-living and pathogenic organisms with large genomes and only missing in a subset of obligate intracellular organisms and other SAR11 strains. We examined global differences in mRNA and protein expression in Ca. P. ubique strain HTCC1062 during nitrogen-limited and nitrogen-replete stationary phase to understand how this thriving organism responds to nitrogen limitation. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating they devote increased resources to the assimilation of nitrogenous compounds. Enzymes for assimilating amine into glutamine (GlnA) and glutamate (AspC, GltBD) were similarly up-regulated.  Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in the control of the nitrogen starvation response. Comparisons of the transcriptome and proteome suggest that Amt is post-transcriptionally repressed during nitrogen limitation, supporting previous studies that computationally identified a novel cis-acting riboswitch upstream of this gene. These observations support the conclusion that Ca. P. ubique has an unusually simple regulatory system that enables it to increase its capacity for the uptake of nitrogenous compounds in response to nitrogen limitation.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: Batch cultures of P. ubique were grown in a defined arificial seawater media. Three cultures were given no nitrogen amendment, and three other cultures received an excess concentration of NH3. Cultures were harvested for microarray analyses during log and stationary phase for the purpose of observing differences in gene expression related to nitrogen limitation. Proteomic analysis was conducted in parallel and is available at http://omics.pnl.gov .

middle: P

first: Stephen

middle: J

last: Giovannoni


title: Expression analysis of Streptococcus mutans UA159 under Hyperosmotic stress environment

status: Public on Aug 31 2013

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary:
Oral streptococci metabolize carbohydrate to produce organic acids, which not only decrease the environmental pH, but also increase osmolality of dental plaque fluid due to tooth demineralization and consequent calcium and phosphate accumulation. Despite these unfavorable environmental changes, the bacteria continue to thrive. The aim of this study was to obtain a global view on strategies taken by Streptococcus mutans to deal with physiologically relevant elevated osmolality, and perseveres within a cariogenic dental plaque.

We investigated phenotypic change of S. mutans biofilm upon hyperosmotic challenge. We found that the hyperosmotic condition was able to initiate S. mutans biofilm dispersal by reducing both microbial content and extracellular polysaccharides matrix. We then used whole-genome microarray with quantitative RT-PCR validation to systemically investigate the underlying molecular machineries of this bacterium in response to the hyperosmotic stimuli. Among those identified 40 deferentially regulated genes, down-regulation of gtfB and comC were believed to be responsible for the observed biofilm dispersal. Further analysis of microarray data showed significant up-regulation of genes and pathways involved in carbohydrate metabolism. Specific genes involved in heat shock response and acid tolerance were also upregulated, indicating potential cross-talk between hyperosmotic and other environmental stress.

Hyperosmotic condition induces significant stress response on S. mutans at both phenotypic and transcriptomic levels. In the meantime, it may take full advantage of these environmental stimuli to better fit the fluctuating environments within oral cavity, and thus emerges as numeric-predominant bacterium under cariogenic conditions.

overall_design: A six-chip study using total RNA recovered from mid-logarithmic phase of S. mutans UA159 from three separate cultures of strains submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl) and three separate cultures of strains kept under no stress condition.

first: Chengcheng

last: Liu


title: Comparison of the expression profiles of 630E strain and a sigD mutant after 6h of growth.

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. difficile 630E strain vs a sigD mutant after 6h of growth in BHI

overall_design: Two-conditions experiments, 630E strain 6h vs sigD mutant 6h, 4 biological replicates for each condition

first: Imane

last: El Meouche

first: Marc

last: Monot


title: Regulation of sialidase production in clostridium perfringens by the orphan sensor histidine kinase ReeS

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

summary: ReeS, previously named as CPE1512, was originally annotated as the only hybrid sensor histidine kinase/response regulator in Clostridium perfringens.  Further evidence suggests that ReeS is more likely to function as an orphan sensor histidine kinase.  A reeS deletion mutant was constructed and the transcriptome analysed using microarrays.

overall_design: Total RNA was isolated from the reeS mutant and the wild-type control cells during exponential phase growth.  Gene expression levels were compared between the reeS mutant and wild-type strain 13

first: Thomas

last: Hiscox

first: Paul

last: Harrison

first: Anjana

last: Chakravorty

first: Jocelyn

last: Choo

first: Kaori

last: Ohtani

first: Tohru

last: Shimizu

first: Jackie

last: Cheung


title: Wnt signaling pathway gene expression profile in SW480 cells with/without hiNOS overexpression

status: Public on Aug 20 2013

city: Pittsburgh

first: David

middle: A.

last: Geller

state: Pennsylvania

address: 200 Lothrop St. BST W1507

department: Surgery

institute: University of Pittsburgh

summary: Wnt signaling plays important roles in development and cancer. We found hiNOS is a wnt target gene. We tried to clarify the role of the so far iNOS in Wnt signaling in colorectal cancer.

overall_design:
We performed SuperArray limited gene array analysis of SW480 cells with/without hiNOS overexpression. Oligo GEArray expression array systems (cat#OHS-043) SuperArray, Bethesda, MD) consisted of spotted cDNA fragments encoding 114 genes involved in and downstream of Wnt signaling. Control sequences (PUC18, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and β-actin) were also included. These Superarrays were employed to compare wnt signaling genes expression between with iNOS and without iNOS.
Total RNA was isolated by Trizol (Invitrogen) and processed for microarray hybridization following the manufacturer’s instructions. Arrays were visualized by autoradiography, and hybridization signals were scanned and analyzed for density in GEArray Expression Analysis Suite 2.0. The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, and β-actin. To obtain a gene profile, analysis was performed on three separate RNA samples isolated from different SW480 cells, with replicate assays conducted on each RNA preparation.

middle: A

first: Qiang

last: Du


title: Diversity of antibody responses to Borrelia burgdorferi in experimentally-infected beagle dogs

status: Public on Aug 22 2013

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

summary: Lyme borreliosis (LB) is a common infection of domestic dogs in areas where there is enzootic transmission of the agent Borrelia burgdorferi.  Immunodiagnostic assays for canine antibodies to B. burgdorferi are usually based on whole-cell preparations as substrate and, consequently, interpretation of results is confounded by antibody cross-reactivity between borrelial antigens and those of other bacterial species.  To more broadly characterize the antibody responses to B. burgdorferi infection and to assess the diversity in those responses between individual dogs, we examined sera from 32 adult, colony-bred beagle dogs that were experimentally infected with B. burgdorferi through tick bites and compared those on a protein microarray with sera from uninfected dogs in their antibody reactivities to various recombinant chromosome- and plasmid-encoded B. burgdorferi proteins, including 24 of the serotype-defining OspC proteins of North America.  The profiles of immunogenic proteins for the dogs were largely similar to those for humans and natural reservoir rodents.  These included the decorin-binding protein DbpB, BBA36, BBA57, BBA64, fibronectin-binding protein BBK32, VlsE, FlaB and other flagellar structural proteins, Erp proteins, Bdr proteins, and all of the OspC proteins.  In addition, the canine sera bound to the presumptive lipoproteins BBB14 and BB0844, which infrequently elicited antibodies in humans or rodents.  Although the beagle, like most other domestic dog breeds, has a small effective population size and features extensive linkage disequilibrium, the group of animals here demonstrated diversity in antibody responses by measures of antibody levels and specificities for conserved proteins, like DbpB, and polymorphic ones, like OspC.

