title: Comparison of Arabidopsis stem base to first internode transcriptional profiles

city: Vienna

first: Thomas

last: Greb

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute

summary: Subsequently to primary growth, most dicotyledonous plants undergo secondary growth leading to an increased diameter of growth axes. During secondary growth initiation in shoots, a cylindrical meristem, the vascular cambium, is established by the initiation of meristematic activity in interfascicular regions, a process that ultimately leads to the formation of a continuous cylinder of vascular tissue along the shoot axis. In Arabidopsis this happens in a reduced area at the very base of the stem. In this study, a transcriptional comparison between the base and the first internode has been performed in order to asses the physiological state of both sample types and search for potential key regulators of the process.

overall_design: Total RNA was extracted from the base and the first internode from stems of 15cm tall Arabidopsis plants (ecotype Col-0). After RNA amplification, Cy3 or Cy5 targets were produced. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap.

first: Javier

last: Agusti


status: Public on Mar 24 2010

city: San Francisco

first: Sanjay

last: Chandriani

state: CA

address: 513 Parnassus Avenue

country: USA

institute: UCSF

type: Expression profiling by genome tiling array

summary:
[original title] Mock or latently infected KSHV cells (BCBL, SLK and HFF) vs common reference (mixture of RNA from both infected and uninfected cells).
Expression profiling of latently infected cells using a custom tiling microarray.
SLK and HFF cells were infected and selected for rKSHV.219.  Mock infected SLK and HFF cells served as controls for each of these two stably infected cells, respectively.  BJAB cells served as uninfected controls for the BCBL-1 cells.  Biological replicates were harvested and analyzed.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8
Human herpesvirus 8 strain rKSHV.219

platform_organism:
Homo sapiens
Human herpesvirus 8 type M

overall_design: Two condition experiment: mock infected vs. latently infected cells.  Three cell types.

first: Don

last: Ganem


title: Evolutionarily conserved replication timing profiles distinguish cell types and predict long range chromatin interaction

city: Tallahassee

first: Tyrone

last: Ryba

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

summary: Extensive changes in replication timing occur during early mouse development, but their biological significance remains uncertain. To identify evolutionarily conserved features of replication timing and their relationships to epigenetic properties in humans, we profiled replication timing genome-wide in four human embryonic stem cell (hESC) lines, hESC-derived neural precursor cells (NPCs), lymphoblastoid cells, and two independently derived human induced pluripotent stem cell lines (hiPSCs). Results confirm the conservation of coordinately replicated megabase-sized units of chromosomes (replication domains) with stable cell type specific molecular boundaries that consolidate into larger replication domains during differentiation. Replication timing changes encompassed units of 400-800 kb and were coordinated with changes in transcription similar to mouse. Moreover, significant cell-type specific conservation of replication timing profiles was observed across regions of conserved synteny, despite significant species variation in the alignment of replication timing to isochore GC/LINE-1 content. Replication profiling also revealed a closer genome-wide epigenetic alignment of hESCs to mouse epiblast-derived stem cells (mEpiSCs) than to mouse ESCs. Finally, we identify a signature of chromatin modifications marking the boundaries of early replicating domains and a remarkably strong link between spatial proximity of chromatin as measured by Hi-C analysis and replication timing. Together, our results reveal evolutionarily conserved elements of the replication program in mammalian early development, demonstrate the power of replication profiling to identify important epigenetic distinctions between closely related stem cell populations (e.g. ESCs vs. EpiSCs), and strengthen the hypothesis that replication domains are structural and functional units of 3D chromosomal architecture.

overall_design: 8 cell types, with a total of 13 individual replicates (i.e. 5 in duplicates, 3 in single replicates)

first: Ichiro

last: Hiratani


status: Public on Mar 31 2010

city: Singapore

first: Choong Yong

last: UNG

state: Singapore

address: Science Drive 4

department: Biological Sciences Department

country: Singapore

institute: National University of Singapore

summary:
Full title: Mercury-Induced Hepatotoxicity in Zebrafish: In Vivo Mechanistic Insights from Transcriptome Analysis, Phenotype Anchoring and Targeted Gene Expression Validation

In this study, we performed microarray-based expression profiling on liver of zebrafish exposed to 200 µg/L of mercuric chloride for 8-96 h, to identify global transcriptional programs and biological pathways involved in mercury-induced adaptive responses under in vivo environment.

overall_design: We analyzed 12 arrays for mercuric chloride treated zebrafish liver and 12 arrays for control liver.

first: Choong

middle: Y

last: Ung

first: Siew

middle: H

last: Lam

first: Cecilia

last: Winata

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Molecular characterization of a cryptochrome in Neurospora crassa

city: Hanover

first: Chen-Hui

last: Chen

state: NH

address: 702 Remsen

department: Genetics

institute: Dartmouth College

summary:
Cryptochromes were identified in plants and animals where they function as either photoreceptors or circadian clock components. In the filamentous fungus Neurospora, the biological function of cryptochrome has not yet been explored. Here, we demonstrate that Neurospora crassa cryptochrome (Nc cry) is a DASH-type of cryptochrome, capable of  binding FAD and MTHF, whose transcript and protein levels are both strongly induced by blue light in a wc-1 dependent manner. Although the Nc cry transcript is circadian-regulated and antiphasic to frq, knockout strains of Nc cry appears to have a normal clock phenotype. Whole genome microarray and RT-QPCR analysis confirm that Nc cry is not involved in the signal transduction of either early or late light responses and seems to have no transcriptional regulatory activity under our laboratory conditions. Our study concludes that the only cryptochrome in Neurospora crassa is dispensable for the well-characterized blue light sensing cascade and is not part of the circadian clock system.

Keywords: light response

overall_design: Two-color microarray. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.

first: Carol

middle: S

last: Ringelberg

first: Jennifer

last: Loros

first: Jay

middle: C

last: Dunlap


title: Comparative transcriptome and phenotype analysis of Bacillus cereus in response to disinfectant treatments

city: Wageningen

first: Mara

last: Ceragioli

address: Bomenweg

department: Food Microbiology LAb

country: Netherlands

institute: WUR

summary: Antimicrobial chemicals are widely applied to clean and disinfect food-contacting surfaces. However, the cellular response of bacteria, such as Bacillus cereus, to various disinfectants is unclear. In this study, the physiological and genome-wide transcriptional responses of B. cereus ATCC 14579 exposed to four different disinfectants (i.e., benzalkonium chloride, sodium hypochlorite, hydrogen peroxide, and peracetic acid) were analyzed. The physiological response of B. cereus to different concentrations of the disinfectants used was investigated. For each disinfectant, concentrations leading to the attenuation of growth, growth arrest, and cell death were studied in more detail. The simultaneous analysis of the transcriptional responses of B. cereus upon exposure to the different concentrations of disinfectants revealed common responses induced by the four disinfectants. Notably, genes involved in the general and oxidative stress responses were commonly up-regulated. Furthermore, the obtained results indicate that all the disinfectants also induce specific responses. Exposure to benzalkonium chloride, a disinfectant known to induce membrane damage, specifically induced genes involved in the fatty acid metabolism. Benzalkonium chloride induced-membrane damage was confirmed by fluorescence microscopy and fatty acid analysis confirmed that fatty acid composition of cell membrane was affected upon exposure to benzalkonium chloride. Sodium hypochlorite induced genes involved in sulfur and sulfur-containing amino acids metabolism, which correlated with the observed sodium hypochlorite-specific induction of oxidation of sulphydryl groups. Hydrogen peroxide and peracetic acid exposures induced genes involved in DNA damage and the SOS response. Notably, hydrogen peroxide and peracetic acid-treated cells exhibited higher mutation rates corroborating with the induced SOS response. Understanding the mechanisms displayed by microorganisms coping with disinfectants-induced stress may allow for design of more efficient sequential and/or disinfectant combination treatments in food processing environments.

overall_design: Each sample was treated for 10 and 30 min with different disinfectants (i.e., benzalkonium chloride, sodium hypochlorite, hydrogen peroxide, and peracetic acid) and compared with non-exposed cells (i.e., t0). For each disinfectant different concentrations were used: mild concentration, growth arresting concentrations (only for benzalkonium chloride and sodium hypochlorite), and lethal concentrations. The experiments were performed in duplicate and the duplicate samples were hybridized with a dye-swap.

first: Maarten

last: Mols

first: Roy

last: Moezelaar

first: Emilia

last: Ghelardi

first: Sonia

last: Senesi

first: Tjakko

last: Abee


title: Gene expression analysis in Eight Homo sapiens Cell lines

status: Public on Mar 25 2010

city: Huntsville

first: Preti

last: Jain

state: AL

address: 601 Genome Way

institute: Hudsonalpha Institute for Biotechnology

summary: Gene expression profiles for ~20,000 genes using Illumina Homo sapiensRef-8 v2

overall_design: Cell lines were picked to match cell lines that were assayed in a complimentary set of transient transfection promoter activity assays.  Gene identifiers on the BeadArrays were matched to promoter predictions from SwitchGear Genomics (www.switchdb.com; score>20) for transcripts that were not associated with alternative promoters. The eight cell lines are:  Ags, HeLa, HepG2, HT1080, HCT116, T98G, U87MG, and G402.

first: David

last: Johnson

first: Richard

middle: M

last: Myers

first: Devin

last: Absher


title: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: fluoranthene

status: Public on Mar 23 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

country: United Kingdom

institute: Cardiff University

summary:
Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to fluoranthene (FA).

