title: MicroRNA expression data in mouse fetal lungs

status: Public on Nov 26 2013

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

country: USA

institute: University of Pittsburgh

summary: Microarray data of mouse postnatal lungs between day 1 and 6 weeks of age. The results provide a general insight into the microRNA expression profile during the alveolar phase of lung development.

overall_design: We obtained lung tissue of healthy postnatal mice, 4-5 replicates at each time point. Time points were day1, day4, day7, day14, and day 42.

middle: V

first: Namasivayam

last: Ambalavanan

first: Naftali

last: Kaminski


title: Penicillium marneffei:  Gene expression profiling during the dimorphic switch

status: Public on Nov 21 2013

city: University of Melbourne

first: Alex

last: Andrianopoulos

state: Victoria

address: Royal Parade

department: Department of Genetics

country: Australia

institute: University of Melbourne

summary: Penicillium marneffei (Talaromyces marneffei) is an opportunistic human pathogen that can grow in a multicellular hyphal form at 25°C or a unicellular fission yeast form at 37°C, and can switch between these two forms in response to temperature. The yeast form is found in infected individuals and represents the pathogenic phase. In response to specific environmental cues, the hyphal form can undergo asexual development (conidiation) the produce a differentiated multicellular structure called a conidiophore which produces dormant spores (conidia). Inhaled conidia initiate infection. To identify genes that are important during the early stages in the transition from hyphal to yeast and yeast to hyphal cells transcriptional profiling was performed with a custom microarray consisting of ~42% of the predicted P. marneffei genes and RNA from P. marneffei hyphal cells switched to growth at 37°C for 6 hours (hyphal-yeast switch) and yeast cells switched to growth at 25°C for 6 hours (yeast-hyphal switch).

overall_design: A custom microarray consisting of short, random genomic fragments from P. marneffei (~42% of the predicted genes) was generated using PCR products of the inserts from two independent DNA libraries constructed from genomic DNA of the P. marneffei type strain FRR2161. PCR products from previously cloned P. marneffei genes with known expression profiles were included as controls on the microarray. Total RNA from hyphal cells before and after switching to growth at 37°C for 6 hours (hyphal-yeast switch) and yeast cells before and after switching to growth at 25°C for 6 hours (yeast-hyphal switch) were used in pairwise combinations on the microarrays. Three biological replicate cultures were prepared for each experiment.

first: Shivani

last: Pasricha

first: David

last: Canovas

first: Luke

last: Pase

first: Nathamon

last: Ngaosuwankul

first: Alicia

last: Oshlack

first: Gordon

middle: K

last: Smyth


title: Mechanical loading and gene expression - Microarray study

city: amsterdam

first: Nathalie

last: Bravenboer

address: de Boelelaan 1117

department: Clinical Chemistry

country: Netherlands

institute: VU Medical Center

summary: Skeletal integrity in humans and animals is maintained by daily mechanical loading. It has been widely accepted that osteocytes function as mechanosensors. Many biochemical signaling molecules are involved in the response of osteocytes to mechanical stimulation. The aim of this study was to identify genes involved in the translation of mechanical stimuli into bone formation. The four-point bending model was used to induce a single period of mechanical loading (comprising 300 cycles (2 Hz) using a peak magnitude of 60 N) on the right tibia, while the contra lateral left tibia served as control. Six hours after loading, the effects of mechanical loading on gene-expression were determined with microarray analysis. Protein expression of differentially regulated genes was evaluated with immunohistochemistry. Nine genes were found to exhibit a significant differential gene expression in LOAD compared to  control. MEPE, Garnl1, V2R2B, and QFG TN1 olfactory receptor were up-regulated, and creatine kinase (muscle form), fibrinogen-B beta-polypeptide, monoamine oxidase A, troponin-C and kinesin light chain-C were down-regulated. Validation with real-time RT-PCR analysis confirmed the up regulation of MEPE and the down-regulation of creatine kinase (muscle form) and troponin-C in the loaded tibia. Immunohistochemistry showed that the increase of MEPE protein expression was already detectable six hours after mechanical loading. In conclusion, these genes probably play a role during translation of mechanical stimuli six hours after mechanical loading. The modulation of MEPE expression may indicate a connection between bone mineralization and bone formation after mechanical stimulation.

overall_design: Two groups: LOAD vs contralateral control and SHAM vs contralateral control (n=5/group)

first: Christianne

middle: M

last: Reijnders

first: Huib

middle: W

last: van Essen

first: Birgitte

middle: T

last: van Rens

first: Johannes

middle: H

last: van Beek

first: Bauke

last: Ylstra

first: Marinus

middle: A

last: Blankenstein

first: Paul

last: Lips


title: Expression data from the Arabidopsis root epidermis mutants

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

summary: The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation.  The goal of this study was to define the transcript changes in the root epidermis of mutants associated with root epidermis cell specification, including mutants that lack a visible phenotypic alteration (try, egl3, myb23, and ttg2).   Transcript levels were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting with the WER::GFP transgene.  These microarray results were used to compare the effects of single and double mutants on the gene regulatory network that controls root epidermal cell fate and differentiation in Arabidopsis.

overall_design: The cells of the developing root epidermis were obtained by growing plant seedlings expressing the WER::GFP transgene under sterile conditions on MS media, cutting off root tips (including all developmental stages), protoplasting the roots, and purifying cells containing GFP using FACS.   The WER::GFP transgene is expressed throughout the developing cells of the root epidermis and the lateral root cap.   Three biological replicates were analyzed for each of the plant lines examined in this study.

first: Angela

last: Bruex

first: Raghu

last: Kainkaryam

first: Peter

last: Woolf


title: Comparative genomics of Helicobacter pylori strains associated with different clinical outcome

status: Public on Nov 10 2013

city: Beijing

first: yuanhai

last: you

address: Changbai road 155,Changping district

country: China

institute: intitute of communicable disease control and prevention,China CDC

type: Genome variation profiling by genome tiling array

summary: In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori(H. pylori) genomes was designed and utilized for comparative genomic profiling of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation were found among these strains, an additional 76 H. pylori stains with different clinical outcomes isolated from various provinces of China were further tested by PCR to demonstrate this distinction. We observed several highly variable regions among strains of gastritis, gastric ulceration and gastric cancer. They are involved in genes associated with bacterial type I, type II and type III R-M system as well as in a virB gene neighboring the well studied cag pathogenic island. Previous studies have reported the diverse genetic characterization of this pathogenic island, but it is conserved in the strains tested by microarray in this study. Moreover, a number of genes involved in the type IV secretion system related to DNA horizontal transfer between H. pylori strains were identified based on the comparative analysis of the strain specific genes. These findings may provide new insights for discovering biomarkers for prediction of gastric diseases.

platform_organism:
Helicobacter pylori 26695
Helicobacter pylori J99
Helicobacter pylori HPAG1
Helicobacter pylori Shi470
Helicobacter pylori G27
Helicobacter pylori P12

overall_design: Here we describe the design and use of a high-density oligonucleotide microarray covering six sequenced H. pylori genomes as well as several sequenced plasmids. The performance of this microarray is evaluated, and its utility is illustrated for the hybridization of genomic DNA in order to compare eight uncharacterized H. pylori strains which have not been sequenced with the six known, sequenced strains. We utilize this microarray to identify variable genomic region among H. pylori strains isolated from patients with different gastroduodenal diseases in a Chinese patient population. H. pylori isolates from 2 patients with chronic superficial gastritis, 2 patients with atrophic gastritis, 2 patients with gastric ulcer, and 2 patients with gastric cancer were studied. All eight strains were isolated from Heilongjiang province of China. A number of variable regions with high genetic diversity was identified. 26 selected genes were validated by large scale PCR in both microarray tested strains while an additional 76 strains were isolated from eight provinces.


title: Reciprocal transcriptional responses in the interaction between Arabidopsis thaliana and Tetranychus urticae.

status: Public on Nov 25 2013

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario

summary:
While pathogen-induced immunity is comparatively well characterized, far less is known about plant defense responses to arthropod herbivores. To date, most molecular-genetic studies of plant-arthropod interactions have focused on insects. However, plant-feeding (phytophagous) mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g., Lepidopteran larvae or aphids). The two-spotted spider mite, Tetranychus urticae, is among the most significant mite pests in agriculture. T. urticae is an extreme generalist that has been documented on a staggering number of plant hosts (more than 1,100), and is renowned for the rapid evolution of pesticide resistance. To understand reciprocal interactions between T. urticae and a plant host at the molecular level, we examined mite herbivory using Arabidopsis thaliana. Despite differences in feeding guilds, we found that transcriptional responses of A. thaliana to mite herbivory generally resembled those observed for insect herbivores. In particular, defense to mites was mediated by jasmonic acid (JA) biosynthesis and signaling. Further, indole glucosinolates dramatically increased mite mortality and development times. Variation in both basal and activated levels of these defense pathways might also explain differences in mite damage and feeding success between A. thaliana accessions. On the herbivore side, a diverse set of genes associated with detoxification of xenobiotics was induced upon exposure to increasing levels of in planta indole glucosinolates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.
We used microarray to assess global gene expresion in Arabidopsis thaliana upon Tetranychus urticae attack in two A. thaliana accessions: Bla-2, resistant to spider mite herbivory and Kon, susceptible to spider mite herbivory.

overall_design: 3 week old Arabidopsis thaliana plants were subjected to Tetranychus urticae attack through application of 10 mites for various periods of time (timecourse scenario) or hundreds of mites for 1 hour (feeding site scenario).