overall_design: Antibody profiling was performed on sera from dogs experimentally-infected with B. burgdorferi and unexposed controls against antigens of B. burgdorferi. Thirty-two serum samples from experimental infections, and 4 unexposed controls were probed on a protein microarray displaying 24 OspC proteins of B. burgdorferi .

first: Deborah

last: Grosenbaugh

first: Alan

last: Barbour


title: Comparison of gene expression profiles between N2 wild-type C. elegans and an nhr-8(hd117) mutant

status: Public on Aug 06 2013

city: Cologne

first: Daniel

last: Magner

address: Joseph-Stelzmann-Str. 9b

institute: Max Planck Institute for Biology of Aging

summary: Transcriptional profiling of N2 vs. nhr-8 mutant worms, aiming to identify direct and indirect targets of the nuclear receptor.

overall_design: Seven independent synchronized populations of N2 and nhr-8(hd117) animals were grown from eggs on low cholesterol plates at 25 degrees C until mid-L3 larval stage and collected for microarray RNA expression analysis.

middle: B

first: Adam

last: Antebi


title: Thermotoga maritima transcription during exponential and stationary phase growth on 1 and 5 g/l yeast extract

status: Public on Aug 28 2013

city: Raleigh

first: Andrew

last: Frock

address: 840 Main Campus Drive, Partners II, Room 3304

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Although proteins and peptides encoded in small open reading frames (ORFs < 100 AA) in microbial genomes can play critical roles as toxins, bacteriocins, transcriptional regulators, signaling molecules, and chaperones, many such ORFs remain annotated as “hypothetical proteins”. In the genome of the hyperthermophilic bacterium, Thermotoga maritima, nearly 2/3 of the 167 small ORFs have no known function. As a strategy for investigating the potential significance of specific small ORFs, growth conditions that could trigger the expression of genes encoding small ORFs were sought. A defined medium supplemented with either 1 or 5 g/L yeast extract was used to track transcriptional response during the transition from exponential to stationary phase.

platform_organism:
Thermotoga maritima
Thermotoga neapolitana
Thermotoga petrophila
Thermotoga sp. RQ2

overall_design: RNA derived from exponential (1E) and stationary (1S) phase cultures grown on 1 g/l yeast extract was compared to RNA derived from exponential (5E) and stationary (5S) phase cultures grown on 5 g/l yeast extract using a four-slide loop design.

first: Clemente

last: Montero

first: Sara

middle: E

last: Blumer-Schuette

first: Robert

last: Kelly


title: Transcriptional profiling of Neurospora crassa conidia undergoing a time-course: Δpp-1 vs WT

status: Public on Aug 09 2013

city: Berkeley

first: Abby

last: Leeder

address: 111 Koshland Hall

institute: UC Berkeley

summary: To study the consequences of transcription factor pp-1 deletion during vegetative cell fusion, we performed whole genome microarrays of WT and Δpp-1 conidia during their initial growth period (3h - 8h).

overall_design: The WT (FGSC2489) and Δpp1 strains were analyzed at five different timepoints. Cy3 and Cy5 dye swaps were performed.

first: Abigail

middle: C

first: Wilfried

last: Jonkers

first: Jingyi

last: Li

first: Monika

last: Fisher

first: N

middle: L

last: Glass


title: Alterations in miRNA levels in the dentate gyrus in epileptic rats

status: Public on Aug 14 2013

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences

summary: Analysis of the dentate gyrus of amygdala electrical stimulation model of temporal lobe epilepsy. Results provide insight into the molecular mechanism underlying epileptogenesis.

overall_design: This study was designed to estimate changes in miRNA expression levels after 7, 14, 30 and 90 days after electrical stimulation of amygdala as a model of temporal lobe epilepsy. The advantage of this study is time matched control (sham operated animals sacrificed at the same age as stimulated animals).

first: Anna

last: Bot

first: Konrad

last: Debski


title: miRNA Expression in Early Porcine Pregnancy

status: Public on Aug 01 2013

city: Hamilton

first: Jocelyn

last: Wessels

state: Ontario

address: 1280 Main Street West

department: Obstetrics and Gynecology

country: Canada

institute: McMaster University

summary: This study examined the expression of pig-specific microRNAs (miRNAs) at gestation day 20 (gd20) of pregnancy in Yorkshire sows. Tissue differences in miRNA expression, and miRNA differences between healthy and arresting embryo attachment sites (i.e., healthy endometrium vs. arresting endometrium; healthy trophoblast vs. arresting trophoblast), were of prime interest. For more information, please refer to the primary research paper.

overall_design: Paired endometrium and trophoblast samples were collected at gestation day 20 from two conceptus attachement sites (1 healthy, 1 arresting) per sow (n=3). Endometrial samples were collected from four non-pregnant sows at mid-estrus.

middle: K

last: Edwards

first: Kasra

last: Khalaj

first: Rami

middle: T

last: Kridli

first: Mallikarjun

last: Bidarimath

first: Chandrakant

last: Tayade


title: Zebrafish transcriptomics in 24 and 36 hpf embryos after knockdown of glucocorticoid receptor translation

city: Waterloo

first: Matt

last: Vijayan

address: 200 University Avenue W

institute: University of Waterloo

summary: To further characterize the roles  of cortisol signaling via the glucocorticoid receptor (GR) in developing zebrafish, we have used morpholino oligonucleotides to knockdown GR protein translation and measured gene expression in RNA extracted from 24 and 36 hours post fertilization (hpf) embryos. The GR morpholino was characterized previously in Nesan et al., 2012, Endocrinology 181, 35-44)

overall_design: Single-cell zebrafish embryos were microinjected with either active morpholino or mispair control. Embryos were frozen at 24 and 36 hpf and total RNA extracted for microarray analysis. Three independent replicates (different breeding events on separate days) were performed for each treatment per timepoint.

first: Dinushan

last: Nesan

first: Mathilakath


title: Gene expression profiling of zebrafish embryos at 5 days post fertilization [Agilent Arrays]

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes.

overall_design: This microarray study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28°C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.  The samples were analyzed in a technical duplicate using a dye swap experiment in order to check for dye bias.

first: H

first: Ron

last: Dirks

first: Annemarie

last: Meijer

first: Wouter

last: Veneman


title: Melita plumulosa toxicant response: What is contaminant mode of action?

status: Public on Jul 11 2013

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

summary: The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to eight different contaminants for 48 hours.

overall_design: RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals.  Each treatment was replicated 5 times.  Alternate arrays were dye swapped.  Data are presented (exposed/unexposed).

first: Hannah

last: Osborn

first: David

last: Spadaro

first: Stuart

last: Simpson


title: Morphine induced sepsis is mediated by abrogation of endotoxin tolerance through modulation of miR-146a, but not miR-155.