DEBtox modelling showed an effect of FA on costs for growth and reproduction (i.e. for production of new and differentiated biomass). The microarray analysis supported this effect, showing an effect of FA on protein integrity and turnover that would be expected to have consequences for rates of somatic growth.

Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes.

overall_design:
Adults of C. elegans strain GE-31 were exposed as biological replicate groups (approx 10,000) to a control and 4 concentrations of fluoranthene from L1 stage. Replicate populations were sampled 12 hours after the on-set of egg laying and hybridised against a common oligonucleotide reference for purposes of normalisation.

All experiments were conducted following a reference design with the reference sample compiled from a mixture of RNA extracted from control and cadmium-, fluoranthene-, atrazine- and copper-exposed worms from L1, L4 and adult life-stages. Use of this reference was intended to provide optimal coverage of the spotted genes.

first: Suresh

last: Swain

first: Jodie

middle: F

last: Wren

first: Stephen

middle: R

last: Sturzenbaum

first: A

middle: J

last: Morgan

first: Tjalling

last: Jager

first: Martijs

last: Jonker

middle: K

last: Hankard

first: Claus

last: Svendsen

first: Jenifer

last: Owen

first: B

middle: A

last: Hedley

first: Mark

middle: L

last: Blaxter

last: Spurgeon


title: Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome 1

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

summary:
Atrazine and bentazon are both photosystem II inhibiting herbicides that interfere with photosynthetic electron transport provoking oxidative stress. While atrazine is lethal to soybean, bentazon does not kill soybeans because of the capability of soybeans to metabolize the herbicide. Gene expression profiling was conducted using cDNA microarrays to understand the responses of soybeans to PSII interruption and concomitant oxidative stress caused by atrazine and bentazon by monitoring expression at 1, 2, 4, and 8 h after treatment (HAT). The microarray study revealed that 6,646 genes were differentially expressed with high statistical significance over the experiment with 88% of them sharing similar expression pattern between the atrazine and bentazon treatments. Many genes related to xenobiotic detoxification and antioxidation such as cytochrome P450s, glutathione-S-transferases, superoxide dismutases, catalases and tocopheral cyclases were induced by the herbicides. The study also discovered plants treated with bentazon started to recover between 4 HAT and 8 HAT as reflected in the decreased amplitude of fold changes of most genes from 4 to 8 HAT. The 12% of the genes that were differentially expressed between atrazine and bentazon were largely related to cell recovery, such as genes related to ribosomal components.
Keywords = stress
Keywords = GST
Keywords = ROS
Keywords = D1 protein
Keywords = Fuzzy k-means
Keywords = plant

Keywords: plant xenobiotic interaction

overall_design: loop design, 12 direct comparisons, 2 technical repeats including dye swaps, 3 biological repeats

first: Jin

last: Zhu

first: William

last: Patzoldt

first: Osman

last: Radwan

first: Patrick

last: Tranel

first: Steven

last: Clough


title: Melanoma Cancer miRNA Blood Profiles

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

summary: This project analyzes peripheral blood profiles of melanoma cancer patients. Since miRNAs are known to be valuable diagnostic markers we asked whether respective patterns of melanoma patients can be detected in peripheral blood samples rather than in biopsies. The project aimed at an improved understanding of complex profiles rather than single markers. Thus, a high-throughput technique was necessary, profiling all known miRNAs integratively. Top markers have been validated by using qPCR.

overall_design: n = 22 normal controls and n = 35 melanoma cancer samples have been screened for the complete miRNA repertoire. The melanoma samples have been collected by two clinicians using the same procedure. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.

first: Petra

last: Leidinger


title: miRNA expression profiling in Cystic Fibrosis Airway Epithelium

city: Beaumont

first: Irene

last: Oglesby

address: ERC, beaumont Hospital

department: Medicine

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Cystic fibrosis (CF) is one of the commonest lethal genetic diseases in which the role of microRNAs (miRNAs) has yet to be explored. We hypothesized that unique miRNA expression profiles exist in CF versus non-CF bronchial epithelial cells so the our aim was to investigate whether unique miRNA expression profiles exist in CF, particularly in CF bronchial epithelial cells and explore their effects on influencing signaling pathways.

overall_design: The expression of 667 miRNAs were measured in bronchial brushings from individuals with and without cystic fibrosis (CFn=5, non-CF n=5).  The 5 CF patient samples have been normalised to the controls so we get a final normalised value for 5 samples only. There are 2 raw data files for samples and controls as there are two cards A and B ran for each sample, for a total of 4 raw data files available on the Series record.


title: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: atrazine

first: Peter

last: Kille

summary:
Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to atrazine (AZ).

For AZ, the physiological mode of action predicted by DEBtox was increased cost for maintenance. The transcriptional analysis demonstrated that this increase resulted from effects on DNA integrity as indicated by changes in the expression of genes chromosomal repair.

Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes.

overall_design:
Adults of C. elegans strain GE-31 exposed as biological replicate groups (approx 10,000) to a control and 4 concentrations of atrazine from L1 stage. Replicate populations were sampled 12 hours after the on-set of egg laying and hybridised against a common reference for purposes of normalisation.

All experiments were conducted following a reference design with the reference sample compiled from a mixture of RNA extracted from control and cadmium-, fluoranthene-, atrazine- and copper-exposed worms from L1, L4 and adult life-stages. Use of this reference was intended to provide optimal coverage of the spotted genes.

first: Suresh

last: Swain

first: Jodie

last: Wren

first: Stephen

last: Sturzenbaum

last: Morgan

last: Jager

first: David


title: Time course of localization of histone modifications, insulators, RNA polymerase II on TNF alpha responsive genes

city: Komaba

first: Shuichi

last: Tsutsumi

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary:
The many modifications involved in transcription are extensively coupled, and levels of histone modifications, insulators, and RNA polymerase II could be measured using genomic tiling microarrays. After 0, 30, 60 min of stimulation of HUVEC with TNF alpha, we crosslinked cells and fixed, then immunoprecipitated to prepare DNA using antibodies for modified histone, insulators and RNA polymerase.
We apply samples collected every 7.5 min to arrays and monitor the growth of several long transcripts.

Keywords: time course

overall_design: Using tumor necrosis factor a (TNF-alpha) to switch on transcription of selected human genes rapidly and synchronously, we apply samples collected every 30 min to arrays

first: Tatsuhiko

last: Kodama

first: Hiroyuki

last: Aburatani

first: Sigeo

last: Ihara

first: Yoshihiro

last: Ohta

first: Youichiro

last: Wada


title: SSHscreen analysis of cowpea drought stress SSH libraries (F&R) to calculate Enrichment ratio 2 and 3 values

status: Public on Mar 22 2010

city: Pretoria

first: Dave

last: Berger

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

summary:
Screening cDNA clones from SSH library by hybridization with cDNA used to construct the library. Treated samples were drought-stressed cowpea plants, and control samples were cowpea plants subjected to a standard watering regime. cDNA clones from forward and reverse libraries are spotted on the same array, but data from each library were analysed separately after normalization using SSHscreen software (http://microarray.up.ac.za/SSHscreen ) to calculate Enrichment Ratio 3 (ER3) and Enrichment Ratio 2 (ER2) values for each clone.
ER3 is a measure of differential expression, and was determined using a set of hybridizations with unsubtracted treated (UT) and unsubtracted control (UC) cDNA. ER2 is a measure of the relative abundance of a clone's transcript in the original tester sample, relative to other transcripts in the sample prior to the SSH process. ER2 for the forward library was determined using a set of hybridizations with subtracted treated (ST) and unsubtracted treated (UT) cDNA. ER2 for the reverse library is determined using a set of hybridizations with subtracted control (SC) and unsubtracted control (UC) cDNA.

overall_design: Direct comparison of UT and UC cDNAs to calculate ER3 values for F and R library, including dye swaps and replicate arrays. Direct comparison of ST and UT cDNAs to calculate ER2 values for F library, including dye swaps and replicate arrays. Direct comparison of SC and UC cDNAs to calculate ER2 values for R library, including dye swaps and replicate arrays.