first: Marie

last: Navarro

first: Kristie

last: Bruinsma

first: Vicente

last: Arbona

first: Maria

middle: E

last: Santamaria

first: Marc

last: Cazaux

first: Nicky

last: Wybouw

first: Edward

middle: J

last: Osborne

first: Cherise

last: Ens

first: Cristina

last: Rioja

first: Vanessa

last: Vermeirssen

first: Ignacio

last: Rubio-Somoza

first: Priti

last: Krishna

first: Isabel

last: Diaz

first: Markus

last: Schmid

first: Aurelio

middle: G

last: Cadenas

first: Yves

last: Van de Peer

first: Miodrag

last: Grbic

first: Richard

last: Clark

first: Thomas

last: Van Leeuwen

first: Vojislava


title: Xenopus laevis embryos and animal caps: Control vs PouV morpholino

status: Public on Nov 12 2013

city: Copenhagen

first: Joshua

last: Brickman

address: Blegdamsvej 3B

department: The Danish Stem Cell Centre (DanStem)

country: Denmark

institute: University of Copenhagen

summary: Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants.

overall_design: Two conditions: Control vs. PouV morpholino; Two tissues: whole embryos, animal caps .Two timepoints: stage 9 and 10.  Biological replicates: 2 control replicates at stage 9  and 10 for whole embryos, 2 control replicates at stage 9 and 10  for animal caps, 2 PVD2 morpholino replicates  at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps

first: Alessandra

last: Livigni

first: Alexei

last: Sharov


title: MicroRNA of exosome in Hand, foot and mouth disease serum samples

status: Public on Nov 27 2013

city: Guangzhou

first: Hong-Ling

last: Jia

state: Guangdong

address: Huangpu Road

institute: Jinan University

summary: The some biomarkers can be found by pairwise comparison. They can distinguish between extremely severe Hand,foot and mouth disease and mild Hand,foot and mouth disease,moreover,they can applied to diagnose extremely severe Hand,foot and mouth disease

overall_design: mild Hand,foot and mouth disease vs.control; extremely severe Hand,foot and mouth disease vs.control; extremely severe Hand,foot and mouth disease vs.mild Hand,foot and mouth disease,verification by qRT-PCR

first: Li

last: Deng

first: H


title: Predicting the evolution of metastatic disease in breast cancer: results from 50 years of autopsies

status: Public on Nov 11 2013

city: Brisbane

first: Peter

last: Simpson

address: Royal Brisbane & Women's Hospital

department: UQ Centre for Clinical Research

institute: The University of Queensland

summary: This is a genomic analysis of breast cancer metastasis using array based CGH and is part of a large study investigating the patterns and evolution of metastases from breast cancer using autopsy material accumulated over the last 50 years from a single institution. The samples used in the genomic profiling comprise the primary breast tumour and multiple matched metastases from each patient. The data demonstrate both the clonal nature of metastatic progression and the role of clonal evolution during progression.

overall_design: This study comprises six patients who died of metastatic breast cancer. For some patients the breast primary tumour and lymph node metastasis was obtained from previous surgical excision, otherwise material was obtained from a resulting autopsy. Each patient set of samples involves the primary breast tumour and multiple metastases, including from lung, liver, lymph node, adrenal gland, brain etc. DNA was extracted from formalin fixed paraffin embedded (FFPE) tissue blocks and analysed for DNA copy number alterations using an Agilent aCGH platform.

first: Margaret

middle: C

last: Cummings

first: Lynne

last: Reid

first: Janani

last: Jayanthan

first: Joanna

last: Skerman

first: Sarah

last: Song

first: Amy

last: McCart Reed

first: Jamie

middle: R

last: Kutasovic

first: Adrienne

middle: L

last: Morey

first: Louise

last: Marquart

last: O’Rourke

first: Sunil

last: Lakhani


title: Tissue-specific response of microRNAs to carcinogenicity and mutagenicity of aristolochic acid in rats

city: Dalian

first: Zhiguang

last: Li

state: Liaoning

address: 9 Lvshun South Road

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Aristolochic acid (AA) is an active component of herbal drugs derived from the Aristolochia species that have been used for medicinal purposes since antiquity.  However, AA is genotoxic and induces tumors in animals and humans.  AA induces mutations and tumors in the kidney but solely mutations in the liver.  To evaluate whether miRNAs could indicate AA’s tissue-specific carcinogenicity and mutagenicity, we first conducted microarray analysis of miRNA expression in kidneys and livers of rats treated with a carcinogenic dose of AA.  Then, miR-21, a biomarker for carcinogenicity, and miR-34a, a biomarker for mutagenicity, the two miRNAs whose expressions were most altered, were evaluated for their expression in the kidney (the AA’s mutagenic and carcinogenic target tissue), liver (the AA’s mutagenic target tissue), and testis, the non-target tissue where neither tumors nor mutation induction was found in previous studies and in this study.  Genomic analysis of miRNA expression for kidney and liver samples showed that miRNA expression was globally changed by the treatment.  Nineteen miRNAs were significantly dysregulated by the treatment in the kidney.  Most of these miRNAs are related to carcinogenesis.  Only one miRNA, miR-34a, was differentially expressed in the liver.  Expression of miR-21 was induced in the kidney by AA treatment in a dose-dependent manner while no changes occurred in the liver or testis, indicating that the kidney is the carcinogenic target.  miR-34a was dose-dependently up-regulated in the kidneys and livers of rats treated with AA, but not in the testis, suggesting that the kidney and liver are mutagenic target tissues, but the testis is not.  Our results demonstrate that miRNA profiles can reflect the AA’s carcinogenicity in a tissue-specific manner while specific miRNAs can signify the target tissues for carcinogenicity or mutagenicity of AA.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Six-week-old Big Blue rats were treated with 0.1, 1.0, or 10.0 mg AA/kg body weight by gavage, five times per week for 12 weeks; Vehicle control rats were gavaged with 0.9% sodium chloride using the same schedule as for the AA-treated rats. Six rats from each treatment group were sacrificed one day after the last treatment. The kidney and liver tissues that were collected and used for the DNA adduct and mutation study (Mei et al, 2006) were used for the miRNA profiling and real-time PCR in this study, which allow us to compare the different endpoints at the same conditions.

first: Fanxue

last: Meng

first: Jian

last: Yan

first: Mugimane

last: Manjanatha

first: Sharon

last: Shelton

first: Stephanie

last: Yarborough

first: Tao

last: Chen


title: Indole Negatively Impacts Predation by Bdellovibrio bacteriovorus HD100 and Its Release from the Bdelloplast

status: Public on Nov 19 2013

city: Ulsan

first: Robert

middle: J.

last: Mitchell

address: 50 UNIST-gil

department: School of Life Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

summary: Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic.

overall_design: Bdellovibrio bacteriovorus HD100 was incubated for 30 min at 30°C in HEPES buffer supplemented with 0,1, and 2 mM indole.  RNA was then extracted from each sample and purified. 100 ng of RNA from each sample were used for microarray experiment. For zero and 1 mM indole treatments, three independant samples were tested while for 2 mM indole treatment, two samples were tested. A total of 8 arrays were used.

first: Mohammed

last: Dwidar

first: Dougu

last: Nam


title: Pathways involved in plant decomposition in Clostridium phytofermentans

status: Public on Nov 20 2013

city: Amherst

first: Jeffrey

last: Blanchard

state: MA

address: 203 Morrill Science Center IVN

institute: University of Massachusetts Amherst

summary: Genomic analysis of the model lignocellulosic biomass degrading bacteria C. phytofermentans indicates that it can degrade, transport, and utilize a wide-range of carbohydrates as possible growth substrates.  Previous experiments characterized the expression of the degradation and transport machinery using custom whole genome oligonucleotide microarrays.  The results indicate that C. phytofermentans utilizes ATP-binding cassette (ABC) transporters for carbohydrate uptake and does not use the sole phosphoenolpyruvate-phosphotransferase system (PTS) for any of the tested substrates.  While some ABC transporters are specific for a single carbohydrate, the expression profiles indicate that others may be capable of transporting multiple substrates.  Distinct sets of Carbohydrate Active Enzymes (CAZy) genes were also up-regulated on specific substrates indicative of C. phytofermentans ability to selectively degrade plant biomass. We also identified a highly expressed cluster of genes which includes seven extracellular glycoside hydrolases and two ABC transporters with unknown specificity.  These results lead to the hypothesis that when grown on plant biomass, C. phytofermentans is capable of degrading and transporting all major carbohydrate components of the plant cell.  To test this, C. phytofermentans was grown on cornstover and switchgrass.  Results from this expression data and HPLC analysis indicates that C. phytofermentans is utilizing multiple substrates.  with multiple sugar ABC transporter clusters and glycoside hydrolases being expressed.  Interestingly all of the transporters were initially identified on disaccharides or oligio-saccharides, and none of the transporters identified as monosaccharide specific transporters were expressed.  This could be an indication that C. phytofermentans prefers to transport oligiosacchrides over monosaccharides.  The results presented here corroborate the genomic data which indicates the breath of the carbohydrate degradation, transport, and utilization machinery of C. phytofermentans.

overall_design: C. phytofermentans was cultured anaerobically on switchgrass and corn stover to determine specific expression patterns.  The data in this series consists three independent RNA preparations from replicate cultures.