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: Endotoxin/LPS tolerance is a tightly regulated phenomenon, which, during infection, prevents systemic hyper-inflammation. Here we report for the first time that morphine reversal of endotoxin tolerance resulting in persistent inflammation thus contributing to septicemia and septic shock. We further report that this regulation is mediated by LPS-induced down-regulation of microRNAs 146a and 155. However, only over-expression of miR-146a, but not miR-155 abrogates morphine mediated hyper-inflammation, while antagonizing miR-146a (but not miR-155) augments morphine mediated hyper-inflammation. Hence, miR-146a could be the potential therapeutic target for morphine-mediated abrogation of endotoxin tolerance.

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

overall_design: All treatments done in vivo. Morphine implanted subcuteniously, LPS administered as intraperitoneal injection.

first: Sabita

last: Roy

first: Anitha

last: Krishnan

first: Sundaram

last: Ramakrishnan

first: Xiaoxiao

last: Zhang


title: The role of Dichaete in transcriptional regulation the of Drosophila midline [prosGal4]

status: Public on Jul 22 2013

first: Steve

last: Russell

address: Tennis Court Road

department: Genetics

country: United Kingdom

institute: University of Cambridge

summary: Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, specifically looking at targets in the midline using dominant negative constructs expressed via the UAS/Gal4 system, using prosGal4 to drive expression in developing neuroblasts.

overall_design: 4 independent biological replicates. 3.5-4.5h old embryos were collected, and the RNA was extracted using Trizol. The UAS-dominant negative construct expressing embryos were compared to UAS-GFP expressing controls. Construct expression was driven using prosGal4.

first: Jelena

last: Aleksic

first: Bettina

last: Fischer


title: The role of Dichaete in transcriptional regulation of Drosophila embryogenesis

summary: Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, by looking at the disruption of gene expression in Dichaete mutants.

overall_design: Stage 10-11 embryos (5 and 7.5 hours after egg laying) from a cross between Dr72/TM3, twi-GAL4 UAS-Gfp Dr513/TM3, twi-GAL4 UAS-Gfp, were hand picked under a fluorescence dissecting microscope.  GFP negative homozygous Dichaete mutant embryos and their heterozygous single GFP positive siblings were collected and approximately 150 embryos per sample were stored frozen in Trizol


title: Grazing-induced expression of seaweed genes

status: Public on Jun 19 2013

city: Bremerhaven

first: Carla

last: Flöthe

address: Am Handelshafen 12

institute: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

summary: The aim of this study was to elucidate which changes in gene expression are related to the induced anti-herbivory response in the brown seaweed Fucus vesiculosus. Microarray hybridizations were used to identify genes differentially expressed in response to grazing by the isopod Idotea baltica. This study shows that modifications in gene expression occur simultaneously to a reduced palatability and that defence induction entails reallocation of resources from primary to secondary metabolism with down-regulation of photosynthesis and degradation of storage compounds.

overall_design: Total RNA of Fucus vesiculosus pieces that were or were not previously grazed by Idotea baltica for 15 and 18 days (3 biological replicates each) was hybridized against pooled RNA from 4 F. vesiculosus pieces that were collected before onset of grazing (day 0).

first: Markus

last: Molis

first: Inken

last: Kruse

first: Florian

last: Weinberger

first: Uwe

last: John


title: MicroRNA-gene expression network in murine liver during Schistosoma japonicum infection

status: Public on Jun 12 2013

city: Beijing

first: Pengfei

last: Cai

address: #9 Dong Dan San Tiao

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences

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

summary: Schistosomiasis japonica remains a significant public health problem in China and Southeast Asian countries. The most typical and serious outcome of the chronic oriental schistosomiasis is the progressive granuloma and fibrosis in the host liver, which has been a major medical challenge. However, the molecular mechanisms that underlie the hepatic pathogenesis induced by schistosomal egg deposition have not yet been well-defined. Using microarrays, we quantified the temporal gene expression profiles in the liver of Schistosoma japonicum-infected BALB/c mice at day 15, 30, and 45 post infection (pi) with that from uninfected mice as controls. Meanwhile, microRNA expression profiles from the same samples were decoded by parallel solexa sequencing. Gene expression alternation associated with liver damage was observed even at early stage of infection (e.g., pi 15), which became more magnificent onset of egg deposition within the liver tissue. Up-regulated genes were dominantly associated with inflammatory infiltration of liver during S. japonicum infection, whereas down-regulated genes primarily led to the hepatic functional disorders. More than 130 miRNAs were differentially expressed during S. japonicum infection, and dynamic miRNA-gene co-expression network has been constructed during the development of hepatic pathology.

overall_design: A four chip study using total RNA recovered from liver tissues of BALB/c mice which were percutaneously infected with 30 ± 2 cercariae of S. japonicum at day 0, 15, 30, and 45 post infection, respectively.

first: Qijun

last: Chen


title: ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes (ChIP-Chip)

status: Public on Jul 01 2013

city: Chapel Hill

first: Julian

last: Rozenberg

address: Brinkhous-Bullitt Bldg., CB#7525

department: Pathology and Lab Medicine

institute: University Of North Carolina

type: Genome binding/occupancy profiling by genome tiling array

summary:
Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation
Chromatin immunoprecipitation (ChIP) of RNAP II, CREB C/EBPb and cJun in undifferentiated or differentiated keratinocytes demonstrate recruitment of RNAP II to promoters bound by combination of specific transcription factors

overall_design: comparison of undifferentiated and differentated keratinocytes

last: Rozenbereg

first: Charles

last: Vinson


title: Influence of growth rate and methanogenic partner on syntrophic metabolism of Desulfovibrio G20 (comparative transcriptional analysis of Desulfovibrio G20 grown under various syntrophic conditions relative to respiratory growth)

status: Public on May 02 2013

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

summary: Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis or Methanospirillum hungatei in chemostats at a low growth rate of 0.027h-1.

overall_design: 7 samples of Desulfovibrio alaskensis strain G20 grown in syntrophic coculture on lactate with either Methanococcus maripaludis (4 replicates) or Methanospirillum hungatei (3 replicates), and 5 samples of sulfate-limited monoculture growth of strain G20 on lactate.

first: Birte

last: Meyer

first: Adam

last: Deutschbauer

last: Arkin

first: David

last: Stahl


status: Public on Apr 30 2013

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

institute: Lund University

summary:
Abstract: A large part of the nitrogen in forest soils is found in recalcitrant organic matter-protein complexes. Ectomycorrhizal fungi are thought to have a key role in the decomposition and mobilization of nitrogen from such complexes. The knowledge on the functional mechanisms of these processes, and how they are regulated by carbon from the host plant and the availability of more easily available forms of nitrogen sources are limited. We used spectroscopic analyses and transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus. Amendments of glucose triggered the assimilation of nitrogen and the decomposition of the litter material. Concomitantly, the expression of genes encoding enzymes involved in oxidative (i.e. Fenton chemistry) degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism were upregulated in concert. Addition of ammonium had minute effects on both the expression of transcripts and decomposition of litter material, and only when glucose was present. Based on the spectroscopic analyses, three major types of chemical modifications of the litter material were observed. Each of them was correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggests that the expression of the decomposition and nitrogen assimilation machinery of ectomycorrhizal fungi can be firmly regulated by the host carbon supply, i.e. priming, and that the availability of inorganic nitrogen as such has limited effects on the saprotrophic activities.
Rineau F, Shah F., Smits M.M., Persson P., Johansson T., Carleer R., Troein C., Tunlid A. (2013) Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus (submitted)

overall_design:
A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 467991) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of various soil-derived substrates.
Transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus.