first: Nanette

last: Coetzer

first: Inge

last: Gazendam


title: Gene expression profiles of beta-cell enriched tissue obtained by Laser Capture Microdissection from subjects with type 2 diabetes

status: Public on Mar 20 2010

city: Boston

first: Lorella

last: Marselli

state: MA

address: One Joslin Place

department: Joslin Diabetes Center and the Department of Medicine

institute: Harvard Medical School

summary: Changes in gene expression in pancreatic beta-cells from type 2 diabetes could provide insights into their abnormal insulin secretion and beta-cell turnover. The laser capture microdissection technique was used to acquire beta-cells from pancreatic tissue sections obtained from type 2 diabetic (T2D) and non-diabetic controls. We found that 4% of analyzed transcripts were differentially expressed between the two groups at the lower confidence bound cutoff of 1.2, and, among the differentially expressed transcripts, 62% were up-regulated and 38% down-regulated in samples of T2D subjects compared to non-diabetic controls. We observed: 1) changes in expression of genes linked to glucotoxicity, in particular, up-regulation of LDHA and PCK1, and down-regulation of GPD2, ME1 and ACLY; 2) evidence of oxidative stress, documented by up-regulation of metallothionein genes; 3) few changes in the major genes associated with cell cycle, apoptosis or endoplasmic reticulum stress; 4) differential expression of genes associated with pancreatic regeneration, most notably up-regulation of members of the regenerating islet gene (REG) family and metalloproteinase 7; and 5) differential expression of some genes found in genome wide association studies to be related to T2D (IGF2BP2, TSPAN8, and HNF1B were up-regulated, while JAZF1 and SLC30A8 were down-regulated). In conclusion, this study has identified many novel changes in pancreatic beta-cell gene expression that enhance the understanding of the pathogenesis of T2D.

overall_design: The gene expression profile of beta-cells obtained from cadaver pancreases of 10 control and 10 type 2 diabetic subjects was evaluated. Beta-cells were acquired from pancreatic tissue sections using the laser capture microdissection technique. RNA was extracted, amplified, biotinylated and hybridized to GeneChip Human X3P Array (Affymetrix). Array data were normalized and analysis was performed using the DNA-Chip Analyzer software.

first: Jeffrey

last: Thorne

first: Sonika

last: Dahiya

first: Dennis

last: Sgroi

first: Arun

last: Sharma

first: Susan

last: Bonner-Weir

first: Piero

last: Marchetti

first: Gordon

last: Weir


title: Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum 2

first: min

last: li

summary:
White mold disease, caused by Sclerotinia sclerotiorum (Lib) de Bary, can be a serious disease of crops grown under cool moist environments. In many plants, like soybean [Glycine max (L.) Merr.], complete genetic resistance does not exist. To identify possible genes involved in defense against this pathogen, and to determine possible physiological changes that occur during infection, a microarray screen was conducted using stem tissue to evaluate changes in gene expression between partially resistant and susceptible soybean genotypes at 8 and 14 hours post inoculation. RNA from 15 day old inoculated plants was labeled and hybridized to soybean cDNA microarrays. ANOVA identified 1270 significant genes from the comparison between time points and 105 genes from the comparison between genotypes. Selected genes were classified into functional categories. The analyses identified changes in cell-wall composition and signaling pathways, as well as suggesting a role for anthocyanin and anthocianidin synthesis in the defense against S. sclerotiorum. In-silico mapping of both the differentially expressed transcripts and of public markers associated with partial resistance to white mold, provided evidence of several differentially expressed genes being closely positioned to white mold resistance markers, with the two most promising genes encoding a PR-5 and anthocyanidin synthase.
Keywords = white mould
Keywords = necrotroph
Keywords = oxalic acid
Keywords = defense
Keywords = ANOVA
Keywords = PI 194639
Keywords = plant

Keywords: plant microbe interaction

overall_design: 1 comparison, 2 technical repeats including dye swaps, 3 biological repeats

first: Bernarda

last: Calla

first: Tri

last: Vuong

first: Osman

last: Radwan

first: Glen

last: Hartman

first: Steven

last: Clough


title: Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum 1


title: Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum 4

overall_design: loop design, 4 comparisons, 2 technical repeats including dye swaps, 3 biological repeats


title: Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome 2

first: Jin

last: Zhu

first: William

last: Patzoldt

first: Patrick

last: Tranel


title: Expression data from broiler chickens in response to the combined stressors of catching, transport and slaughter

status: Public on Mar 19 2010

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

summary:
The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples.
We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS.

overall_design: We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.

first: Louise

last: Sherlock

first: D

last: Wathes

first: Christopher


title: PBMC IFNg Dose Reponse

city: London

first: Simon

last: Waddell

department: Division of Cellular and Molecular Medicine St. George's

institute: University of London Tooting

summary:
PBMC response to three concentrations of IFNg (0.006, 0.6 and 60 pM) from 0-12h.
Abstract:  Background Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles.
Results: We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons a, b, w and g, IL12 and TNFa; and (2) characterise the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNg stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNg and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFa stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNg, and emergent properties associated with IFN-mediated activation of mixed cell populations.
Conclusions: This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the detection and definition of host immune responses in a variety of disease settings.
PBMC extraction and stimulation Human primary peripheral blood mononuclear cells (PBMCs) were purified from whole blood of healthy donors using Ficoll-Paque PLUS (GE Healthcare) according to manufacturers instructions. PBMCs were incubated at 1.5-2.0 x 106 cells/well for 24 h before stimulation in RPMI 1640 medium supplemented with 10% heat-inactivated foetal calf serum and 2 mM L-glutamine (Invitrogen) at 37C, 5% CO2. Cells were treated with 0.006 pM, 0.6 pM or 60 pM recombinant IFNg (R&D Systems), and sampled at time intervals from 0.5 h to 12 h after stimulation. Additionally, cells were treated with 0.1 % BSA/PBS alone and used for untreated (mock) control time courses.  RNA extraction and amplification Total RNA was extracted in TRIzol LS (Invitrogen) followed by standard chloroform purification and isopropanol precipitation. RNA was resuspended in RNase-free water, quantitated on the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) and stored at -80C. 500 ng total RNA was amplified using the MessageAmp modified Eberwine linear amplification procedure (Applied Biosystems). All samples to be compared were extracted and amplified together.  Microarray analysis 4 ug amplified RNA was labelled with Cy5-dUTP (GE Healthcare) and combined with 3 ug of Cy3-labelled reference cDNA derived from a pool of RNA derived from a panel of 11 human cell lines (Stratagene Universal Human Reference RNA). The samples were washed and concentrated using MinElute columns (Qiagen) and competitively hybridised to custom printed cDNA microarrays containing 37,632 elements for approximately 18,000 unique human genes. The hybridised slides were scanned using a GenePix 4000A microarray scanner (Axon Instruments). Comparative spot intensities were calculated from the images, and areas of poor quality excluded from further analysis using GenePix Pro 6.0 (Axon Instruments). Data were deposited in the Stanford Microarray Database. Analysis was restricted to cDNA elements with a regression correlation of > 0.6, fluorescence intensities of > 2.5 fold signal/background in Cy3 or Cy5 channels and a minimum signal intensity of > 100 in both channels for at least 80% of the arrays. The expression ratios were normalised for array variation, and the data zero-transformed using a custom-designed Microsoft Excel macro (C. Liu, Stanford). The statistical package SAM (Significance Analysis of Microarrays, version 1.15) was used to identify genes significantly differentially expressed in the normalised data sets by pairwise comparison with a minimum 2 fold cutoff at a false discovery rate of < 1% of the median. The transformed datasets were then hierarchically clustered using Cluster 2.11 and the results displayed using Treeview 1.60.

overall_design: A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).


title: PBMC Cell Subset Stimulation

summary:
PBMC cell subsets were treated with 0.6 pM IFNg for 0-24h and compared to mock-treated time series.
Abstract:  Background Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles.
Results: We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons a, b, w and g, IL12 and TNFa; and (2) characterise the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNg stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNg and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFa stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNg, and emergent properties associated with IFN-mediated activation of mixed cell populations.
Conclusions: This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the detection and definition of host immune responses in a variety of disease settings.