first: James

last: Hayes


title: Genome and transcriptome of Clostridium phytofermentans catalyst for the direct conversion of plant feedstocks to fuels

summary: Clostridium phytofermentans was recently isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways.  The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates.  The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer.  These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome.  Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield.  The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products.  These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.

overall_design: C. phytofermentans was cultured anaerobically on different carbohydrates sources to determine carbohydrates specific expression patterns.  The data in this series consists two independent RNA preparations from replicate cultures.

first: Elsa

last: Petit


title: MicroRNA analysis of breast cancer cell lines

status: Public on Nov 28 2013

city: New Orleans

first: Reza

last: Izadpanah

state: Louisiana

address: 1430 Tulane Avenue

department: Heart and Vascular Institute

institute: Tulane University

summary: Membrane vesicles released by neoplastic cells into extracellular medium contain potential of carrying arrays of oncogenic molecules including proteins and microRNAs (miRNA). Extracellular (exosome-like) vesicles play a major role in cell-to-cell communication. Thus, the characterization of miRNAs of exosome-like vesicles is imperative in clarifying intercellular signaling as well as identifying disease markers. microarray analysis identified several oncogenic miRNA between the two types vesicles.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Exosome-like vesicles were isolated using gradient centrifugation from MCF-7 and MDA-MB 231 cultures. Sample-derived miRNA expression was analyzed on Miltenyi's miRXplore™ platform. The RNA was isolated from two replicate samples of MDA-MB231 and MCF7 cell lines. The miRNAs extracted from all four samples were labeled with Hy5 and hybridized against Hy3-labeled Universal Reference miRNA (UR). Candidate miRNAs were identified. In this report, the re-ratios of MDA1 or MDA2 relative to a virtual pool of both MCF7 samples 1 and 2 were used for further analyses.   1- Reratio No. 7 MDA 1 vs MCF7 1+2  reratios of (MDA 1 vs UR) and (MCF7 1 vs UR + MCF7 2 vs UR)  7970041, (7970039 + 7970040)    2- Reratio No. 8 MDA 2 vs MCF7 1+2  reratios of (MDA 2 vs UR) and (MCF7 1 vs UR + MCF7 2 vs UR)  7970042, (7970039 + 7970040)  Exosome-like vesicles were isolated using gradient centrifugation from MCF-7 and MDA-MB 231 cultures. Sample-derived miRNA expression was analyzed on Miltenyi's miRXplore™ platform. The RNA was isolated from two replicate samples of MDA-MB231 and MCF7 cell lines. The miRNAs extracted from all four samples were labeled with Hy5 and hybridized against Hy3-labeled Universal Reference miRNA (UR). Candidate miRNAs were identified. In this report, the re-ratios of MDA1 or MDA2 relative to a virtual pool of both MCF7 samples 1 and 2 were used for further analyses.   1- Reratio No. 7 MDA 1 vs MCF7 1+2  reratios of (MDA 1 vs UR) and (MCF7 1 vs UR + MCF7 2 vs UR)  7970041, (7970039 + 7970040)    2- Reratio No. 8 MDA 2 vs MCF7 1+2  reratios of (MDA 2 vs UR) and (MCF7 1 vs UR + MCF7 2 vs UR)  7970042, (7970039 + 7970040)


title: Oncorhynchus mykiss liver and muscle cells: Small vs. Large neomale offspring

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

state: Ontario

address: Science Complex, University of Guelph

department: Intergrative Biology

institute: University of Guelph

summary: Transcriptional profiling of rainbow trout liver and muscle cells comparing small fish with large fish within a population of neomale offspring.

overall_design: Small vs. large-fish liver and muscle cells from neomale offspring. Biological replicates: 4 small replicates, 4 large replicates.

first: Moira

last: Ferguson

first: Roy

last: Danzmann


title: The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool

status: Public on Nov 15 2013

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travelling, climate changes and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. For many of them, the disease symptoms are similar to each other, as well as to other more common diseases, making them difficult to diagnose. A rapid identification will help to decide about specific treatment and appropriate case management. Real-time PCR is commonly used for specific virus detection in clinical samples. A diagnostic microarray containing probes for all human viruses, could replace hundreds of specific PCR-reactions and identify all viruses by one assay and thereby remove the need for a clear clinical hypothesis. We show that the Microbial Detection Array successfully identifies emerging viruses present in both non-clinical and clinical samples.

sample_organism:
Cowpox virus
Monkeypox virus
Orf virus
Eastern equine encephalitis virus
dengue virus type 2
West Nile virus
Yellow fever virus
Rift Valley fever virus
Toscana virus
Dengue virus
sandfly fever Sicilian virus
synthetic construct
Chikungunya virus
Human poliovirus sp.
Usutu virus
Marburgvirus
Zaire ebolavirus
Sandfly fever Naples virus
Hepacivirus hominis
Mammarenavirus lassaense
Orthohantavirus dobravaense
Orthohantavirus hantanense
Orthohantavirus puumalaense
Orthohantavirus seoulense
Orthohantavirus sinnombreense
Orthonairovirus haemorrhagiae

overall_design: Fifteen clinical samples and 27 non-clinical samples (cell culture supernantants or purified viral DNA or RNA) were analyzed for presence of emerging viruses using the MDA microarray.

first: Maiken

last: Rosenstierne

first: Majken

last: Olesen

first: Anna

last: Pappa

first: Olivier

last: Engler

first: Sebastien

last: Plumet

first: Ali

last: Mirazimi

first: Manfred

last: Weidmann

first: Matthias

last: Niedrig

first: Anders

last: Fomsgaard

first: Lena

last: Erlandsson


title: Differential genes in adipocytes induced from polycystic ovary syndrome-derived and non- polycystic ovary syndrome-derived human embryonic stem cells

status: Public on Nov 22 2013

city: Zhengzhou

first: Fang

last: Wang

address: 1st of Jianshe Road

institute: The first affiliated hospital of zhengzhou university

summary: To explore the molecular mechanisms of obesity and insulin resistance in the patients with polycystic ovary syndrome (PCOS) at the level of human embryonic stem cells (hESCs).Three PCOS-derived and one non-PCOS-derived hESC lines were induced into adipocytes, and then total mRNA was extracted from these adipocytes. The differential genes between PCOS-derived and non-PCOS-derived adipocytes were identified with GeneChip, and then were validated with real-time PCR.There were 153 differential genes. Of the 153 genes, 91 genes were up-regulated and 62 down-regulated. Nuclear receptor subfamily 0, group B, member 2 (NR0B2) was an up-regulated gene, and GeneChip software system indicated that it was associated with obesity and diabetes.

first: Yingpu

last: Sun


title: Transcriptional profiling of left ventricle and peripheral blood cells in rats with post-myocardial infarction

city: Warszawa

first: Dorota

middle: Anna

last: Tulacz

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics of the Polish Academy of Sciences

summary:
Myocardial infarction (MI) often results in left ventricular (LV) remodeling followed by heart failure (HF). It is of great clinical importance to understand the molecular mechanisms that trigger transition from compensated LV injury to HF and to identify relevant diagnostic biomarkers. In this study, we performed transcriptional profiling of LVs in rats with a wide range of experimentally induced infarct sizes and of peripheral blood mononuclear cells (PBMCs) in animals that developed HF.
We used microarrays to investigate gene expression in the left ventricle (LV) accompanying myocardial infarction and concomitant heart failure (HF) in a well validated model of post-infarcted heart failure and to evaluate their reflection in peripheral blood mononuclear cells (PBMCs)

overall_design: Myocardial infarction (MI) was induced in male Wistar rats by ligation of the proximal left coronary artery. The sham-operated group (control group) was subjected to the same protocol, except that the suture was not tied around the proximal left coronary artery. Sham-operated rats (n=6) and rats with small (n=6), moderate (n=6), and large (n=5) MI size were included into the experiment two months after the operation. Then, left ventricules and blood samples were obtained for RNA extraction and hybridization on Affymetrix microarrays. Microarrays were used to compare the LV and PBMCs transcriptomes of control and experimental animals. The development of heart failure was estimated by echocardiography and catheterization.

first: Beata

last: Burzynska

first: Monika

last: Gora

first: Urszula

last: Mackiewicz

first: Michal

last: Maczewski


title: Profiling and bioinformatics analysis of hsa-miRNAs involved in A549 strain of human alveolar epithelial type II cell line infected with A/Zhejiang/DTID-ZJU02/2009(H1N1)

status: Public on Nov 06 2013

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

institute: NWSUAF

summary: A/Zhejiang/DTID-ZJU02/2009(H1N1) is a strain of the swine-origin influenza A(H1N1) virus isolated during the human swine flu outbreak of 2009. To analyze the miRNA expression profiles of A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) at 0, 24, 48, and 72 h post-infection (hpi) and investigate the relation between the miRNA expression profile and its pathogenesis, Human MicroRNA Array v2.0 was applied. At 24 hpi, 174 miRNAs were detected to change their expression compared with 0 hpi, 28 of them increased and 146 decreased. At 48 hpi, 214 changed miRNAs were detected, 21 of them increased and 193 decreased. At 72 hpi, 282 changed miRNAs were detected, 19 of them increased and 263 decreased. Targets of the 21 significantly differentially expressed miRNAs were analyzed by bioinformatics technology. The function categories of the predicted targets were analyzed by GO(Gene ontology) annotation. The signaling pathways involving the changed miRNAs were analyzed by KEGG(Kyoto Encyclopedia of Genes and Genomes) and GO annotation. Four key signaling pathways were identified, namely, the MAPK, apoptosis, JAK_STAT, and toll-like receptor signaling pathways. The apoptosis and MAPK signaling pathways were activated by all miRNAs, whereas the JAK_STAT and toll-like receptor signaling pathways were activated by some miRNAs but inhibited by the others, suggesting balance in the host–virus interaction. We also constructed and analyzed the protein-protein interaction network of all the predicted targets and found some key nodes. This finding provides a picture of miRNA expression in A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) as complete as possible, which may provide important information for investigation of H1N1 pathogenesis and therapeutic method.