first: Anders

last: Tunlid


title: Transcriptome analysis of MENX‑associated rat pituitary adenomas identifies novel molecular mechanisms involved in the pathogenesis of human pituitary gonadotroph adenomas

status: Public on Jul 10 2013

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Gonadotroph adenomas comprise 15–40 % of all pituitary tumors, are usually non-functioning and are often large and invasive at presentation. Surgery is the first-choice treatment, but complete resection is not always achieved, leading to high recurrence rates. As gonadotroph adenomas poorly respond to conventional pharmacological therapies, novel treatment strategies are needed. Their identification has been hampered by our incomplete understanding of the molecular pathogenesis of these tumors. Recently, we dem¬onstrated that MENX-affected rats develop gonadotroph adenomas closely resembling their human counterparts. To discover new genes/pathways involved in gonadotroph cells  tumorigenesis, we performed transcriptome profiling of rat tumors versus normal pituitary. Adenomas showed overrep¬resentation of genes involved in cell cycle, development, cell differentiation/proliferation, and lipid metabolism. Bioinfor¬matic analysis identified downstream targets of the transcrip¬tion factor SF-1 as being up-regulated in rat (and human) adenomas. Meta-analyses demonstrated remarkable similari¬ties between gonadotroph adenomas in rats and humans, and highlighted common dysregulated genes, several of which were not previously implicated in pituitary tumorigenesis. Two such genes, CYP11A1 and NUSAP1, were analyzed in 39 human gonadotroph adenomas by qRT-PCR and found to be up-regulated in 77 and 95 % of cases, respectively. Immunohistochemistry detected high P450scc (encoded by CYP11A1) and NuSAP expression in 18 human gonado¬troph tumors. In vitro studies demonstrated for the first time that Cyp11a1 is a target of SF-1 in gonadotroph cells and promotes proliferation/survival of rat pituitary adenoma pri¬mary cells and cell lines. Our studies reveal clues about the molecular mechanisms driving rat and human gonadotroph adenomas development, and may help identify previously unexplored biomarkers for clinical use.

overall_design: We compared five control animals and 16 homozygous mutants (p27Kip1/Cdknb1)

first: Ilaria

last: Marinoni

first: Martin

last: Irmler

first: Misu

last: Lee

first: Natalia

last: Pellegata


title: Transcriptomic profiling of Campylobacter jejuni strains: IA3902 vs NCTC11168

status: Public on Mar 29 2013

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

summary: A highly pathogenic Campylobacter jejuni clone has recently emerged as the major cause of Campylobacter-associated sheep abortion in the U.S. and is also associated with foodborne gastroenteritis in humans. A distinct phenotype of this clone is its ability to induce bacteremia and abortion. To facilitate understanding the pathogenic mechanisms of this hyper virulent clone,  the differences in global gene expression patterns between this hyper virulent clone (IA3902) and a non-abortifacient strain (NCTC 11168) were compared by DNA microarray.

overall_design: One-condition experiment,  IA3902 vs NCTC11168. Biological replicates: 3 IA3902 , 3 NCTC11168. One replicate per array.

first: Zuowei

first: Peng

last: Liu

first: Zhangqi

last: Shen

first: Orhan

last: Sahin

first: Qijing

last: Zhang


title: Transcriptional profiling of Neurospora crassa cells containing MAK2Q100G allele: Exposure to ATP-analog (1NM-PP1) vs control

status: Public on Jun 01 2013

first: Abby

last: Leeder

summary: To study the consequences of MAK-2 activity modulation during vegetative cell fusion, we took advantage of a previously constructed allele of MAK-2 (MAK-2Q100G) to specifically perturb kinase signaling during germling vegetative cell fusion (inhibition of MAK-2Q100G activity by addition of the ATP analog 1NM-PP1 results in a phenotype indistinguishable from mak-2 deletion strains). Whole genome microarrays of mak-2Q100G cells following 20 min 1NM-PP1 treatment were performed.

overall_design: Two-condition experiment, Neurospora crassa cells containing MAK2Q100G allele treated with 1NM-PP1 inhibitor vs untreated control. Cy3 and Cy5 dye swaps were performed.

first: Abigail

first: Wilfried

last: Jonkers

first: Jingyi

last: Li

first: Monika

last: Fisher

first: N

last: Glass


title: Transcriptome profiling of the basal region of poplar stems during the early gravitropic response

status: Public on Apr 12 2013

city: Tunis

first: Wassim

last: Azri

address: Campus universitaire

country: Tunisia

institute: Biology

summary: Young poplar stems show a preponderantly primary growth in the top internodes and differential cambium activity in the basal internodes after inclination with some tension wood formed after 45 min. This study was conducted in order to characterize the early changes in gene expression during early stages of the gravitropic response in the poplar.

platform_organism:
Populus trichocarpa x Populus deltoides
Populus tremula x Populus alba

overall_design: Hybridizations were performed to compare gravistimulated poplar stems (basal region) after 45 min of inclination and untreated control stems. Two biological replicates were done. Two hybridizations with a dye swap for each tree pair were done, making a total of four hybridizations.


title: Transcriptional dynamics elicited by a short pulse of Notch activation.

status: Public on Dec 31 2012

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

summary: Cellular responses to signalling pathways are often highly dynamic, however most analyses of developmental signalling pathways focus on a single endpoint. Here we have analyzed the temporal changes in transcription following a short Notch activation treatment and have related these to the recruitment of the Notch pathway transcription factor, CSL [Suppressor of Hairless, Su(H), in Drosophila], and to the state of RNA Polymerase II (Pol II) binding. A total of 154 genes showed significant differential expression over time and their expression profiles stratified into 14 clusters based on temporal and quantitative differences in their responses. These differences were partially reflected in the profiles of Pol II and Su(H) binding. However neither could fully account for the different response profiles. Furthermore, the timing of the different responses was unaffected by more prolonged Notch activation. Instead our data suggest that regulatory relationships between genes that segregate into different response clusters can partially account for the stratification. Thus feed-forward repression, where products of early responding Enhancer of split bHLH genes (E(spl)bHLH) inhibit expression of endogenous repressors, is one mechanism that explains the profile of genes that exhibit delayed up-regulation. E(spl)bHLH genes may therefore be responsible for co-ordinating the Notch response of a wide spectrum of other targets, explaining their critical functions in many developmental and disease contexts.

overall_design: DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols. Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. The cells were stimulated for 5 minutes before washing out EDTA using normal culture media. The cells were then collected at 18 time points at 0’, 5’, 10’, 15’, 20’, 25’, 30’, 35’, 40’, 50’, 60’, 70’, 80’, 90’, 100’, 110’, 120’ and 150’ after stimulation in 4 independent time trials. For control samples, for each time trial, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples and then collected at equivalent times. For each trial 50 µg of the untreated control RNA sample of each time point was pooled to create a trial specific reference sample. Samples from trials #1 and #3 were labelled with Cy5 and trails #2 and #4 as dye-swap with Cy3.