PBMC extraction and stimulation Human primary peripheral blood mononuclear cells (PBMCs) were purified from whole blood of healthy donors using Ficoll-Paque PLUS (GE Healthcare) according to manufacturers instructions. PBMCs were incubated at 1.5-2.0 x 106 cells/well for 24 h before stimulation in RPMI 1640 medium supplemented with 10% heat-inactivated foetal calf serum and 2 mM L-glutamine (Invitrogen) at 37C, 5% CO2. Cells were treated with 0.006 pM, 0.6 pM or 60 pM recombinant IFNg (R&D Systems), and sampled at time intervals from 0.5 h to 12 h after stimulation. Additionally, cells were treated with 0.1 % BSA/PBS alone and used for untreated (mock) control time courses.  RNA extraction and amplification Total RNA was extracted in TRIzol LS (Invitrogen) followed by standard chloroform purification and isopropanol precipitation. RNA was resuspended in RNase-free water, quantitated on the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) and stored at -80C. 500 ng total RNA was amplified using the MessageAmp modified Eberwine linear amplification procedure (Applied Biosystems). All samples to be compared were extracted and amplified together.  Microarray analysis 4 ug amplified RNA was labelled with Cy5-dUTP (GE Healthcare) and combined with 3 ug of Cy3-labelled reference cDNA derived from a pool of RNA derived from a panel of 11 human cell lines (Stratagene Universal Human Reference RNA). The samples were washed and concentrated using MinElute columns (Qiagen) and competitively hybridised to custom printed cDNA microarrays containing 37,632 elements for approximately 18,000 unique human genes. The hybridised slides were scanned using a GenePix 4000A microarray scanner (Axon Instruments). Comparative spot intensities were calculated from the images, and areas of poor quality excluded from further analysis using GenePix Pro 6.0 (Axon Instruments). Data were deposited in the Stanford Microarray Database. Analysis was restricted to cDNA elements with a regression correlation of > 0.6, fluorescence intensities of > 2.5 fold signal/background in Cy3 or Cy5 channels and a minimum signal intensity of > 100 in both channels for at least 80% of the arrays. The expression ratios were normalised for array variation, and the data zero-transformed using a custom-designed Microsoft Excel macro (C. Liu, Stanford). The statistical package SAM (Significance Analysis of Microarrays, version 1.15) was used to identify genes significantly differentially expressed in the normalised data sets by pairwise comparison with a minimum 2 fold cutoff at a false discovery rate of < 1% of the median. The transformed datasets were then hierarchically clustered using Cluster 2.11 and the results displayed using Treeview 1.60.

overall_design: A cell type comparison design experiment design type compares cells of different type for example different cell lines.


title: Direct regulation of myocardial triglyceride metabolism by the cardiomyocyte circadian clock

city: Birmingham

first: Molly

middle: Bray

last: Bray

address: 720 20th Street S

institute: Univ of Alabama at Birmingham

summary: Maintenance of circadian alignment between an organism and its environment is essential to ensure metabolic homeostasis. Synchrony is achieved by cell autonomous circadian clocks. Despite a growing appreciation of the integral relation between clocks and metabolism, little is known regarding the direct influence of a peripheral clock on cellular responses to fatty acids. To address this important issue, we utilized a genetic model of disrupted clock function specifically in cardiomyocytes in vivo (termed cardiomyocyte clock mutant (CCM)). CCM mice exhibited altered myocardial response to chronic high fat feeding at the levels of the transcriptome and lipidome as well as metabolic fluxes, providing evidence that the cardiomyocyte clock regulates myocardial triglyceride metabolism. Time-of-day-dependent oscillations in myocardial triglyceride levels, net triglyceride synthesis, and lipolysis were markedly attenuated in CCM hearts. Analysis of key proteins influencing triglyceride turnover suggest that the cardiomyocyte clock inactivates hormone-sensitive lipase during the active/awake phase both at transcriptional and post-translational (via AMP-activated protein kinase) levels. Consistent with increased net triglyceride synthesis during the end of the active/awake phase, high fat feeding at this time resulted in marked cardiac steatosis. These data provide evidence for direct regulation of triglyceride turnover by a peripheral clock and reveal a potential mechanistic explanation for accelerated metabolic pathologies after prevalent circadian misalignment in Western society.

overall_design:
Comparison of gene expression in hearts taken from wildtype and transgenic FVB/N mice.
WT and CCM (transgenic mice lacking a functional circadian within cardiomyocytes only) mice were fed a high fat diet for 16 weeks ad libitum. Gene expression in hearts from these animals was subsequently measured at ZT 18 (middle of the active phase).

first: Jun-Yu

last: Tsai

first: Petra

last: Kienesberger

first: Thomas

last: Pulinilkunnil

first: Mary

last: Sailors

first: David

last: Durgan

first: Carolina

last: Villegas-Montoya

first: Anil

last: Jahoor

first: Rodrigo

last: Gonzalez

first: Merissa

middle: E

last: Garvey

first: Brandon

middle: B

last: Boland

first: Zachary

last: Blasier

first: Tracy

last: McElfresh

first: Vijay

last: Nannegari

first: Chi-Wing

last: Chow

last: Heird

first: Margaret

middle: P

last: Chandler

first: Jason

last: Dyck

first: Martin

last: Young


title: PBMC Cytokine Comparison

first: Simon

last: Waddell

summary:
Treatment of PBMC with 0.6 pM cytokine from 0-24h
Abstract:  Background Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles.
Results: We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons a, b, w and g, IL12 and TNFa; and (2) characterise the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNg stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNg and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFa stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNg, and emergent properties associated with IFN-mediated activation of mixed cell populations.
Conclusions: This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the detection and definition of host immune responses in a variety of disease settings.
PBMC extraction and stimulation Human primary peripheral blood mononuclear cells (PBMCs) were purified from whole blood of healthy donors using Ficoll-Paque PLUS (GE Healthcare) according to manufacturers instructions. PBMCs were incubated at 1.5-2.0 x 106 cells/well for 24 h before stimulation in RPMI 1640 medium supplemented with 10% heat-inactivated foetal calf serum and 2 mM L-glutamine (Invitrogen) at 37C, 5% CO2. Cells were treated with 0.006 pM, 0.6 pM or 60 pM recombinant IFNg (R&D Systems), and sampled at time intervals from 0.5 h to 12 h after stimulation. Additionally, cells were treated with 0.1 % BSA/PBS alone and used for untreated (mock) control time courses.  RNA extraction and amplification Total RNA was extracted in TRIzol LS (Invitrogen) followed by standard chloroform purification and isopropanol precipitation. RNA was resuspended in RNase-free water, quantitated on the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) and stored at -80C. 500 ng total RNA was amplified using the MessageAmp modified Eberwine linear amplification procedure (Applied Biosystems). All samples to be compared were extracted and amplified together.  Microarray analysis 4 ug amplified RNA was labelled with Cy5-dUTP (GE Healthcare) and combined with 3 ug of Cy3-labelled reference cDNA derived from a pool of RNA derived from a panel of 11 human cell lines (Stratagene Universal Human Reference RNA). The samples were washed and concentrated using MinElute columns (Qiagen) and competitively hybridised to custom printed cDNA microarrays containing 37,632 elements for approximately 18,000 unique human genes. The hybridised slides were scanned using a GenePix 4000A microarray scanner (Axon Instruments). Comparative spot intensities were calculated from the images, and areas of poor quality excluded from further analysis using GenePix Pro 6.0 (Axon Instruments). Data were deposited in the Stanford Microarray Database. Analysis was restricted to cDNA elements with a regression correlation of > 0.6, fluorescence intensities of > 2.5 fold signal/background in Cy3 or Cy5 channels and a minimum signal intensity of > 100 in both channels for at least 80% of the arrays. The expression ratios were normalised for array variation, and the data zero-transformed using a custom-designed Microsoft Excel macro (C. Liu, Stanford). The statistical package SAM (Significance Analysis of Microarrays, version 1.15) was used to identify genes significantly differentially expressed in the normalised data sets by pairwise comparison with a minimum 2 fold cutoff at a false discovery rate of < 1% of the median. The transformed datasets were then hierarchically clustered using Cluster 2.11 and the results displayed using Treeview 1.60.

overall_design: A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.


title: Transcriptional Response of Rhodococcus aetherivorans I24 to Polychlorinated Biphenyl-Contaminated Sediments.

city: Cambridge

first: Matt

last: Cahill

address: Downing Street

institute: University of Cambridge

summary: We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons.  Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were up-regulated in the various treatments. In medium and in sediment, PCBs elicited the up-regulation of a common set of 100 genes, including chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were up-regulated in response to PCBs or biphenyl.   This study is one of the first which utilizes microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions which more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. In addition, the identification of numerous genes expressed in contaminated soil specifically may have implications for the development of biosensors. Finally, comparative genomic and transcriptomic analyses suggest that the mere presence of orthologs of the required enzymes may not be sufficient to confer a vigorous biphenyl/PCB metabolism.

overall_design: RNA was isolated from cells incubated in the following: sediment from a PCB-contaminated industrial site, uncontaminated sediment from a comparable site, and defined media supplemented with glucose (3 g/L), glucose and biphenyl (3 g/L, 4.5 μM), or glucose and PCBs (3 g/L, 5 mg/L Aroclor 1254). In all cases, there were 3 biological replicates and 2 technical replicates (repeat hybridizations). A total of 3524 genes are represented on the arrays; of these, 41 and 176 are found on the plasmids pRA2 and pRA3, respectively. On average, there are 3 distinct 24nt probes per gene.