overall_design: the miRNA expression profiles of A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) at 0, 24, 48, and 72 h post-infection (hpi) were analyzed  and the relation between the miRNA expression profile and its pathogenesis was  investigated.

first: Zhang

last: Deli


title: Seeking genes responsible for developmental origins of health and disease from the fetal mouse liver following maternal food restriction [Methylation]

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

type: Methylation profiling by genome tiling array

summary: Non-optimal fetal environments resulting in low birth weight have epidemiologically been associated with a higher risk of adult diseases. In animal models, maternal undernutrition has successfully demonstrated that offspring owed increased risks for adult diseases. In mice, shorten life span was also demonstrated in offspring following maternal undernutrition. In the present study, we treated pregnant mice with 50% food restriction (FR), and performed global gene expression and promotor DNA methylation profiling on the fetal livers. Considering that effects of food restriction is opposite between before and after birth, we further searched genes which are regulated oppositely against adult calorie restriction (CR) and commonly against aging. Among searched genes, trib1 has already been demonstrated to contribute to a risk of cardiovascular disease, hypertriglyceridaemia and insulin resistance. The present result suggests that expression of trib1 is affected by maternal nutrition, and is one of the most responsible genes for developmental origins of metabolic syndrome. In addition, lepr was also down-regulated by maternal FR, suggested a potential role of this gene in induction of obesity and diabetes. Promotor DNA methylation profiling as well as gene expression profiling revealed that glucocorticoid receptor target genes were regulated by maternal FR. This finding supports previous studies that suggest an important role for glucocorticoid in developmental origins of metabolic syndrome. In the immune system, most of the genes related to interferon were down-regulated in their expression with up-regulation of their promoter DNA methylation. The profiling also suggested diminished NF-κB signalling. These results suggested that maternal FR affected development of the immune system. We presented here a list of genes responsible for developmental origins of health and disease, which were regulated oppositely against adult CR, and commonly against aging, and also affected their promotor DNA methylation. The present list hopefully contributes to prediction of risks for non communicable diseases, and also prediction of prenatal environment of nutrition from offspring materials.

overall_design: Here we carried out global gene expression profiling analysis on the fetal mouse liver following maternal 50% FR. Considering that opposite effects of nutrition between the fetus and adult, we further analyzed our fetal array data by comparing with data from their mothers, and array data on the effect of CR and aging in previous reports using adult rodent tissues. In addition, we performed global DNA methylation analysis using mouse promoter microarray, and compared the results with data of the gene expression analysis. Finally, we presented a list of candidate genes responsible for DOHaD.

first: Tetsuo

last: Ogawa

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Tomomi

last: Saito

first: Makiko

last: Kuwagata

first: Seiji

last: Shioda


title: Transcription profiling of sweet orange in response to PthA4-dependent infection

city: Gainesville

first: Jeffrey

middle: B.

last: Jones

state: FL

address: 1453 Fifield Hall

department: Plant Pathology

institute: University of Florida

summary: We used this microarray data to survey the differentially expressed genes in sweet orange by comparing leaf tissues challenged with wild type X. citri ssp. citri (Xcc) strain 306 and leaf tissues challenged with pthA4 gene defeciency mutant Xcc306ΔpthA4at 6 h and 48 h post inoculation.The deletion of pthA4 gene reduced the virulence of Xcc306, and eliminated pustule formation. The citrus gene expression changes after inoculation of these two isogenic strains represent PthA4-mediated molecular events in a susceptible reaction.

overall_design: Xcc306 wild-type strain and pthA4 gene deletion mutant Xcc306ΔpthA4 were used to inoculate fully expanded young leaves in sweet orange (Citrus sinensis)  at the concentration of 5 X 108 cfu/ml using syringe with needle in a quarantine greenhouse facility at the Citrus Research and Education Center, Lake Alfred, FL. The leaves were harvested 6 hours and 48 hours after inoculation for RNA isolation. To allow stringent statistical data analysis, three biological replicates were conducted and three technical replicates were pooled for each strain. RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The quantity and quality of RNA were determined on a ND-8000 Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington,DE). Microarray labeling, hybridization, washing, scanning, and data analysis were performed at ICBR facility at University of Florida in Gainesville. Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language. Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package. Differentially expressed genes with fold change higher than 3 and an adjusted P-value (FDR) less than 0.05 were considered as differentially expressed genes at a statistically significant level.

first: Yang

last: Hu

first: Nian

middle: B


title: Penicillium marneffei:  Gene expression profiling of hyphal and yeast cells and during conidiation

city: University of Melbourne

first: Alex

last: Andrianopoulos

address: Royal Parade

institute: University of Melbourne

summary: Penicillium marneffei (Talaromyces marneffei) is an opportunistic human pathogen that can grow in a multicellular hyphal form at 25°C or a unicellular fission yeast form at 37°C, and can switch between these two forms in response to temperature. The yeast form is found in infected individuals and represents the pathogenic phase. In response to specific environmental cues, the hyphal form can undergo asexual development (conidiation) the produce a differentiated multicellular structure called a conidiophore which produces dormant spores (conidia). Inhaled conidia initiate infection. To identify genes that are ‘phase or cell-state specific’ transcriptional profiling was performed with a custom microarray consisting of ~42% of the predicted P. marneffei genes and RNA from P. marneffei hyphal, yeast and conidiation cell types.

overall_design: A custom microarray consisting of short, random genomic fragments from P. marneffei (~42% of the predicted genes) was generated using PCR products of the inserts from two independent DNA libraries constructed from genomic DNA of the P. marneffei type strain FRR2161. PCR products from previously cloned P. marneffei genes with known expression profiles were included as controls on the microarray. Total RNA from hyphal, yeast or conidiation cell types was prepared and used in pairwise combinations (conidiation versus hyphal cells, conidiation versus yeast cells and hyphal versus yeast cells) on the microarrays. Three biological replicate cultures were prepared for each experiment.

first: Shivani

last: Pasricha

first: David

last: Canovas

first: Luke

last: Pase

first: Nathamon

last: Ngaosuwankul

first: Alicia

last: Oshlack

first: Gordon

middle: K

last: Smyth


title: Effects of an antipsychotic (Olanzapine) involves alterations in gene specific DNA methylation

first: Melkaye

last: Melka

summary:
Antipsychotic drugs are commonly used to treat psychosis, mood disorders, and anxiety. While there is indirect evidence that some component of the antipsychotic effect of these drugs may involve modulation of dopamine transmission, their mechanism of action is poorly understood. We hypothesized that antipsychotic drugs mediate their effects via epigenetic modulation. Here we tested the effect of an antipsychotic, olanzapine, on the methylation status of genes following chronic treatment. These effects have been revealed through significantly increased (p<0.01) DNA methylation of genes involved in dopaminergic and non-dopaminergic pathways including the glutamatergic, GABAergic, cholinergic, neuregulin and ErbB signaling pathways. The affected genes included GLS in hippocampus, NR1 in cerebellum and GLUD1 and NR2B in liver. Further, from a set of genes in the 22q11.2 micro-deletions that has been previously implicated in psychosis, 22 genes showed increased methylation following olanzapine treatment. Ingenuity Pathway Analysis (IPA) revealed that chronic olanzapine treatment significantly affected several important pathways such as CREB and CDK5 signaling (p=1.4E-05). Also, DNA replication, recombination and repair, cellular movement and cell cycle have been identified as the top networks affected by olanzapine.
The results suggest that these downstream effects, aside from D2 blockade, may play a critical role in the biological actions of antipsychotics. These include altered expressions of relevant genes involved in GABAergic, glutamatergic, cholinergic, neuregulin and ErbB signaling pathways. Epigenetic mechanisms involving changes in DNA methylation could, therefore, explain the delay and individualized non-specificity of biological effects of olanzapine. The results also suggest that DNA methylation may play a role in the process of therapeutic efficacy of olanzapine by altering the transcriptome via tissue-specific methylation of genes involved in schizophrenia signaling pathways.

overall_design: comparison of olanzapine treated rats vs. control rats for genome-wide DNA methylation changes

first: Nagalingam

last: Rajakumar

first: Richard

last: O'Reilly

first: Shiva

middle: M

last: Singh


title: Gene expression profiling of hepatitis B- and hepatitis C-related hepatocellular carcinoma using graphical Gaussian modeling

status: Public on Nov 14 2013

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary: Gene expression profiling of hepatocellular carcinoma (HCC) and background liver has been studied extensively; however, the relationship between the gene expression profiles of different lesions has not been assessed. We examined the expression profiles of 34 HCC specimens (17 hepatitis B virus [HBV]-related and 17 hepatitis C virus [HCV]-related) and 71 non-tumor liver specimens (36 chronic hepatitis B [CH-B] and 35 chronic hepatitis C [CH-C]) using an in-house cDNA microarray consisting of liver-predominant genes. Graphical Gaussian modeling (GGM) was applied to elucidate the interactions of gene clusters among the HCC and non-tumor lesions. Gene expression profiling of HCC and non-tumor lesions revealed the predisposing changes of gene expression in HCC. This approach has potential for the early diagnosis and possible prevention of HCC.