first: Ben

last: Housden

first: Audrey

middle: Q

last: Fu

first: Alena

last: Krejci

first: Fred

last: Bernard

first: Bettina

last: Fischer

first: Simon

last: Tavaré

first: Steven

last: Russell


title: Gene expression profiling for 2 cell samples

status: Public on Dec 15 2012

city: shanghai

first: fang

last: ke

address: road chongqing 280

institute: shanghai jiao tong tong university

summary: Mesenchymal stem cells (MSCs) exhibit immunosuppressive properties. However the homing mechanisms underlying MSC trafficking to target tissues remain elusive. Here we report that skin-derived MSCs (S-MSCs) secrete high levels of interleukin-6 (IL-6), inhibit T helper (Th)1- and Th17-cell differentiation, and possess IL-6-dependent immunomodulatory capacity in inflammatory microenvironment. Disruption of the il6 locus or its signaling transducer gp130 blocks voltage-operated calcium (Ca2+) channels (VOCC) critically required for cell contraction involved in the sequential adhesion and de-adhesion events during S-MSC migration. IL-6 directly regulates CaV2.3 encoded by cacna1e of R-type Ca2+ channels through the JAK3/STAT3 signaling pathway. Deletion of il6 or silencing CaV2.3 gene expression leads to a severe defect in S-MSC’s homing and immunosuppressive function in vivo. Thus, this unexpected requirement of autocrine IL-6 for activating CaV2.3 Ca2+ channels uncovers a previously unrecognized link between IL-6 signaling and the VOCC, and provides novel mechanistic insights for the immunomodulatory activities of S-MSCs.

overall_design: A two chip study using total RNA recovered from three mixed S-MSCs derived from WT mice and three mixed S-MSCs derived from IL6KO mice.

first: Honglin

last: Wang

first: Fang

last: Ke


title: Mammary carcinomas in WAP-SV40 transgenic mice [gene expression]

status: Public on Oct 31 2012

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: Transgenic expression in mice of two synergistically acting SV40 early region encoded proteins, large (LT) and small (sT) tumor antigens, in the mammary epithelium recapitulates loss of p53 and Rb function and deregulation of PP2A-controlled mitogenic pathways in human breast cancer. In primiparous mice, WAP-promoter driven expression of SV40 proteins induces well and poorly differentiated mammary adenocarcinomas. We performed a correlative aCGH and gene expression analysis of 25 monofocal tumors, representing four histopathological grades, to explore the molecular traits of SV40-induced mammary tumors and to emphasize the relevance of this tumor model for human breast tumorigenesis.

overall_design: Gene expression analysis of 25 mammary carcinoma samples of two different WAP-SV40 mouse lines, T1 and NP8. Three involuted mammary gland tissues were included in the study as reference samples.

first: Genrich

last: Tolstonog

first: Benjamin

last: Otto

first: Wolfgang

last: Deppert


title: Expression analysis of Tim-3 knockdown RAW264.7 cell

status: Public on Dec 05 2012

first: Gencheng

last: HAN

address: 27 Taiping Road, Haidian District

department: Department of Immunology

institute: Beijing Institute of Basic Medical Sciences

summary:
Investigation of whole genome gene expression level changes in a Tim-3 knockdown RAW264.7 cell, compared to control siRNA transfected RAW264.7 cell. The Tim-3 knockdown of this cell render it hyper-reactive to TLR stimulation.
Tim-3 knockdown analyzed in this study are further described in Li Y, Feng J, Geng S, Geng S, Wei H, Chen G, Li X, Wang L, Wang R, Peng H, Han G, Shen B, Li Y.  2011. The N- and C-terminal carbohydrate recognition domains of galectin-9 contribute differently to its multiple functions in innate immunity and adaptive immunity. Mol Immunol. 48(4):670-7. (PID 21146220)

overall_design: A six chip study using total RNA recovered from Tim-3 knockdown and control RAW264.7 cells. There are 135,000 probes in a chip,each chip measures the expression level of 27526 genes of mouse from Nimblegen. Fold-change screening between the two groups obtained from the experiment. The threshold used to screen up or down regulated genes is Fold change＞＝2.0

first: Yunbin

last: Zhang

first: Xiaona

last: Xu


title: Hypoxia transcriptomic time-series data in three different cancer cell lines

status: Public on Oct 12 2012

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Tumour hypoxia exhibits a highly dynamic spatial and temporal distribution and is associated with increased malignancy and poor prognosis.
Assessment of time-dependent gene-expression changes in response to hypoxia may thus provide additional biological insights and help with patient prognosis.

overall_design: Transcriptome profiling was performed for 3 cell lines derived from diverse tumour-types after hypoxic exposure at 8 time-points.

first: M

middle: H

last: Starmans

first: K

first: S

last: Haider

first: A

last: Kasprzyk

first: R

last: Seigneuric

middle: G

last: Magagnin

last: Koritzinski

first: P

last: Boutros

first: B

last: Wouters

last: Lambin


title: Modulation of primary cell function of host Pseudomonas bacteria by conjugative plasmid pCAR1

status: Public on Dec 25 2012

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Impacts of plasmid carriage on its host cell were comprehensively analyzed using conjugative plasmid pCAR1 in the three different kinds of hosts, Pseudomonas putida KT2440, P. aeruginosa PAO1, and P. fluorescens Pf0-1. Various analyses of the host phenotype showed that pCAR1 carriage reduced host fitness, swimming motility, and resistances to osmotic- or pH-stress, and brought about the alterations of primary metabolic capacities in the TCA cycle or those several steps away from the TCA cycle in the host cells. Growth phase-dependent transcriptome analyses were performed with the classification of the annotated genes based on their identities among the three hosts and their putative functions. pCAR1 carriage affected host transcriptome more greatly at the transition and stationary phases in each host. The transcriptome responses were more similar between KT2440 and PAO1 than between other host combinations, and many genes, such as for ribosomal proteins, F-type ATPase, and RNAP core, in both strains were commonly not suppressed in their stationary phases. These responses may have resulted in the reduction of host fitness, motility, and stress resistances. Host-specific responses to plasmid carriage were transcriptional changes of genes on putative prophage or foreign DNA regions. The extent of the impacts in host phenotypes and transcriptomes was similarly the largest in KT2440 and the lowest in Pf0-1. The host alterations controlled by pCAR1 carriage are important for understanding the fate of the plasmid and its host, plasmid maintenance, expression of plasmid genes, the host cell physiology, and host survivability in the environment.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas fluorescens
Pseudomonas putida

platform_organism:
Pseudomonas
Pseudomonas putida KT2440
Pseudomonas fluorescens Pf0-1
Pseudomonas aeruginosa PAO1

overall_design:
The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring KT2440 and non-pCAR1 harboring KT2440 were compared.
The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring PAO1 and non-pCAR1 harboring PAO1 were compared.
The growth-dependent change of chromosomal RNA maps from exponential to early stationary phases of pCAR1-harboring Pf0-1 and non-pCAR1 harboring Pf0-1 were compared.
The growth-dependent change of RNA maps from exponential to early stationary phases of plasmid pCAR1possessed by 3 kinds of hosts were compared.