first: Edoardo

last: Puglisi

first: Philip

last: Lessard

first: Ettore

last: Capri

first: Anthony

last: Sinskey

first: John

last: Archer

first: Paolo

last: Boccazzi


title: MicroRNA Profiling Analysis of Differences between the Melanoma of Young Adults and Older Adults

city: Pittsburgh

first: Monica

last: Panelli

state: PA

address: 5117 Centre Ave

department: Hematology-Oncology

institute: Hillman Cancer Center, University of Pittsburgh

summary: This study represents the first attempt to perform a profiling analysis of the intergenerational differences in the microRNAs (miRNAs) of melanocytic neoplasms in young adult and older adult groups. Our comparative miRNA profiling provides a novel characterization of the miRnomes of melanocytic neoplasms and melanomas of different age groups and identifies a set of potential diagnostic and potential clinico-pathologic biomarkers that may serve as targets for development of novel miR-based modalities in cancer diagnosis and treatment. An exploratory miRNA analysis of 666 miRs was conducted on  formalin fixed and  paraffin embedded tissues  from 10 adults and  10 young adults including conventional melanoma and  melanocytic  neoplasms of uncertain biological significance. Age-matched benign melanocytic nevi were used as controls. The comparative profiling was intentionally performed at two extremes of age, i.e., less than 30 years (Mel 30) and greater than 60 years (Mel 60). Primary melanoma in patients greater than 60 years old was characterized by the increased expression of miRs regulating TLR-MyD88-NF-kappaB pathway (hsa-miR -199a), RAS/RAB22A pathway (hsa-miR-204); growth differentiation and migration (hsa-miR337), epithelial mesenchymal transition EMT (let-7b, hsa-miR-10b/10bSTAR(*)),  invasion and metastasis (hsa-miR-10b/10bSTAR(*), hsa-miR-30a/e*, hsa-miR-29c*; cellular matrix components (hsa-miR-29c*); invasion-cytokinesis (hsa-miR 99b*) compared to melanoma of younger patients. miR 211 was dramatically downregulated in primary melanoma compared to nevi controls, decreased with increasing age and was among the miRs linked to metastatic processes and potentially targeting the inflammatory receptor CCR10; Primary melanoma in young adult patients was characterized by the increased expression of hsa-miR-449a and decreased expression of hsa-miR146b, hsa-miR 214*. Among the miRs expressed at higher levels in control nevi, compared to adult or young adult melanoma, was hsa-miR 574-3p. Only 2 miRs distinguished adult from young adult-pediatric nevi, hsa-miR374a* and has-miR-566. MiR 30a* appeared to be a strong marker of differentiation in clinical stages I-II adult and pediatric melanoma, and could predict classification of melanoma tissue in the two age groups. Furthermore, lymph node status in  the two age groups was characterized by the statistically significant expression of hsa-miR-30a* and hsa-miR-204 (F-test, p-value <0.001).

overall_design: Archival paraffin blocks of melanocytic neoplasms studied at the University of Pittsburgh Cancer Institute (UPCI) were retrieved from the files of  the Health Sciences Tissue Bank (HSTB) database and disbursed by UPCI HSTB according to UPCI-IRB regulations. Ten primary FFPE-tissues (including melanocytic neoplasms of uncertain biological potential) were obtained from two cohorts of patients respectively segregated according to age: Cohort A - > 60 years and Cohort B - <30 years and utilized for microRNA profiling. These two case cohorts were separated by at least 30 years, thereby representing an adequate basis for an intergenerational study. Additionally, 6 benign nevi were used as homologous controls (3 from adults and 3 from young adult patients, respectively). A total of 26 lesions (20 test specimens + 6 controls) were analyzed. Primary diagnostic workup and verification of the diagnosis of primary neoplasms was performed by two independent reference pathologists. Total RNA was isolated from all lesions from (at average) 30 5µm sections, and these were obtained specifically from areas that contained at least 70% viable tumor (identified by a pathologist). RNA quality was assessed using Nanodrop and the Agilent Bioanalyzer (OD 260/280 and 260/230 (Table 1)). The overall microRNA profiling of these two groups (adult and young adult) included a total of 56 Taqman ® microRNA Low density arrays (TLDAs).  Each group included 10 melanocytic neoplasm samples (older adult melanoma, AM, pediatric and young adult melanoma PM) and 3 control nevi specimens (adult nevi, AN, pediatric nevi, PN). The assays were run in 3 batches for processing and a calibrator RNA was included in each batch for normalization. For each specimen, 2 TLDA were run, TLDA panel A and TLDA panel B.

first: Drazen

last: Jukic

first: Uma

middle: N

last: Rao

first: Lori

last: Kelly

first: Jihad

last: Skaf

first: Laura

last: Drogowski

last: Kirkwood


title: Expression data from cid14 delta and air1 delta strains

status: Public on Mar 17 2010

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Expression profiling of cid14 delta and air1 delta cells shows that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1.

overall_design: Gene expression in the mutants was compared to the parent wild-type strain. 2 biological replicates were performed for each strain.

first: Claudia

last: Keller


title: Localized complement activation in the development of protective immunity against Ostertagia ostertagi infections in cattle

status: Public on Mar 18 2010

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary: The gastrointestinal nematode Ostertagia ostertagi is one of major causal agents that contribute to production inefficiency in cattle industry in the temperate region of the world. One of pathophysiological factors that lead to reduced weight gain and milk yield is altered gastrointestinal functions, resulting from considerable tissue damage in the abomasal mucosa during infections. Protective immunity to Ostertagia ostertagi infections in cattle develops very slowly. Resistance to reinfection becomes manifest only after a prolonged period of exposure. Mechanisms underlying the development of protective immunity remain largely unexplored. Immune animals, with significantly reduced worm burdens, were developed after multiple drug-attenuated experimental infections and were compared to the primary infected group and their respective uninfected controls. In this study, transcriptomic analysis identified 3 signaling pathways, the complement system, leukocyte extravasation and acute phase responses, significantly impacted during both primary and repeat infections.  The markedly increased mRNA levels of complement components C3, factor B (CFB), and factor I (CFI) in the abomasal mucosa of the infected cattle were confirmed using quantitative PCR. Western blot analysis established the presence of elevated levels of activated C3 proteins in the mucosa. One of the iniators of local complement activation could be related with secretory IgA and IgM because infections significantly upregulated expression of J chain (IGJ) as well as polymeric Ig receptor (PIGR) and an IgM-specific receptor (FAIM3), suggesting sustained increase in both synthesis and transepithelial transport of IgA and IgM during the infection. The elevated levels of pro-inflammatory cytokines, such as IL-4 and IL-1β, during the infection may be involved in gene regulation of complement components. Our data suggested enhanced tissue repair and mucin secretion in immune animals may also contribute to protective immunity. Our results presented the first piece of evidence that local complement activation may be involved in the development of long term protective immunity and provided a novel mechanistic insight into resistance against Ostertagia ostertagi in cattle.

overall_design: There were four treatment groups: naive control (never infected), primary infection, drug-attenuated control, and drug-attenuated 5th reinfection. Each group had 4 biolgical replicates. A total of 16 arrays were used for this experiment. The 2 major contrast were 1). The primary infection vs naive control; and 2). The drug-attenuated 5th reinfection vs the drug-attenuated control.

first: Yali

last: Hou

first: Congjun

first: Louis

last: Gasbarre


title: Gene expression and gene ontology analysis of the transcriptional changes occurring in spinal cord from the G93A SOD1 gene mutant rat

status: Public on Mar 16 2010

first: ANDREA

last: MALASPINA

state: England

address: 4 Newark Street

department: Neuroscience

institute: Institute of Cell and Molecular Science

summary: We have investigated the process of disease-induced functional perturbation and the related transcriptional changes occurring in thoraco-lumbar spinal cord extracted from Sprague-Dawley rats heterozygous for the G93A SOD1 gene mutation (Emerging Model 2148 Het Male, Taconic USA; Wyeth and Amyotrophic Lateral Sclerosis Association 2002) using spinal cord from wild type females littermates as reference tissues. Rats were obtained from a breeding project at Taconic Breeding Services (USA). We have applied large-scale gene expression analysis to define the pattern or transcriptional changes occurring in spinal cord from the G93A SOD1 rat model from a pre-symptomatic stage, at disease onset and at end-stage disease, using Bead Array analysis (Illumina, San Diego, USA). We have pooled spinal cord from N:5 transgenic rats for each of the time points considered, using the same pools of spinal cord from sex and age-matched WT rats as reference. In this specific project, the aim was to obtain a gene ontology (GO) pathway analysis of the transcriptional changes induced by the G93A SOD1 mutation in rat spinal cord. Hence, we have opted for a sample pooling strategy, well aware that in so doing, we would not obtaineed information about individuals genes variation across the samples in study but an overall view of the activation of multi-genes molecular signals.

overall_design: Total RNA was isolated from the spinal cords of mutant (G93A SOD1 gene mutation) female rats sacrificed at a pre-symptomatic stage (10-week old), at disease onset and at end stage disease and from age and sex-matched wild type (WT) littermates. RNA samples obtained from spinal cord extracted from rats of the same genetic types and sacrificed at the same time points (e.g. 5 RNA samples from mutant spinal cord from end-stage rats; 5 RNA samples from mutant spinal cord from rats at disease onset; 5 RNA samples from mutant pre-symptomatic rats and 5 RNA samples from spinal cord obtained from age-matched WT rats sacrificed at each of the 3 time points) were pooled and used for gene expression analysis and Ontology analysis of the expression profiles.