first: Teruyuki

last: Ueda

first: Katsuhisa

last: Horimoto

first: Sachiyo

last: Aburatani

first: Shigeru

first: Taro

last: Yamashita

first: Yoshio

last: Sakai

first: Mikiko

last: Nakamura

first: Hajime

last: Takatori

last: Sunagozaka

first: Shuichi

last: Kaneko


title: Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K4me3

status: Public on Nov 08 2013

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC.
To further elucidate the functional relatedness of the active H3K4me3 and repressive H3K27me3 histone remodeling in HCC, we performed H3K4me3 and H3K27me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues.

overall_design: Comparison of  ChIP-on-chip results between tumor(C) and  adjacent tissues(N) from three HCC specimens with H3K4me3

first: Bin

last: Xu

first: Shu-bin


title: Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K27me3

status: Public on Nov 13 2013

summary:
Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC.
To further elucidate the functional relatedness of the repressive H3K27me3 and active H3K4me3 histone remodeling in HCC, we performed H3K27me3 and H3K4me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues.

overall_design: Comparison of  ChIP-on-chip results between tumor(C) and  adjacent tissues(N) from three HCC specimens with H3K27me3


title: FGF21-Induced Gene Expression in Mouse Adipose Tissues

status: Public on Nov 18 2013

city: Boston

first: eric

last: muise

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

summary: FGF21 is a novel secreted protein with robust anti-diabetic, anti-obesity, and anti-atherogenic activities in preclinical species. In the current study, we investigated the signal transduction pathways downstream of FGF21 following acute administration of the growth factor to mice. Focusing on adipose tissues, we identified FGF21-mediated downstream signaling events and target engagement biomarkers. Specifically, RNA profiling of adipose tissues and phosphoproteomic profiling of adipocytes, following FGF21 treatment revealed several specific changes in gene expression and post-translational modifications, specifically phosphorylation, in several relevant proteins. Affymetrix microarray analysis of white adipose tissues isolated from both C57BL/6 (fed either regular chow or HFD) and db/db mice identified over 150 robust potential RNA transcripts and over 50 potential secreted proteins that were changed greater than 1.5 fold by FGF21 acutely. Phosphoprofiling analysis identified over 130 phosphoproteins that were modulated greater than 1.5 fold by FGF21 in 3T3-L1 adipocytes. Bioinformatic analysis of the combined gene and phosphoprotein profiling data identified a number of known metabolic pathways such as glucose uptake, insulin receptor signaling, Erk/Mapk signaling cascades, and lipid metabolism. Moreover, a number of novel events with hitherto unknown links to FGF21 signaling were observed at both the transcription and protein phosphorylation levels following treatment. We conclude that such a combined "omics" approach can be used not only to identify robust biomarkers for novel therapeutics but can also enhance our understanding of downstream signaling pathways; in the example presented here, novel FGF21-mediated signaling events in adipose tissue have been revealed that warrant further investigation.

overall_design: Three mouse strains (C57BL6 on chow diet, C57BL6 on high fat diet, and db/db on chow diet) were treated with either vehicle, wild-type FGF21, or pegylated FGF21 acutely or for several days and three white adipose tissues (IWAT, EWAT, RPWAT) and brown adipose tissue (BAT) were profiled on custom Affymetrix microarrays. The primary goal was to identify robust and consistent acute target engagement biomarkers of FGF21 activation in white adipose tissues.

first: Eric

last: Muise


title: Temperature-related gene expression reaction norms in brown trout

city: Aarhus

first: Michael

last: Hansen

address: Ny Munkegade 114

institute: Aarhus University

summary: Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta) populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if similar reaction norm patterns were present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C) representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population × temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We were able to identify 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Brown trout populations from three rivers in Denmark were studied: the Karup (KAR), Norring Moellebaek (NOR) and Lilleaa Rivers (LIL). These rivers experience different temperature regimes during the period lasting from egg incubation until fry emergence. During the autumn of 2004 and the winter of 2004/2005, adults from the three populations were collected by electro fishing. The fish were stripped for milt and eggs to establish an F1 generation. In autumn/winter 2008/2009, mature F1s were used to establish F2 offspring for each of the three populations. For KAR and LIL, 20 full-sib families were established, whereas for NOR, 15 full-sib families were established. Eggs from each full sib family were divided into two pools that were incubated at 5 and 8¡C in separate hatching troughs. At the time of first feeding (ca. 750-780 day-degrees), 10 individuals from each family and temperature were collected and transferred to separate tubes containing RNAlater (QIAGEN, Hilden, Germany). A 32K cDNA microarray developed for salmonids by cGRASP was used for the analyses. Ten families were randomly selected from each population. From each family two individuals were analyzed for each temperature (5 and 8oC, respectively), amounting to a total of 120 individuals. Of the two individuals from each temperature treatment within a family, one was labeled with CY5 and the other with CY3. For each family there were two comparisons of individuals representing different temperatures, but with dyes swapped between comparisons.

first: Kristian

last: Meier

last: Normandeau

first: Karen-Lise

middle: D

last: Mensberg

first: Jane

last: Frydenberg

first: Peter

middle: F

last: Larsen

first: Dorte

last: Bekkevold

first: Louis

last: Bernatchez


title: eQTL Mapping of the Drosophila Female Head Transcriptome

city: Columbia

first: Elizabeth

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

summary: A dataset of ~600 RIL crosses using RILs from the Drosophila Synthetic Population Resource to be used for genomewide eQTL mapping. All samples are from female heads.

overall_design: 54 arrays with 12 samples per array resulting in data for 596 RIL crosses.

first: Anthony

last: Long

first: Stuart

last: Macdonald


title: The prognostic and predictive value of a six-microRNA-based classifier in stage II colon cancer

status: Public on Nov 29 2013

city: Guangzhou

first: Zhenhua

last: Chen

address: NO.58,ZhongShan 2nd Road

department: Urology

institute: The First Affiliated Hospital,Sun Yat-sen University

summary: microRNA profiling of  colon tumor tissues vs adjacent normal tissues

overall_design: 40 paired tumor and adjacent normal tissues of stage Ⅱ colon caner

first: Junhang

last: Luo

first: Dan

last: Xie

first: Huiyun

last: Wang


title: Gene expression analysis of lentivirally-transduced rhesus macaque CD34+ cells long-term following transplant

status: Public on Nov 05 2013

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: The occurrence of clonal perturbations and leukemia in patients transplanted with retrovirally-transduced autologous hematopoietic stem and progenitor cells (HSPCs) has stimulated extensive investigation, demonstrating that proviral insertions perturb adjacent proto-oncogene expression. Although enhancer-deleted lentiviruses are less likely to result in insertional oncogenesis, there is evidence that they may perturb transcript splicing, and one patient with a benign clonal expansion of lentivirally-transduced HPSC has been reported.  The rhesus macaque model provides an opportunity for informative long-term analysis to ask whether transduction impacts on long-term HSPC properties. We utilized two techniques to examine whether lentivirally-transduced HSPCs from eight rhesus macaques transplanted 1-13.5 years previously are perturbed at a population level, comparing telomere length as a measure of replicative history and gene expression profile of vector positive versus vector negative cells. There were no differences in telomere lengths between sorted GFP+ and GFP- blood cells, suggesting that lentiviral transduction did not globally disrupt replicative patterns. Bone marrow GFP+ and GFP- CD34+ cells showed no differences in gene expression using unsupervised and principal component analysis. These studies did not uncover any global long-term perturbation of proliferation, differentiation, or other important functional parameters of transduced HSPCs in the rhesus macaque model.

overall_design: CD34+ hematopoietic stem and progenitor cells were purified from bone marrow aspirates obtained from 4 rhesus macaques 3-9 years following transplantation with lentivirally-transduced autologous hematopoietic stem and progenitor cells. All lentiviral vectors contained the GFP marker gene.  The CD34+ cells from each animal were sorted via flow cytometry into GFP+ and GFP- fractions, and RNA from these cells was used for Affymetrix gene expression analysis as detailed below. There were two samples, GFP+ and GFP-, from each of 4 animals.

first: Stephanie

last: Sellers

first: Cynthia

last: Dunbar


title: Expression data from rat livers - Naproxen and NO-Naproxen treatment

city: Milwaukee

first: Yan

last: Lu

state: WI

address: 8701 Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary:
To characterize naproxen and NO-naproxen, their effects on gene expression in livers of treated rats was examined. We have previously worked with liver and could therefore identify a moderate to strong antioxidant response element signature. There were two goals to this study: 1) to determine whether naproxen and NO-naproxen yield similar gene expression profiles, which would imply that their effects are mediated by the parent NSAID, and 2) to determine whether NO-naproxen, due to the release of NO, might cause increases in expression of genes associated with the antioxidant response element (ARE).
In this dataset, we include the expression data obtained from liver of untreated rats and rats treated with naproxen (400mg/kg diet) or NO-naproxen (550mg/kg diet) for 7 days.

overall_design: Total 12 samples were analyzed. We generated the following comparisons: NO-Naproxen vs. Control and Naproxen vs. Control.  Genes with a p-value < 0.05 and a fold-change ≥1.5 were selected.