first: Yurika

last: Takahashi

first: Masaki

last: Shintani

first: Noriyuki

last: Takase

first: Yuka

last: Kazou

first: Fujio

last: Kawamura

first: Hirofumi

last: Hara

first: Hiromi

last: Nishida

first: Hisakazu

last: Yamane


title: Spermatozoal mRNA is reproducibly detected in purified D. melanogaster sperm.

status: Public on Apr 24 2012

first: Bettina

last: Fischer

department: Systems Biology Centre

institute: Unversity of Cambridge

summary: It is now well established that mature mammalian spermatozoa carry a population of mRNA molecules, at least some of which are transferred to the oocyte at fertilisation.  However, the function of the sperm transcriptome remains largely unclear.  To shed light on the evolutionary conservation of this feature of sperm biology, we analysed highly purified populations of mature sperm from the fruitfly, Drosophila melanogaster.  As with mammalian sperm, we found a consistently enriched population of mRNA molecules that are not likely to be derived from contaminating somatic cells or immature sperm.  Using tagged transcripts for three of the spermatozoal mRNAs, we demonstrate that they are transferred to the oocyte at fertilisation and can be detected at least until the onset of zygotic gene expression.  We find a remarkable conservation in the functional annotations associated with fly and human spermatozoal mRNAs, in particular a highly significant enrichment for transcripts encoding Ribosomal Proteins.  The identification of a conserved set of spermatozoal transcripts opens the possibility of using the power of Drosophila genetics to address the function of this enigmatic class of molecules.

overall_design: RNA extracted from three biological replicates of purified sperm (Sperm rep1, Sperm rep2 and Sperm rep3) was used as a template for oligo-dT-primed reverse transcription, amplification, labelling of dye swapped technical replicates and hybridisation to long oligonucleotides microarrays. As a control, RNA from two biological replicates of dissected adult testis plus accessory glands (Testis_rep1, Testis_rep2) was amplified, labelled (dye-swap technical replicate) and hybridised to similar arrays. To help with the spot-finding of the arrays genomic DNA was co-hybridised in some cases (this genomic DNA data was excluded from further analysis). Genes with an intensity level below 200 in at least one channel across the Sperm or Testis set were removed (5579 transcripts present in all three sperm replicates, 5358 transcripts from the testis/accessory gland samples and 4295 transcripts common to both data sets). Then the quantile normalisation was independently applied to the Sperm replicate samples and Testis replicates.

first: Elizabeth

last: Wasbrough

first: Lisa

last: Meadows

first: Owen

last: Randlet

first: Steve

last: Dorus

first: Timothy

last: Karr

first: Steven

last: Russell


title: miRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus

status: Public on Jul 03 2012

city: Seattle

first: Mei

last: Xu

address: 1959 NE Pacific ave N

institute: University of Washington

summary: The distinct phenotypic and prognostic subclasses of human hepatocellular carcinoma (HCC) are difficult to reproduce in animal experiments.  Here we have used in vivo gene targeting to insert an enhancer-promoter element at an imprinted chromosome 12 locus in mice, thereby converting ~1 in 20,000 normal hepatocytes into a focus of HCC with a single genetic modification.   A 300 kb chromosomal domain containing multiple mRNAs, snoRNAs and microRNAs was activated surrounding the integration site.   An identical domain was activated at the syntenic locus in a specific molecular subclass of spontaneous human HCCs with a similar histological phenotype, which was associated with partial loss of DNA methylation.   These findings demonstrate the accuracy of in vivo gene targeting in modeling human cancer, and suggest future applications in studying various tumors in diverse animal species.  In addition, similar insertion events produced by randomly integrating vectors could be a concern for liver-directed human gene therapy.

overall_design: Three individual liver tumor samples and their adjacent normal-looking liver tissue were used for miRNA array analysis

first: Pei-Rong

last: Wang

first: Sara

last: Toffanin

first: Yi

last: Li

first: Josep

middle: M

last: Llovet

first: David

middle: W


title: Long oligo- and cDNA-based microarray gene expression in nine porcine muscle tissues using a common reference design

status: Public on Oct 30 2012

city: Aarhus

first: Henrik

last: Hornshøj

address: Brendstrupgårdsvej 100

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

summary:
The introduction of long oligonucleotide-based probes has led to many comparative studies of these two platforms in mammals, but remains to be performed for pig. Further, the characteristics of global gene expression in diverse porcine muscle tissues have not been yet been fully established. This is the first global gene expression study of a collection of nine porcine muscle tissues consisting of cardiac and various skeletal muscle types using both cDNA-based and long oligonucleotide-based microarray platforms. The expression profiles from the two platforms agree in differentiating between cardiac, skeletal red, skeletal intermediate and skeletal white muscle types by producing almost identical hierarchical expression clusters. The clusters from both platforms also reveal that gene expression profiles of the skeletal intermediate type are more similar to the red type than to the white type. Analysis of the ability to identify differentially expressed genes based on gene set analysis and GO term integration show a platform overlap of at least 80% for the cardiac-skeletal comparisons and a platform overlap of at least 58% for the skeletal red-white comparisons. Interestingly, the oligonucleotide platform was always able to identify more GO terms associated with differential expression than the cDNA platform. We further examined the skeletal red-white expression differences and found many GO biological processes that are known to be associated with these phenotypes including calcium ion transport, glycolysis, fatty acid beta-oxidation and muscle contraction. In addition, the expression of genes involved in differentiation between slow (red) and fast (white) muscle types such as MYBPC1, TNNI1, TNNT3 and ATP2A1 is highly regulated between red and white type muscles. Not previously shown to be associated with this tissue difference we found the biological process post-Golgi vesicle-mediated transport. Similar results were obtained with GO classes cellular components and molecular functions. Using the gene expression profiles from the oligonucleotide platform we presented and applied an approach for predicting alternatively spliced transcripts across cardiac and skeletal type muscles. One of the predicted transcripts from the gene named UBE2C has been shown to have six transcript variants in human, but they are not expressed in a cardiac-skeletal specific manner as we have observed here. We speculate that one of our oligonucleotide probes for this gene is able to detect only three of these variants whereas the other detects all six variants and that these variants are expressed in a cardiac-skeletal muscle specific manner. These results supports some of the advantages of using oligonucleotide-based microarray platforms for global gene expression profiling and the observed differences in gene expression among muscle tissues contribute to the understanding of the molecular processes behind porcine muscle biology.
Keywords: tissue comparison, platform comparison

overall_design: Muscle tissue samples from heart (HEA), Vastus intermedius (VIN), Infraspinatus (ISP), Supraspinatus (SSP), Biceps femoris (BFE), Longissimus dorsi (LDO), Semimembranosus (SME), Semitendinosus (STE) and Triceps brachii (TBR). A common reference sample was constructed by combining all samples. The exact same tissue samples were used for expression profiling with cDNA microarrays and 70-mer long oligonucleotide microarrays.

last: Hornshoj

first: Jakob

last: Hedegaard

first: Frank

last: Panitz

first: Christian

last: Bendixen


title: Mammary carcinomas in WAP-SV40 transgenic mice

first: Thomas

last: Streichert

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: The RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

summary: To investigate the regulatory targets of the RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

overall_design: Single factor (genotype) with dye swaps.