first: Andrea

last: Malaspina

middle: V

last: Priestley


title: MicroRNA expression profiling of the porcine developing brain

city: Frederiksberg C

first: Agnieszka

last: Podolska

address: Grønnegårdsvej 3 2nd floor

department: Department of Basic Animal and Veterinary Sciences

country: Denmark

institute: Faculty of Life Sciences, University of Copenhagen,

summary: MicroRNA expression profiling with use of microRNA microarrays was performed on porcine developing brain. Two tissues, cortex and cerebellum were sampled at each of three different developmental stages: gestation day 50 (F50), gestation day 100 (F100) and three months old (named adult), respectively. The aim was to find developmental stage as well as the tissue specific microRNA candidates and validate them with qPCR.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Samples containing both small RNA and total RNA were subjected, respectively. One replicate per array was made from each developmental stage/tissue, for each isolation method. Fetus gestation day 50 cortex total RNA was run in four replicates. Fetus gestation day 50 cortex small RNA was run in two replicates.

first: Bogumil

last: Kaczkowski

first: Peter

last: Busk

first: Thomas

last: Litman

first: Susanna

last: Cirera

first: Merete

last: Fredholm


title: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: cadmium

last: Kille

summary:
Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to cadmium.

For Cd, the physiological mode of action as indicated by DEBtox model fitting was an effect on energy assimilation from food, suggesting that the transcriptional response to exposure should be dominated by changes in the expression of transcripts associated with energy metabolism and the mitochondria. While evidence for effect on genes associated with energy production were seen, an ontological analysis also indicated an effect of Cd exposure on DNA integrity and transcriptional activity.

Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes.

overall_design:
Adults of C. elegans strain GE-31 exposed as biological replicate groups (approx 10,000) to a control and 4 concentrations of cadmium from L1 stage. Replicate populations were sampled 12 hours after the on-set of egg laying and hybridised against a common oligonucleotide reference for purposes of normalisation.

All experiments were conducted following a reference design with the reference sample compiled from a mixture of RNA extracted from control and cadmium-, fluoranthene-, atrazine- and copper-exposed worms from L1, L4 and adult life-stages. Use of this reference was intended to provide optimal coverage of the spotted genes.

first: Suresh

last: Swain

first: Jodie

last: Wren

first: Stephen

last: Sturzenbaum

first: A

last: Morgan

first: Tjalling

last: Jager

first: Martijs

last: Jonker

last: Hankard

first: Claus

last: Svendsen

first: Jenifer

last: Owen

first: B

last: Hedley

first: Mark

last: Blaxter

first: David

last: Spurgeon


title: Long non-coding RNA HOTAIR reprograms chromatin state to promote breast cancer metastasis

city: Stanford

first: Rajnish

last: Gupta

address: CCSR Room 2155

institute: Stanford University

summary: Large intervening noncoding RNAs (lincRNAs) are pervasively transcribed in the genome yet their potential involvement in human disease is not well understood4,5. Recent studies of dosage compensation, imprinting, and homeotic gene expression suggest that individual lincRNAs can function as the interface between DNA and specific chromatin remodeling activities. Here we show that lincRNAs in the HOX loci become systematically dysregulated during breast cancer progression. The lincRNA termed HOTAIR is increased in expression in primary breast tumors and metastases, and HOTAIR expression level in primary tumors is a powerful predictor of eventual metastasis and death. Enforced expression of HOTAIR in epithelial cancer cells induced genome-wide re-targeting of Polycomb Repressive Complex 2 (PRC2) to an occupancy pattern more resembling embryonic fibroblasts, leading to altered histone H3 lysine 27 methylation, gene expression, and increased cancer invasiveness and metastasis in a manner dependent on PRC2. Conversely, loss of HOTAIR can inhibit cancer invasiveness, particularly in cells that possess excessive PRC2 activity. These findings suggest that lincRNAs play active roles in modulating the cancer epigenome and may be important targets for cancer diagnosis and therapy.

overall_design: Comparision of MDA-MB-231 Breast Cancer Cells expressing vector or HOTAIR.  Each cell line was subjected to ChIP-chip with anti-H3K27, SUZ12, and EZH2 and interrogated on whole genome promoter arrays

first: Howard

middle: Y

last: Chang


title: Performance Evaluation of Commercial miRNA Expression Array Platforms

city: Austin

first: Sachin

last: Sah

state: TX

address: 2150 Woodward St, Suite 100

institute: Asuragen Inc.

summary: This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance.  The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific.   Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
synthetic construct
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Performance of four (4) commercially available miRNA platforms was evaluated using 7 placenta samples spiked with synthetic microRNA spikes (in Latin-square design) absent in placenta. Platforms were primarily evaluated for accuracy and specificity.

first: Michael

last: Wilson

first: Deepa

last: Eveleigh

first: Matthew

last: McCall

first: Rafael

last: Irizarry


title: High-throughput screening for Salmonella avirulent mutants that retain targeting of solid tumors

city: San Diego

first: nabil

last: arrach

address: 10905 Road to the cure

department: Viori

institute: Burnham Institute for Medical Research

summary: Salmonella has a natural ability to target a wide range of tumors in animal models. However, strains used for cancer therapy have generally been selected only for their avirulence rather than tumor-targeting ability. To select Salmonella strains that are avirulent and yet efficient in tumor-targeting, a necessary criteria for clinical applications, we measured the relative fitness of 41,000 Salmonella Typhimurium transposon insertion mutants growing in mouse models of human prostate cancer and melanoma. Two classes of potentially safe mutants were identified. Class 1 mutants showed reduced fitness in normal tissues and unchanged fitness in tumors (e.g., mutants in htrA, SPI-2, and STM3120). Class 2 mutants showed reduced fitness in tumors and normal tissues (e.g., mutants in aroA and aroD). Class 1 mutants are more suitable for delivery of therapeutics for cancer therapy.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design:
A library of 41,000 Salmonella mutants containing mini-Tn5 transposon insertions was constructed and pooled. The pool was injected into six human prostate (PC3) and six melanoma (MDA-MB-435) tumors growing subcutaneously in nude mice, and injected intravenously into three tumor-free mice. Bacteria were recovered after two days from tumors and spleens, livers, and lungs of tumor-free mice.
During in vivo selection, defective mutants in genes contributing to fitness in the selective environment are lost from the pool. Differences in the mutant pool composition before (input pool) and after selection (output pool) can be detected using microarray hybridization: Transposons were used that carry the T7 promoter sequence, allowing the specific amplification of genomic sequences adjacent to each insertion, which are then mapped on the Salmonella genome using a gene microarray

first: Nabil

last: Arrach

first: Pui

last: Cheng

first: Ming

last: Zhao

first: Carlos

last: Santiviago

first: Robert

last: Hoffman

last: McClelland


title: Identification of subtypes in HER2-positive breast cancer reveals a gene signature prognostic of outcome

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary:
Purpose
HER2 gene amplification or protein overexpression (HER2+) defines a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. We aimed to investigate the heterogeneous biological appearance and clinical behavior of HER2+ tumors using molecular profiling.

Materials and Methods
Hierarchical clustering of gene expression data from 58 HER2-amplified tumors of various stage, histological grade and estrogen receptor (ER) status was used to construct a HER2-derived prognostic predictor that was further evaluated in several large independent breast cancer data sets.

Results
Unsupervised analysis identified three subtypes of HER2+ tumors with mixed stage, histological grade and ER-status. One subtype had a significantly worse clinical outcome. A prognostic predictor was created based on differentially expressed genes between the subtype with worse outcome and the other subtypes. The predictor was able to define patient groups with better and worse outcome in HER2+ breast cancer across multiple independent breast cancer data sets and identify a sizable HER2+ group with long disease-free survival and low mortality. Significant correlation to prognosis was also observed in basal-like, ER−, lymph node positive or high-grade tumors, irrespective of HER2-status. The predictor included genes associated to immune response, tumor invasion and metastasis.