first: Ming

last: You

first: Ronald

last: A. Lubet


title: Differentially regulated genes induced in Mycobacterium by in vitro acid-nitrosative multi-stress

city: Amherst

first: Andrea

last: Cossu

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

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

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycolicibacterium smegmatis MC2 155

overall_design: Refer to individual Series

first: Valentina

last: Rosu


title: Differentially regulated genes induced in Mycobacterium tuberculosis by in vitro acid-nitrosative multi-stress

summary: Transcriptional profile of Mycobacterium tuberculosis in in vitro acid-nitrosative multistress, comparing untreated control cells and bacteria under multi-stress.

overall_design: Two-condition experiment, MTB-K vs. MTB-ACID-NO treated. Biological replicates: 3 controls, 3 Acid-NO treated, independently grown and harvested. In controls and Acid-NO treated cells, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, five replicates per array.


title: Haemophilus ducreyi 35000HPfis relative to 35000HP

status: Public on Nov 04 2013

city: Dallas

first: Eric

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

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

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

first: Maria

last: Labandeira-Rey


title: Afghan Hindu Kush: where Eurasian sub-continent gene flows converge

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

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

summary: Despite being located at the crossroads of Asia, genetics of the Afghanistan  populations have been largely overlooked. It is currently inhabited by five major ethnic  populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal  from a subset of our samples, mitochondrial and Y- chromosome data from over 500  Afghan samples among these 5 ethnic groups. This Afghan data was supplemented  with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia  and updated Pakistani samples (HGDP-CEPH). The data presented here was  integrated into existing knowledge of pan-Eurasian genetic diversity.  The pattern of genetic variation, revealed by structure-like and Principal Component  analyses and Analysis of Molecular Variance indicates that the people of Afghanistan  are made up of a mosaic of components representing various geographic regions of  Eurasian ancestry.  The absence of a major Central Asian-specific component indicates that the Hindu  Kush, like the gene pool of Central Asian populations in general, is a confluence of  gene flows rather than a source of distinctly autochthonous populations that have  arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid  loci.

overall_design: 24 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.

first: Richard

last: Villems


title: Gene expression profiles after infection of zebrafish with Spring Viremia Carp Virus (SVCV)

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary: We describe here transcripts induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in internal organs (pooled spleen, head kidney). Also, transcripts from resistant fishes to viral infection one month after inoculation were studied.

overall_design: Three different experiments were performed to get three biological replicates. Fishes were divided into two groups in each experiment. First group was infected by immersion with SVCV 10^7 pfu/ml, second group was used as a control of non-infected fishes. 6 fishes per group were sacrificed two days post infection, whereas the rest of the infected fishes from the three experiments were maintained for 30 days in the aquariums and then survivors (six for experiment) were sacrificed. This submission includes three biological replicate groups for the non-infected fish and the two days post-infected fish, and two biological replicate groups for the 30 days post-infected fish.

first: Paloma

last: Encinas

first: Pablo

last: García-Valtanen


title: Array CGH with DNA extracted from Candida albicans strains and its derivatives, which is monosomic for chromosome 5

city: Rochester

first: Elena

last: Rustchenko

state: NY

address: 601 Elmwood Ave., Box 712

department: Biochemistry & Biophysics

institute: University of Rochester

summary: Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the derivatives

overall_design: Pair-wise comparison of genomic content between parental strains and their derivatives.

first: Feng

first: Anatoliy

last: Kravets

first: Gabor

last: Bethlendy

first: Stephen

last: Welle


title: Immunosignatures can predict vaccine efficacy

city: Tempe

first: Joseph

middle: Barten

last: Legutki

state: Arizona

address: 1001 S. McAllister Ave

department: Center for Innovations in Medicine

institute: The Biodesign Institute at Arizona State University

summary: Mice were immunized with either formalin fixed Influenza A/PR/8/34 (Killed PR8), the 2006-2007 seasonal influenza vaccine, the 2007-2008 seasonal influenza vaccine, a sublethal infection (live PR8) or mock immunized (PBS).  Array data was used to distinguish the immunogens from each other and predict which of the three inactivated vaccines would be protective against A/PR/8/34 challenge.

overall_design: two replicates of each peptide was printed on 1 CIM_10kv3 peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.

last: Johnston


title: Differentially regulated genes induced in Mycobacterium smegmatis by in vitro acid-nitrosative multi-stress

summary: Transcriptional profile of Mycobacterium smegmatis in in vitro acid-nitrosative multistress, comparing untreated control cells and bacteria under multi-stress.

platform_organism:
Mycobacterium tuberculosis H37Rv
Mycolicibacterium smegmatis MC2 155

overall_design: Two-condition experiment, MSMEG-K vs. MSMEG-ACID-NO treated. Biological replicates: 3 controls, 3 Acid-NO treated, independently grown and harvested. In controls and Acid-NO treated cells, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, three replicates per array.


title: Comparison of the expression profiles of the Clostridium difficile 630E strain after 8h, 14h and 38h of infection in mouse and after 8h, 14h and 38h growth in vitro

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur


title: Comparison of the expression profiles of the 630E strain after 8h, 14h and 38h of infection in mouse

summary: The virulence factors of Clostridium difficile have been studied for many years, but the main in vivo pathogenesis processes of this bacterium has to be investigated. Especially, data on the early mechanisms of C. difficile adaptation to the host is not yet available. The objective of our study was to improve the understanding of the pathogenesis of C. difficile by the analysis of the genome-wide temporal expression of C. difficile genes during the first hours of infection. Three groups of 4 axenic mice each were challenged by vegetative cells of the 630 C. difficile strain, and sacrified at 8, 14, and 38 hours post-infection. Pure prokaryotic RNA was obtained from caecal bacteria. Comparative hybridizations on strain 630 microarrays were done using cDNA issued from an 8-hours in vitro culture as control, with a dye-swap protocol for each sample. Normalisation and statistical analysis of all data were done with different functions of the limma package. The pathogenesis of C. difficile could be seen as a result of the successful metabolic adaptation of the bacteria to its host, contributing to its persistence and multiplication, and the coordinate expression of virulence factors. Analysis of our data enlightened some of these aspects. The results support strongly a two-step infection model, since there is, during the course of infection, a significant increase in the toxins expression contrasting with a decreased expression of most of the putative colonization factors. Several paralogs of the HMW S-layer protein are also down-regulated, some of them could be strong candidates as colonisation factors. Bacterial adaptation to the microenvironment of the host is assessed by the regulation of numerous metabolic pathways, i.e., the upregulation of the ethanolamine catabolic operon or the modulation of several PTS systems. Inactivation of some putative virulence factors identified by this methodology will complete this analysis.

overall_design:
Transcriptional profiling of the C. difficile 630E strain after 8h, 14h or 38h of infection in mouse.
Three-condition experiments: 630E strain 8h, 14h or 38h of infection in mouse vs. 630E strain 8h in culture. 4 biological replicates for each condition in dye swap.

first: Cecile

last: Deneve

first: Laxmee

last: Caleechurn

first: Marc

last: Monot


title: Comparison of the expression profiles of the 630E strain after 8h, 14h and 38h in TY

overall_design:
Transcriptional profiling of the C. difficile 630E strain after 8h, 14h or 38h in TY.
Two-condition experiments: 630E strain 14h or 38h in TY vs. 630E strain 8h in TY. 2 biological replicates for each condition in dye swap.


title: Transcriptional targets of Shewanella oneidensis HnoC (SO_2540)

status: Public on Nov 01 2013

city: San Diego

first: Lars

last: Plate

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis.
Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain.

overall_design: Transcript levels of a WT and hnoC deletion strain were measured after 15 hrs growth, 4 independent replicates were performed for each strain

first: Michael

middle: A

last: Marletta


title: Low paternal dietary folate alters the sperm epigenome and is associated with negative pregnancy outcomes

status: Public on Nov 02 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: Epidemiological studies suggest that a fatherâ€™s diet can influence offspring health. A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome. The epigenome includes heritable information such as DNA methylation. We hypothesized  that the dietary supply of methyl donors would alter epigenetic reprogramming in sperm. This hypothesis was examined by feeding male mice a folate deficient (FD) and folate sufficient (FS) diets and then generating and analyzing DNA methylation profiles of their sperm.

overall_design: C57BL/6 males were fed either the FS or FD diet throughout life (FS, n=32; FD, n=35; 2-3 month old). Pooled gene promoter DNA methylation profiles were generated from the sperm of three FS males and four FD males using the method of MeDIP (Methylated DNA Immunoprecipitation) followed by microarray hybridization.