first: Yogitha

last: Srikhanta

first: Dianna

last: Hocking

first: Judyta

last: Praszkier

first: Ji

last: Yang

first: Marija

last: Tauschek

first: Roy

last: Robins-Browne


title: Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria.

status: Public on Oct 11 2011

first: Hideaki

last: Nojiri

summary: RNA mapping on pCAR1 carried by KT2440, CA10, PAO1, Pf0-1, HS01, and JCM 2778

sample_organism: Pseudomonas chlororaphis subsp. chlororaphis

overall_design: 6 strains/biological entities were compared

first: Masaki

last: Shintani

first: Hiroki

last: Tokumaru

first: Yurika

last: Takahashi

first: Masatoshi

last: Miyakoshi

first: Hisakazu

last: Yamane

first: Hiromi

last: Nishida


title: Microarray gene expression profiles from temperature acclimated atrial, ventricular compact and spongy tissues of Pacific bluefin tuna Thunnus orientalis

status: Public on Apr 01 2012

city: Pacific Grove

first: Nishad

last: Jayasundara

address: 120 Oceanview Blvd

institute: Stanford University

summary: In this study, we examined the transcriptomic responses to temperature acclimation (14oC, 20oC, and 25oC) in atrial and ventricular tissues of Pacific bluefin tuna (PBFT). A global gene expression analysis using a bluefin tuna-specific microarray indicated profound changes in expression of genes associated with energy metabolism, protein turnover, cellular stress response, oxidative stress and apoptosis. A principal component analysis revealed tissue-specific transcriptomic responses to temperature, with atrium at 25oC showing the greatest variation. Overall transcriptomic data suggests that PBFT can optimize cardiac function in the cold by acclimating to 14oC. Capacity to acclimate to colder temperatures potentially underlies this species ability to expand its vertical and horizontal thermal niche and migrate to colder oceans at high latitudes. In contrast, the cardiac phenotype of 25oC acclimated fish infers that PBFT hearts struggle to maintain cellular homeostasis and are subjected to programmed cell death.

overall_design: The goal of this study was to compare transcriptomic response to cold and warm temperature acclimations across cardiac tissues in Pacific bluefin tuna. Fish (n=4) were acclimated to 14C, 20C and 25C, and RNA was extracted from atrial, ventricular compact and spongy tissues. Experimental samples were hybridyzed against a reference pool that contained a mix of RNA from every sample.

first: Luke

last: Gardner

first: Barbara

last: Block


title: Dexamethasone treatment of 3B4.15 T hybridoma cells

status: Public on Jul 13 2012

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

summary:
Investigation of whole genome gene expression level changes in Mus musculus 3B4.15 T hybridoma cells treated with 1microMolar Dexamethasone compared to mock treated cells.
Interleukin-7 receptor alpha (IL-7Rα) is essential for T cell survival and differentiation. Glucocorticoids are potent enhancers of IL-7Rα expression with diverse roles in T cell biology. Here we identify the transcriptional repressor, Growth factor independent-1 (Gfi1), as a novel intermediary in glucocorticoid-induced IL-7Rα upregulation. We found Gfi1 to be a major inhibitory target of dexamethasone by microarray expression profiling of 3B4.15 T-hybridoma cells. Concordantly, retroviral transduction of Gfi1 significantly blunted IL-7Rα upregulation by dexamethasone. To further assess the role of Gfi1 in vivo, we generated bacterial artificial chromosome (BAC) transgenic mice, in which a modified Il7r locus expresses GFP to report Il7r gene transcription. By introducing this BAC reporter transgene into either Gfi1-deficient or Gfi1-transgenic mice, we document in vivo that IL-7Rα transcription is upregulated in the absence of Gfi1 and downregulated when Gfi1 is overexpressed. Strikingly, the in vivo regulatory role of Gfi1 was specific for CD8+, and not CD4+ T cells or immature thymocytes. These results identify Gfi1 as a specific transcriptional repressor of the Il7r gene in CD8 T lymphocytes in vivo.

overall_design: A six chip study using total RNA recovered from three separate flasks of mock treated 3B4.15 cells and three separate flasks of Dexamethasone treated 3B4.15 cells .  Each chip measures the expression level of 44170 target genes


title: Burkholderia pseudomallei transcriptional adaptation in macrophage

status: Public on Dec 31 2011

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: This study reports the expression profile of intracellular B. pseudomallei following infection of human macrophage-like U937 cells. The transcriptome of intracellular B. pseudomallei harvested from macrophage cells over an infection period of 6 hr (1, 2, 4 and 6 hr post-infection) were compared to in vitro grown bacteria to identify genes whose expression is altered in response to intracellular growth.

overall_design: The experimental design of this study involved the total RNA from intracellular B. pseudomallei harvested from infected U937 cells at 4 selected time points with 3 biological replicates each. The microarray data from each time point was compared relative to in vitro grown bacteria in cell culture medium.

first: Sylvia

last: Chieng


title: RNA isolation from mouse skin biopies

status: Public on Oct 05 2011

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

institute: University of Amsterdam

summary: Study to optimize our protocol for isolating RNA from skin biopsies from (hairless) SKH mice using different-diameter biopsy punches. Some mice were also treated with UVB radiation to check its effect on RNA yield.

overall_design: 4 mice total:  2 were irradiated with 300J/m2 UVB and 2 were non-irradiated. Post-mortem skin biopsies with 1.5mm, 2.0mm, and 2.5mm diameter punches were taken from the dorsal region.

first: W

last: Rodenburg

first: A

last: de Vries

first: H

last: de Jong

first: O

first: T

last: Breit


title: Affymetrix Cotton Genome array expression data of cotton fiber at different developmental stages from different varieties of Gossypium hirsutum

status: Public on Mar 20 2012

city: Lucknow

first: Samir

last: Sawant

address: Sikandrabad

department: Centre for Plant and Molecular Breeding

country: India

institute: National Botanical Research Institute

summary:
Cotton fiber were used for the expression analysis at different developmental stages
Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Six developmental stages (0 DPA, 6DPA,9DPA,12DPA,19DPA and 25DPA) of cotton fiber were selected for gene expression studies. The Gene expression profiling of these developmental stages were comparatively analysed in five different genotypes of Gossypium hirsutum. The genotypes namely JKC 725 and JKC 777 were superior in fiber traits as compared to genotypes JKC 703, JKC 737 and JKC 783. Total RNA were extracted from these varieties at six developmental stages. Biotinylated cRNA were synthesized and hybridized on Affymetrix Cotton Genome array according to manufacturer protocol (Affymetrix).Three biological replicates samples were isolated from each developmental stages from five genotypes.