Conclusion
The HER2-derived prognostic predictor provides further insight into the heterogeneous biology of HER2+ tumors and may become useful for improved selection of patients that need additional treatment with new drugs targeting the HER2 pathway.

overall_design: Array comparative genomic hybridization (aCGH) identified 58 breast tumors with amplification of HER2 from a larger cohort of approx 500 tumors breast. Global gene expression profiles were obtained using 70-mer oligonucleotide microarrays. Unsupervised hierarchical clustering of the 58 tumors, using Pearson correlation and complete linkage, identified three main clusters. One cluster showed significantly poorer clinical outcome. Significance of microarray (SAM) analysis was performed to identify 158 genes separating the poor outcome cluster compared to the other two clusters. Gene expression centroids, based on the 158 genes, were created for each cluster for validation in independent breast cancer data sets.

first: Markus

last: Ringner

last: Vallon-Christersson

first: Göran

last: Jönsson

first: Pär-Ola

last: Bendahl

first: Karolina

last: Holm

first: Adalgeir

last: Arason

first: Haukur

last: Gunnarsson

first: Cecilia

last: Hegardt

first: Bjarni

last: Agnarsson

first: Lena

last: Luts

first: Dorthe

last: Grabau

first: Mårten

last: Fernö

first: Per-Olof

last: Malmström

first: Oskar

middle: T

last: Johannsson

first: Niklas

last: Loman

first: Rosa

last: Barkardottir

first: Ake

last: Borg


title: Universal microarray for pattern-based bacterial species identification

city: Waedenswil

first: Frederique

last: Pasquer

address: Schloss

department: Plant Protection

institute: Agroscope Changins-Waedenswil Research Station ACW

summary: Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Hybridisation patterns of DNA from bacterial type strains (E. coli strains K12 and B, Pantoea agglomerans strains ATCC27155T and C9-1, Pantoea stewartii pv stewartii strain DC283, Salmonella Typhimurium strains LT2 and DT204 and Micrococcus luteus) were compared to each other. Using GeneSpring v7.3.1, cluster analyses were performed as well as ANOVA in order to determine the more discriminative probes out of our 95,000-probe panel.

first: Cosima

last: Pelludat

first: Brion

last: Duffy

first: Juerg

last: Frey


title: Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum 3

city: Urbana

first: min

last: li

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

summary:
White mold disease, caused by Sclerotinia sclerotiorum (Lib) de Bary, can be a serious disease of crops grown under cool moist environments. In many plants, like soybean [Glycine max (L.) Merr.], complete genetic resistance does not exist. To identify possible genes involved in defense against this pathogen, and to determine possible physiological changes that occur during infection, a microarray screen was conducted using stem tissue to evaluate changes in gene expression between partially resistant and susceptible soybean genotypes at 8 and 14 hours post inoculation. RNA from 15 day old inoculated plants was labeled and hybridized to soybean cDNA microarrays. ANOVA identified 1270 significant genes from the comparison between time points and 105 genes from the comparison between genotypes. Selected genes were classified into functional categories. The analyses identified changes in cell-wall composition and signaling pathways, as well as suggesting a role for anthocyanin and anthocianidin synthesis in the defense against S. sclerotiorum. In-silico mapping of both the differentially expressed transcripts and of public markers associated with partial resistance to white mold, provided evidence of several differentially expressed genes being closely positioned to white mold resistance markers, with the two most promising genes encoding a PR-5 and anthocyanidin synthase.
Keywords = white mould
Keywords = necrotroph
Keywords = oxalic acid
Keywords = defense
Keywords = ANOVA
Keywords = PI 194639
Keywords = plant

Keywords: plant microbe interaction

overall_design: loop design, 4 comparisons, 2 technical repeats including dye swaps, 3 biological repeats

first: Bernarda

last: Calla

first: Tri

last: Vuong

first: Osman

last: Radwan

first: Glen

last: Hartman

first: Steven

last: Clough


title: Liver sinusoidal endothelium: a microenvironment-dependent differentiation program in rat including the novel junctional protein liver endothelial differentiation-associated protein-1

status: Public on Mar 15 2010

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Liver sinusoidal endothelium (LSEC) is a prime example for organ-specific microvascular differentiation and functions. Disease-associated capillarization of LSEC in vivo and dedifferentiation of LSEC in vitro indicate the importance of the hepatic microenvironment. To identify the LSEC-specific molecular differentiation program in the rat, we used a two-sided gene expression profiling approach comparing LSEC freshly isolated ex vivo with both lung microvascular endothelial cells (LMEC) and with LSEC cultured for 42h. The LSEC signature consisted of 48 genes both down-regulated in LMEC and in LSEC upon culture (FC>7 in at least one comparison); qRT-PCR confirmation of these genes included numerous family members and signalling pathway-associated molecules. The LSEC differentiation program comprised distinct sets of growth (wnt2, Fzd4, 5, 9, wls, VEGFR1, 2, 3, Nrp2) and transcription factors (Gata4, Lmo3, Tcfec, Maf) as well as endocytosis-related (Stabilin-1/2, Lyve1 and Ehd3) and cytoskeleton-associated molecules (Rnd3/RhoE). Specific gene induction in cultured LSEC versus freshly isolated LSEC as well as LMEC (Esm-1, Aatf) and up-regulation of gene expression to LMEC levels (CXCR4, Apelin) confirmed true transdifferentiation of LSEC in vitro. In addition, our analysis identified a novel 26 kDa single-pass transmembrane protein, liver endothelial differentiation-associated protein (Leda)-1, that was selectively expressed in all liver endothelial cells and preferentially localized to the abluminal cell surface. Upon forced over-expression in MDCK cells, Leda-1 was sorted baso-laterally to E-cadherin-positive adherens junctions suggesting functional involvement in cell adhesion and polarity. Conclusion: Comparative microvascular analysis in rat identified a hepatic microenvironment-dependent LSEC-specific differentiation program including the novel junctional molecule Leda-1.

overall_design: Highly pure liver sinusoidal endothelial cells (LSEC) and lung microvascular endothelial cells (LMEC) were isolated by enzymatic digestion, density gradient centrifugation and MACS sorting and subjected to RNA extraction and affymetrix hybridization without any culturing step (LSEC_0h, LMEC_0h). LSEC were also plated on collagen coated dishes and RNA extraction and Affymetrix hybridization was carried out after 2h and 42h in culture (LSEC_2h, LSEC_42h).

first: Cyrill

last: Géraud

first: Kai

last: Schledzewski

first: Alexandra

last: Demory

first: Diana

last: Klein

first: Miriam

last: Kaus

first: Francis

last: Peyre

first: Konstantin

last: Evdokimov

first: Shun

last: Lu

first: Astrid

last: Schmieder

first: Sergij

last: Goerdt


title: Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

summary:
Background:
Lactococcus garvieae is a bacterial pathogen that affects different animal species and human.  Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study the genomic content of L. garvieae CECT 4531 was analyzed by bioinformatic tools and microarray-based comparative genomic hybridizations (CGH) experiments, using Lactococcus lactis subsp. lactis IL1403 and Streptococcus pneumoniae TIGR4 as reference microorganisms.
Results:
The combination and integration of in silico analyses and in vitro (CGH) experiments performed between the reference microorganisms allowed establishing an inter-species hybridization framework with a detection threshold based on the sequence similarity ≥70%. With this threshold value, 267 genes were identified as having an analogue in L. garvieae, most of which (n = 258) have been documented for the first time in this pathogen. Most of these genes are related to ribosomal, sugar metabolism or energy conversion systems. Some identified genes could be involved in the pathogenesis of L. garvieae infections.
Conclusions:
In this study a comparative analysis based on microarray interspecies hybridization and the use of bioinformatic tools were used for the first time to study the genetic content of L. garvieae CECT 4531. Towards this approach, we identified 267 potentially present genes in L. garvieae CECT 4531, some of which could be involved in the pathogenesis of L. garvieae infections, such as als or mycA. These results provide the first insight into the genome content of L. garvieae.

sample_organism:
Streptococcus pneumoniae
Lactococcus lactis subsp. lactis
Lactococcus garvieae

platform_organism:
Streptococcus pneumoniae
Lactococcus lactis subsp. lactis Il1403