first: Lambrot

last: Romain

first: Xu

last: Chen

first: Saint-Phar

last: Shawna

first: Chountalos

last: George

first: Cohen

last: Tamara

first: Paquet

last: Marilene

first: Suderman

last: Matthew

first: Hallett

last: Michael

first: Kimmins

last: Sarah


title: Pregnancy-associated genes contribute to antiluteolytic mechanisms in ovine coprus luteum

city: Fort Collins

first: Thomas

last: Hansen

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: Ovine interferon-tau (IFNT) is released from the conceptus by Day 12 of pregnancy and disrupts pulsatile release of endometrial prostaglandin F2 alpha (PGF), thereby protecting the corpus luteum (CL). IFNT may also have endocrine action through inducing interferon stimulated genes (ISGs) in the CL. The hypothesis that gene expression differs in CL collected from pregnant (P) and non-pregnant (NP) ewes by Day 14 due to the lytic action of PGF during the estrous cycle or the presence of a conceptus was tested. RNA was isolated on Days 12 and 14 in NP or P ewes (n = 3 ewes/group) and analyzed using the Affymetrix bovine microarray (24,000 targets).  Differential gene expression (>1.5 fold, P < 0.05) was confirmed using semi-quantitative real time PCR (RTPCR). Serum progesterone concentrations decreased (P < 0.05) from 1.7 ng/ml on Day 12 to 1.3 ng/ml by Day 14 in NP ewes suggesting initiation of luteolysis; and remained > 1.7 ng/ml in Day 12 and 14 P ewes indicating that the conceptus protected the CL from luteolysis. Early luteolysis from Day 12 to 14 NP was associated with differential expression of 683 genes, including SERPINE1 and THBS1.  Presence of a conceptus from Day 12 to 14 also induced expression of 743 genes, i.e., ISGs (ISG15, MX1), PTX3, and IL-6 and stabilized expression of VEGF and LHR genes. In conclusion, pregnancy circumvents luteolytic pathways, and activates or stabilizes genes associated with interferon, chemokine, cell adhesion, cytoskeletal, angiogenic and epithelial to mesynchymal transition pathways in the CL.

overall_design: There are 12 samples that were analyzed for the microarray, no duplicates and we increased the sample size to 50 for the RTPCR.  This Series contains the Affymetrix array data only (not RT-PCR data).

first: Jared

last: Romero

first: Alfredo

middle: Q

last: Antoniazzi

first: Natalia

middle: P

last: Smirnova

first: Brett

middle: T

last: Webb

first: Fang

last: Yu

first: John

middle: S

last: Davis


title: Circulating miRNAs as novel marker of pulmonary hypertension

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

summary:
We determined pattern of miRNAs of mild-to-severe human pulmonary arterial hypertension and compared the with health controls using microarray and subsequently validated by QPCRs
Manuscript Title: Circulating miRNAs as novel marker for pulmonary hypertension.  (Under Revision Plos One  Manuscript ID: PONE-D-12-38535)

overall_design: Performed microRNA microarray from one healthy and one severe PH patient and compared the results using additional samples by qPCR for other miRNAs

first: Chuanyu

last: Wei

first: Heather

last: Henderson

first: Christopher

last: Spradley

first: Il-Kwon

last: Kim

first: Nayeon

last: Hong

first: Alejandro

middle: C

last: Arroliga

first: Sudhiranjan

last: Gupta


title: Expression data from cell lines treated with enavatuzumab and human IgG1 control

status: Public on Oct 31 2013

city: Redwood City

first: Josue

last: Samayoa

address: 1500 Seaport BLVD

institute: AbbVie Biotherapeutics Inc.

summary:
Cancer lines were treated with enavatuzumab and a human IgG1 control (MSL109) in vitro.  Samples were extracted at various time points and analyzed via genechip.
We used microarrays to examine gene expression patterns following treatment with enavatuzamab.  Expression changes over time were compared with corresponding data from samples treated with a control.

overall_design: 16 samples were analyzed for each cell line, with duplicate samples at 4 different time points (from 6 hours to 3 days) for each of the 2 treatments (enavatuzumab and control).

first: Purcell

last: James

first: Kim

last: Han

first: Tanlimco

last: Sonia

first: Doan

last: Minhtam

first: Fox

last: Melvin

first: Lambert

last: Peter

first: Chao

last: Debra

first: Sho

last: Mien

first: Wilson

last: Keith

first: Starling

last: Gary

first: Culp

last: Patricia

first: Samayoa

last: Josue


title: Microarray analysis of miRNAs involved in Porcine Alveolar Macrophages at the early stage of porcine reproductive and respiratory syndrome virus infection [LCS_miRPig_18]

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

institute: NWSUAF

summary: By analyzing the changes of miRNAs of piglet PAMs at different time points after PRRSV infection,we can find porcine miRNAs associated with viral infection and possible target sites in both PRRSV and pig genome and their roles in protection against viral infections. Then these targets will screened by bioinformatics methods to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level .

overall_design: PAM cells were inoculated with HuN4, and were collected at 12h and 24h post-inoculation (pi), respectively. The uninfected cells served as mock-infected cells.The miRNA chip was according to the porcine miRNA sequences in Sanger miRBase Release 18.0 (http://www.sanger.ac.uk/Software/Rfam/mirna/)added with some miRNAs we found in reference. Then we confirmed the expression change of some important miRNAs by qRT-PCR

first: Zhang

last: Deli


title: Microarray analysis of miRNAs involved in Porcine Alveolar Macrophages at the early stage of porcine reproductive and respiratory syndrome virus infection


city: University Park

first: Timothy

last: McNellis

state: PA

address: 318 Buckhout Lab

department: Plant Pathology and Environmental Microbiology

institute: The Pennsylvania State University

summary: 48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5' were analyzed by microarray to identify gene expression differences between the individuals to correlate gene expression patterns with phenotypic traits segregating in the population

overall_design: 48 individual apple trees were assayed once each using RNA isolated from a single shoot tip from each tree.  There were no biological or technical replicates in the experiment. There was no control sample, since all 48 were compared to each other.

middle: W

first: Philip

middle: J

last: Jensen

first: Gennaro

last: Fazio

first: Craig

last: Praul


title: Integrated approach to explore the mechanisms of aromatase inhibition and recovery on fathead minnow ovaries

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Aromatase, a member of the cytochrome P450 superfamily, is a key enzyme in estrogen synthesis and is responsible for the aromatization of androgens into estrogens. Here, we used an integrated approach to better understand the effects of aromatase inhibition as well as the mechanisms involved in the adaptation and recovery process. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase. We used transcriptomics, metabolomics, and network inference to understand changes and infer connections at the transcript and metabolite level in the ovary. Other apical endpoints such as plasma estradiol, testosterone, and vitellogenin levels were also measured. An integrated analysis of the data revealed changes in gene expression consistent with increased testosterone. Metabolites such as glycogen and taurine were strongly correlated with increased testosterone levels.  Comparison of in vivo and ex vivo data suggested the accumulation of steroidogenic enzymes, including aromatase, as a mechanism to compensate for aromatase inhibition.

first: Natàlia

last: Garcia-Reyero

first: Drew

middle: R

last: Ekman

first: Daniel

middle: L

last: Villeneuve

last: Collette

first: David

last: Bencic

first: Gerald

last: Ankley

first: Edward

last: Perkins


title: Streptococcus sanguinis gene expression at late-log growth phase

city: Richmond

first: Xiuchun

last: Ge

state: VA

address: 521 North 11th Street

institute: Virginia Commonwealth University

summary: We found that many of the genes for which mutants could not be obtained using promoterless aphA-3 gene replacement were annotated as acquired via horizontal gene transfer or as encoding hypothetical proteins. We were curious about the explanation of this finding. The expression of these genes was therefore examined by microarray analysis. The microarray data showed many had undetectable expression. This led us to suspect that many of the unrecoverable mutants might have resulted from insufficient expression of the promoterless aphA-3 gene.

overall_design: S. sanguinis cultures at late log growth phase at 37 oC under microaerobic condition were used for microarray analysis. RNA from each of three independent samples was isolated by RNeasy mini kit (Qiagen, Valencia, CA). Spotted microarray slides were obtained from the Pathogen Functional Genomics Resource Center at JCVI. Each gene had four repeats in one spotted microarray slides. The microarray was performed according to the manufacturer’s protocol. Each sample was divided into two parts and labeled by Cy5 and Cy3 dyes respectively for microarray. The microarray data were analyzed by programs TIGR Spotfinder and Midas to obtain the ratio of one dye to another dye for gene relative expression. Additionally, the ratio of dye intensity to background in a microarray slide was obtained after Spotfinder analysis. Absolute expression of each gene was represented by the average ratio of dye intensity to background for each slide.

first: Ping

last: Xu


title: Candida albicans response to spaceflight (NASA STS-115)

city: Bozeman

first: Sheila

last: Nielsen

state: MT

address: 317 Leon Johnson Hall

department: Immunology and Infectious Disease

institute: Montana State University

summary: This study presents the first global transcriptional profiling and phenotypic characterization of the major human opportunistic fungal pathogen, Candida albicans, grown in spaceflight conditions. Microarray analysis revealed that C. albicans subjected to short-term spaceflight culture differentially regulated 454 genes compared to synchronous ground controls, which represented 8.4% of the analyzed ORFs. Spaceflight-cultured C. albicans induced genes involved in cell aggregation (similar to flocculation), which was validated by microscopic and flow cytometry analysis. We also observed enhanced random budding of spaceflight-cultured cells as opposed to more normal bipolar budding patterns for ground samples, in accordance with the gene expression data. Furthermore, genes involved in antifungal agent and stress resistance were differentially regulated in spaceflight, including induction of ABC transporters and members of the major facilitator family, downregulation of ergosterol-encoding genes, and upregulation of genes involved in oxidative stress resistance. Finally, downregulation of genes involved in the actin cytoskeleton was observed. Interestingly, the transcriptional regulator Cap1 and over 30% of the Cap1 regulon was differentially expressed in spaceflight-cultured C. albicans. A potential role for Cap1 in the spaceflight response of C. albicans is suggested, as this regulator is involved in random budding, cell aggregation, actin cytoskeleton, and oxidative stress resistance; all related to observed spaceflight-associated changes of C. albicans. While culture of C. albicans in microgravity potentiates a global change in gene expression that could induce a virulence-related phenotype, no increased virulence in a murine intraperitoneal (i.p.) infection model was observed. This study represents an important basis for the assessment of the risk that commensal flora could play during spaceflight missions. Furthermore, since the low fluid-shear environment of microgravity is relevant to physical forces encountered by pathogens during the infection process, insights gained from this study could identify novel infectious disease mechanisms, with downstream benefits for the general public.