first: P

last: Kavita

first: Deepti

last: Nigam

first: Alok

last: Ranjan

first: Ridhi

last: Goel

first: Rajeev

last: Tripathi

first: Mehar

last: Asif


title: Gene expression in tissues of Mus musculus with innate immunity stimulation

status: Public on Mar 01 2011

city: Fukuoka

first: Hisanori

last: Nishio

address: Maidashi 3-1-1, Higashi-ku

department: Pediatrics

institute: Kyushu University

summary: This is an investigation of whole genome gene expression level in tissues of mice stimulated by LPS, FK565 or LPS + FK565 in vivo and ex vivo. We show that parenteral administration of a pure synthetic Nod1 ligand, FK565, induces site-specific vascular inflammation in mice, which is prominent in aortic root including aortic valves, slight in aorta and absent in other arteries. The degree of respective vascular inflammation is associated with persistent high expression of proinflammatory chemokine/cytokine genes in each tissue in vivo by microarray analysis, and not with Nod1 expression levels. The ex vivo production of proinflammatory chemokine/cytokine by Nod1 ligand is higher in aortic root than in other arteries from normal murine vascular tissues, and also higher in human coronary artery endothelial cells (HCAEC) than in human pulmonary artery endothelial cells (HPAEC), suggesting that site-specific vascular inflammation is at least in part ascribed to an intrinsic nature of the vascular tissue/cell itself.

overall_design: A fourty chip study using total RNA recovered from four isolated tissues of mice which were stimulated by various reagents. Aortic root, pulmonary artery, aorta and spleen of mice in 3 groups: 1) intraperitoneal injection of 20μg of LPS priming only, 2) oral administration of FK565 (100μg) for consecutive days, 3) oral administration of FK565 (100μg) for consecutive days 1 day after LPS priming, at day 2, 4, and 7. And six chip study using total RNA recovered from three isolated vascular tissues of mice which were stimulated by FK565 (10μg/mL) ex vivo.

first: Kazuyuki

last: Ikeda

first: Shunsuke

last: Kanno

first: Sagano

last: Onoyama

first: Tamami

last: Tanaka

first: Koichi

last: Kusuhara

first: Yukari

last: Fujimoto

last: Fukase

first: Katsuo

last: Sueishi

first: Toshiro

last: Hara


title: Population transcriptomics of Drosophila melanogaster females

status: Public on Dec 23 2010

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

institute: University of Munich

summary: To investigate the effect of sex on within- and between-population variation in gene expression, we performed a microarray analysis of adult females from 16 strains of Drosophila melanogaster, including eight strains from the putative ancestral range in sub-Saharan Africa and eight strains from a European population. The results were compared to those of a previous study of adult male gene expression variation among the same strains (GSE8843).

overall_design: We used dual-channel microarrays to compare genome-wide expression profiles in adult females from 16 inbred strains derived from two natural populations. In total, 56 hybridizations were performed including dye-swaps. The hybridization scheme consisted of a balanced loop design, which allowed an unbiased comparison of relative expression levels within and between populations.

first: Lena

last: Müller

first: Rayna

last: Stamboliyska

first: Sarah

middle: S

last: Saminadin-Peter

first: Wolfgang

last: Stephan

first: John

last: Parsch


title: Chronic activation of the epithelial immune system of the fruit fly's salivary glands has a negative effect on organismal growth and induces a peculiar set of target genes

status: Public on Mar 18 2010

city: Kiel

first: Ahmed

middle: Abdelsadik Mohammed

last: Kahlil

state: SH

address: Olshausenstraße 40

department: Zoophysiology

institute: Christian-Albrechts-Universität

summary: Epithelial and especially mucosal immunity represents the first line of defence against the plethora of potential pathogens trying to invade via the gastrointestinal tract. The salivary glands of the fruit fly are an indispensable part of the gastrointestinal tract, but their contribution to the mucosal immunity has almost completely been neglected. Our major goal was to elucidate if the fly's salivary glands are able to mount an immune response and what the major characteristics of this immune response are.

overall_design: Ectopic activiation of the Immune deficiency pathway in the larval salivary glands using the Gal4/UAS-system of Brand and Perrimon. The activation was induced by the overexpression of the pattern recognition receptor PGRP-LCx using a driver line which was specific for the salivary glands.In general four replicates were performed including dye-swaps in two-colour arrays.

last: Abdelsadik

first: Thomas

last: Roeder


title: sRNAs in Rhizobium etli differentially expressed during free-living and host-associated growth

status: Public on Nov 17 2009

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

type: Non-coding RNA profiling by genome tiling array

summary: 89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions.

overall_design: In order to study expression in the free-living state, wild-type R. etli CFN42 was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, 0.7 and 6 hours after reaching the maximum OD, representing early/late exponential and stationary phase, respectively. In order to study gene expression during host-associated growth, common bean plants (Phaseolus vulgaris cv. Limburgse vroege) were cultivated and inoculated as described previously. Nodules were harvested 2 and 3 weeks after inoculation and the bacteroids were purified by differential centrifugation.

first: Maarten

last: Vercruysse

last: Fauvart

first: Jan

last: Michiels

first: Lore

last: Cloots


title: Biomarkers for Down Syndrome screening in murine fetal liver and placenta

status: Public on May 11 2011

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary:
The Ts1Cje mouse strain (Sago, 1998) contains a segmental trisomy of mouse chromosome 16 orthologous to the region of human chromosome 21 commonly associated with Down Syndrome.
In this study, fetuses were obtained from wildtype mothers bred with either wildtype or Ts1Cje males.
Gene expression profiles in fetal liver and placenta of wildtype and Ts1Cje fetuses were compared, to identify potential markers for application in human prenatal DS screening.

overall_design: A 48 array study with 24 arrays for placenta and 24 for fetal liver. For each tissue we used RNA from 24 individual embryos, i.e. six male and six female embryos from both genotypes.


title: Condition-dependence of the sexually dimorphic transcriptome in Drosophila melanogaster

status: Public on Feb 01 2010

first: Minyoung

last: Wyman

state: ON

address: 25 Willcocks Street

department: Ecology & Evolutionary Biology

institute: University of Toronto

summary: Sexually dimorphic traits are by definition exaggerated in one sex, which may arise from a history of sex-specific selection – in males, females, or both. If this exaggeration comes at a cost, exaggeration is expected to be greater in higher condition individuals (condition-dependent). Although studies using small numbers of morphological traits are generally supportive, this prediction has not been examined at a larger scale. We test this prediction across the trancriptome by determining the condition-dependence of sex-biased (dimorphic) gene expression. We find that high-condition populations are more sexually dimorphic in transcription than low-condition populations. High condition populations have more male-biased genes and more female-biased genes, and a greater degree of sexually dimorphic expression in these genes. Also, condition-dependence in male-biased genes was greater than in a set of unbiased genes. Interestingly, male-biased genes expressed in the testes were not more condition-dependent than those in the soma. By contrast, increased female-biased expression under high condition may be have occurred because of the greater contribution of the ovary-specific transcripts to the entire mRNA pool. We did not find any genomic signatures distinguishing the condition-dependent sex-biased genes. The degree of condition-dependent sexual dimorphism (CDSD) did not differ between the autosomes and the X-chromosome. There was only weak evidence that rates of evolution correlated with CDSD. We suggest that the sensitivity of both female-biased genes and male-biased genes to condition may be akin to the overall heightened sensitivity to condition that life-history and sexually selected traits tend to exhibit. Our results demonstrate that through condition-dependence, early life experience has dramatic effects on sexual dimorphism in the adult transcriptome.

overall_design: There were 8 biologically distinct samples. Each was replicated 6 times for a total of 48 biological samples on 24 arrays. There was no reference or control sample as a loop design was used.  Each of the 48 samples are represented separately.

first: Aneil

middle: F

last: Agrawal

first: Locke

last: Rowe