overall_design:
Cells were grown for 24 hours on the space shuttle or as ground-based controls, preserved in RNALater, and stored at -80C.  Four samples of each flight- and ground-based controls were harvested for microarray analysis.
GAP is Group Activation Pack and each GAP contains 8 FPAs.  The numbers represent the # assigned to the particular GAP and the number assigned to the specific FPA (1-8) within the indicated GAP. The same hardware is used for the flight samples and the ground samples.

last: Nielsen-Preiss

first: Aurélie

last: Crabbé


title: Identification of anther expressing genes in cotton (Gossypium hirsutum)

city: Delhi

first: Pradeep

middle: Kumar

last: Burma

state: Delhi

address: Benito Juarez Road

department: Department of Genetics

country: India

institute: University of Delhi South campus

summary: This study was initiated with the objective of identifying the anther/tapetum specific promoters from cotton floral buds. Cotton is an important commercial crop. Hybrid cotton varieties are developed to obtain improved yield and fiber quality. Most of the hybrid seed production in cotton is carried out by hand emasculation, which requires large amount of manpower, resulting in high cost of hybrid seed. We are developing barnase-barstar based male sterility system, which would be a better alternative for hybrid development. The tapetum specific promoters are main requirement for such a system.  The study was thus carried out to identify genes expressed in the anthers.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Cotton bud sizes were correlated with  tapetum development. RNA was isolated from following tissues:  • Anther tissues from buds at pre-meiotic stage of development (Tapetum absent)  • Buds without anther tissues at pre-meiotic stage of development  • Anther tissues from buds during meiosis  (Tapetum present)  • Buds without anther tissues during meiosis  • Anther tissues from buds at post-meiotic stage of development (Tapetum degenerated)  • Buds without anther tissues at post-meiotic stage of development  • Leaf tissues  • Seedling 5 days after germination  Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following  Affymetrix protocols. Three biological replicates were maintained.

first: K

last: Paritosh

first: D

last: Pental

first: P


title: Toxicogenomic analysis of ionic silver and silver nanoparticles on the fathead minnow and implications to human health

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Nanoparticles are compounds of emerging concern with largely unknown risks for human and ecological health. It is crucial to evaluate their potential biological impact to prevent unintended adverse effects on human health and the environment. We analyzed the transcriptional effects of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) and silver nitrate (AgNO3) on the fathead minnow (Pimephales promelas) to understand their potential toxicity and adverse outcomes. We also tested the feasibility of the fathead minnow as an alternative species to elucidate potential adverse effects on humans. Fathead minnow females were exposed to either 4 µg/L of AgNO3 or 70 µg/L of PVP-AgNPs for 96h. Microarray analyses were performed on liver and brain. Functional analysis identified potential toxicity pathways and molecular initiating events (MIEs) that were confirmed with functional assays. Data suggested that AgNO3 and PVP-AgNPs had both common and distinct transcriptional effects. The nanoparticles were linked to neurotoxicity and oxidative stress, and identified as a dopamine receptor antagonist. Silver nitrate was also identified as a potential neurotoxicant and was confirmed as adrenergic and cannabinoid receptors antagonist.  While silver nitrate and PVP-AgNPs were both potential neurotoxicants, they appeared to act through different MIEs. Fathead minnow is a promising alternative species to elucidate potential adverse effects of relevance to human health.

overall_design: We analyzed the transcriptional effects of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) and silver nitrate (AgNO3) on the fathead minnow (Pimephales promelas) to understand their potential toxicity and adverse outcomes. FHM were obtained from Aquatic Biosystems (Fort Collins, CO), held in aerated dechlorinated tap water and fed three times daily with Zeigler® AquaTox Feed Gardners, PA, USA). Fathead minnow females were exposed to either 4 µg/L of AgNO3 or 70 µg/L of PVP-AgNPs (Luna Innovations, Blackburn, VA) for 96h at 24°C ± 1 with a 90% water change at 48 hours. Microarray analyses were performed on liver and brain.

first: Alan

last: Kennedy

first: B

last: Escalon

first: Jennifer

middle: G

last: Laird

first: Arun

last: Rawat

first: Stephan

last: Wiseman

first: Markus

last: Hecker

first: Jeffery

last: Steevens


title: Microarray analysis of miRNAs involved in Porcine Alveolar Macrophages at the early stage of porcine reproductive and respiratory syndrome virus infection [LCS_miRPig_17]

first: Li

last: Dengyun

summary: By analyzing the changes of miRNAs of piglet PAMs 6h after PRRSV infection,we can find porcine miRNAs associated with viral infection and possible target sites in both PRRSV and pig genome and their roles in protection against viral infections. Then these targets will screened by bioinformatics methods to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level .

overall_design: PAM cells were isolated from 60d old healthy piglets and  inoculated with HuN4,a strain of highly pathogenic porcine reproductive and respitory syndrome  virus (HP-PRRSV) and were collected at 6h post-inoculation (pi). The uninfected cells served as mock-infected cells.The miRNA chip was according to the porcine miRNA sequences in Sanger miRBase Release 17.0 (http://www.sanger.ac.uk/Software/Rfam/mirna/)added with some miRNAs we found in reference. Microarray hybridization and data analysis helps to find  the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level .

first: Zhang

last: Deli


title: Gene expression data of mRNA from skeletal muscle sample of pig DL and Pi breed

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
The skeletal muscle development in swine begins at embryogenesis.
Simultaneously, 24,123 probe-sets were screened, analysed for differential expression between different breeds (german landrace and pietrain) at different stages of development (35, 63, 91 dpc and adult stage).

overall_design: RNAs of skeletal muscle from german landrace and pietrain at 35, 63, 91 dpc and adult stages were hybridized to Affymetrix GeneChip Porcine Genome Array.

first: Siriluck

last: Ponsuksili


title: Regulation of onco and tumor suppressor miRNA by mTORC1 inhibitor PRP-1 in human chondrosarcoma

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary:
The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 not treated (Control)  and JJ012 chondrosarcoma cell line treated with  antitumorigenic neuropeptide PRP-1. The goal was to  elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays,was performed. performed.211 unique gene targets were detected for downregulated miRNAs and 104 unique target genes for upregulated miRNAs with 28 target genes  common for both. out of 122 upregulated and 109 downregulated , total 9 differentially statistically significant miRNAs(3 upregulated and 6 downregulated) fitting P<0.05 by Benjamini Hochberg  were detected   when comparing chondrosarcoma cell line  treted to not treated control  using human Exiqon arrays with biological triplicates.: miR192, regulating cell cycle checkpoinrts   was upregulated in treated samples 4 fold, miR125b, known as tumor suppressor in sarcomas was upregulated 4.87 fold. miR20a was upregulated 5.29 , known to form  complexes with Argonaute proteins-part of  RNA induced silencing complex (RISC)
Downregulated miRNas included miR509-3p (12.88 fold), its targets Yap, Rac1 and Yes1 known to be associated with Src kinase activity; miR589 was downregulated 7.46 fold , targets Src adaptors'. miR 302c was downregulated6.46 fold  and miR199a=5p -5.66 fold , that acted as oncogenes in sarcomas. miR584 involved on cell migration  and TGFbeta signaling was downregulated 4.78 fold

overall_design: Comparison of miRNA expression between control   samples and samples treated with antiproliferative cytostatic mTORC1 inhibitor PRP-1  cytokine  in human chondrosarcoma  JJ012 cell line

last: Galoian

first: T

last: Guettouche

last: Issac

first: A

last: Qureshi

first: H

last: Temple


title: Agilent-013282 array CGH on NCI-60 cancer cell lines

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

summary: The NCI-60 cancer cell lines have been used for studying cancer pathogenesis and for drug discovery. This dataset adds to the growing number of datasets on various genomic platforms that have been made public on Cellminer (http://discover.nci.nih.gov/cellminer/)

overall_design: 60 cell lines (including PR:DU145 and its drug resistant derivative PR:RC01) were arrayed. LC:A549 was done with 8 replicates. LC:NCI_H226 was done on one array. All others were done with 2 replicates. All cell lines with 2 or more replicates were done with dye flips

first: William

last: Reinhold

first: John

middle: N

last: Weinstein


title: DamID for MBD3 in human breast cancer cell lines [Tiling Arrays]

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

summary: Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS).  Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression.

overall_design: DamID experiment was performed in human breast cancer cell lines (MCF-7 and MDA-MB-231) in triplicate. Samples were hybridized to NimbleGen Human Whole-Genome Tiling Arrays (0701_HG18_TILE_05_HX1 and 100718_HG18_TILE_05_HX1).  MBD3-Dam material was hybridized over Dam-only control.

first: Takashi

last: Shimbo

first: Paul

last: Wade

first: Ruchir

last: Shah


title: DamID for MBD3 in human breast cancer cell lines [Promoter_Arrays]

overall_design: DamID experiment was performed in human breast cancer cell lines (MCF-7 and MDA-MB-231) in duplicate. Samples were hybridized to Nimblegen 2.1M Deluxe promoter array.  MBD3-Dam material was hybridized over Dam-only control.