overall_design:
Array-based comparative genome hybridization (CGH):
The L. lactis subsp. lactis IL1403 and S. pneumoniae TIGR4 microarrays used for the CGH analysis were purchased from Eurogentec (Serain, Belgium). The L. lactis microarray contains 4608 spots: 2126 duplicated ORFs, 32 negative controls and 324 empty spots. The S. pneumoniae microarray contains 4608 spots: 2087 duplicated ORFs, 224 negative controls and 210 empty spots.
The CGH experiments were performed by means of competitive hybridizations using DNA of L. lactis subsp. lactis IL1403 or S. pneumoniae TIGR4, depending on the array as positive controls. DNAs to be hybridized on the same array were labelled with Cy3-dUTP and Cy5-dUTP, respectively. For each microarray hybridization reaction, aliquots (1–2 µg) of labelled genomic DNAs of reference (labelled with Cy3) and test (labelled with Cy5) strains, were mixed in 45 µl EGT hybridization solution (Eurogentec, Serain, Belgium) and denatured at 65ºC for 2 min. The hybridization mixture was then loaded onto a microarray slide, covered with a coverslip and incubated at 38ºC overnight. Following hybridization, the slides were washed in 2 X SSC, 0.5% SDS for 5 min followed by 5 min in 1 X SSC, 0.25% SDS. Finally, slides were rinsed in 0.2 X SSC and dried by centrifugation.
The results presented herein represent a compilation of sixteen separate CGH experiments: L. lactis subsp. lactis IL1403 arrays (reference microorganism) were hybridized with S. pneumoniae TIGR4 (test microorganism) (n=2); S. pneumoniae TIGR4 arrays (reference microorganism) were hybridized with L. lactis subsp. lactis IL1403 (test microorganism) (n=2); L. lactis subsp. lactis IL1403 arrays (reference microorganism) were hybridized with L.garvieae CECT 4531 (test microorganism) (n=8); S. pneumoniae TIGR4 arrays (reference microorganism) were hybridized with L.garvieae CECT 4531 (test microorganism) (n=4).
Data acquisition and analysis:
The microarray was scanned after hybridization using a Scanarray HT microarray scanner (Perkin-Elmer). The signal intensity of the two fluors was determined using ImaGene software (BioDiscovery, El Segundo, CA, USA). Microarray data were analysed using ImaGene software, Microsoft Excel and an in-house designed and built Microsoft Access database [30]. Gene calling was based on a signal-to-noise ratio (SNR) > 3 for each spot. After CGH experiments, a gene was considered to show a positive result when it was present in at least three of the four CGH assays. In the case of the L. garvieae CECT 4531 hybridizations with L. lactis subsp. lactis IL1403 arrays, it was necessary to perform a greater number of assays (n=8) due to the poor quality of one of the array batches used. Thus, the criteria chosen to determine a positive result in this case was when the gene was present in at least five of the eight CGH assays.

first: Mónica

last: Aguado-Urda

middle: H

first: José

last: Fernández-Garayzábal

first: Fernando

last: Martín-Sánchez

first: Alicia

last: Gibello

first: Lucas

last: Domínguez

first: Mar

last: Blanco


title: M1T1 Streptococcus pyogenes (isolate 5448) WT and Animal-passaged variant in vitro and in vivo

city: Cairo

first: Ramy

middle: Karam

last: Aziz

address: Qasr-El-Einy Street

department: Microbiology and Immunology

country: Egypt

institute: Faculty of Pharmacy, Cairo University

summary: Microarray analysis was performed on in vitro and in vivo-derived RNA from the well characterized S. pyogenes strain 5448 WT and animal-passage variant

overall_design: Cyclic design with dye swap and biological replicates

first: Mark

last: Walker

first: Malak

last: Kotb


title: Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (GoldenGate methylation)

status: Public on Mar 11 2010

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

summary: Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC. Importantly, we found that the global pattern of copy number alterations in these tumors was significantly associated with tumor methylation profiles. However at the local level, gene promoter regions did not exhibit a correlation between copy number and methylation , and the spectrum of genes affected by each type of alteration was unique. A case-series of 19 tumors and matched blood referents were hybrizided to Affymetrix Human Mapping 500k arrays and copy number was determined via HMM with Copy Number Analysis Tool v4.0.1.

overall_design:
This study was designed to investigate the relationship between copy number and DNA methylation alterations in head and neck squamous cell carcinoma. Data in this submission relates to the methylation
portion only. Each patient tumor has been de-identified and assigned a number (1-19). We included 11 normal head and neck samples, procured through the National Research Disease Interchange,  that were used for reference when comparing tumor to normal.  One ug of tissue DNA extracted using the Qiagen Blood and Tissue Kit was bisulfite-modified using a Zymo Research EZ DNA Methylation Kit. Samples were processed and arrayed on the Illumina GoldenGate Methylation Cancer Panel 1 at the University of California-San Francisco Institute for Genetics, Genomic Core Facility.

first: Karl

last: Kelsey

first: E

last: Houseman


title: Transcriptome analysis of the eukaryotic-type ser/thr kinase PknB in Staphylococcus aureus

city: Wuerzburg

first: Stefanie

last: Donat

address: Roentgenring 11

department: Institute for Molecular Infection Biology

institute: University of Wuerzburg

summary: The function of the Staphylococcus aureus eukaryotic-like serine/threonine protein kinase PknB was investigated by transcriptome analysis using DNA-microarray technology and biochemical assays. The transcriptional profile reveals a strong regulatory impact of PknB on the expression of genes encoding proteins which are involved in purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, and glutamine synthesis.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus N315

overall_design:
To investigate the functional role of PknB in S. aureus DNA microarray experiments were performed. In this experiment, the impact of the deletion of PknB was investigated.
Each experiment was performed 5 times including a dye swap resulting in five chips per competitive comparison to increase reproducibility. All hybridizations were done with equal amounts of cDNA probes.

first: S.


title: Transcriptomic Profiling of Salmonella enterica Enteritidis and Typhimurium under Chlorine Based Oxidation

status: Public on Mar 10 2010

city: SUMMIT

first: SIYUN

last: WANG

address: 6502 S ARCHER ROAD

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

summary: Investigation of whole genome gene expression level changes in Salmonella enterica serova Enteritidis and Typhimurium under chlorine treatment

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: An eighteen chip study using total RNA isolated from three separate cultures of (1) S. Enteritidis in BHI broth (2) S. Typhimurium in BHI broth (3) S. Enteritidis in BHI broth w/ 130 ppm chlorine (4) S. Typhimurium in BHI w/ 130 ppm chlorine (5) S. Enteritidis in BHI broth w/ 390 ppm (6) S. Typhimurium in BHI broth w/ 390 ppm. Each chip measures the expression level of 5,027 ORFs covering the whole genome of S. Enteritidis and S. Typhimurium.

first: Siyun

last: Wang

first: Kaiping

last: Deng

first: Adam

last: Phillippy

first: Xiaoqian

last: Rui

first: Mary

last: Tortorello

first: Wei

last: Zhang


title: Development of the Restriction Site Tiling Analysis (RSTA) method: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

status: Public on Mar 13 2010

city: Pacific Grove

first: Melissa

last: Pespeni

address: 120 Oceanview Blvd.

department: Biology

summary:
Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform.
We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).

overall_design:
Genomic DNA from each individual was extracted, randomly sheared, then divided in half.  Half was restriction digested and labeled with Cy3, half was treated as control and labeled with Cy5.
Labeled DNA from a single individual was then competitively hybridized to the custom, species-specific array that had probe sequences designed to be centered on known restriction cut sites.
Resulting log ratio data reflected the three possible genotypes in clusters when arrays from multiple individuals were examined at a given polymorphic locus.

first: Thomas

last: Oliver

first: David

last: Garfield

first: Manoj

last: Samanta

first: Stephen

middle: R

last: Palumbi


title: Genome-wide DNA methylation in normal and IUGR pancreatic islets

status: Public on Mar 09 2010

city: Bronx

first: Reid

middle: F

last: Thompson

state: NY

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression and epigenetic regulation.  We studied cytosine methylation throughout the genome in pancreatic islets from a rat model of uteroplacental insufficiency, providing a novel and detailed assessment of the genomic distribution and locus-specific patterns of DNA methylation in normal islets as well as the changes that occur as a consequence of IUGR.  Utilizing a high throughput approach to study DNA methylation at almost 1 million unique sites throughout the genome, we found ~1,400 changes in methylation (IUGR compared to control) with an estimated false discovery rate of 4.2%.  These epigenetic differences were observed in IUGR male rats at 7 weeks of age, preceding the development of diabetes in this model.  Therefore, these epigenetic differences represent candidates for mediating the pathogenesis of metabolic disease that occurs later in life in these animals.  Moreover, many of the changes we identify are located near genes that regulate processes known to be abnormal in IUGR islets, such as vascularization, β-cell proliferation, insulin secretion, and cell death.  Consistent changes in mRNA expression were identified at some of the epigenetically-dysregulated genes including Fgfr1, Gch1, Pcsk5, and Vgf.  Globally, epigenetic dysregulation occurred preferentially at conserved intergenic sequences, which are candidate cis-regulatory elements driving differential expression of nearby genes. These results provide insights into the complex developmental consequences of IUGR, and suggest that changes in DNA methylation could mediate a constellation of changes in both gene expression and pancreatic islet development and function, with relevance to T2DM.

overall_design: Direct comparison of DNA methylation in 8 samples consisting of isolated, pooled pancreatic islets from 7-week-old male offspring belonging to 4 IUGR and 4 control litters (Sprague-Dawley rats).  Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

middle: J

last: Fazzari

first: Hong

middle: S

last: Niu

first: Nir

last: Barzilai

first: Rebecca

last: Simmons

first: John

last: Greally


title: The Submergence Tolerance Regulator Sub1A Mediates Stress-responsive Expression of AP2/ERF Transcription Factors

city: Davis

first: Ki-hong

last: Jung

address: one shields

department: Plant pathology

institute: UC DAVIS

summary:
Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1):

We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators.  Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation.

Keywords: Abiotic stress tolerance response

overall_design: Three-condition experiment, M202(Sub1) vs wild type control (M202) at three durations of submergence (0d, 1d and 6d). Biological replicates: 2,  independently grown and harvested. Technical replicates replicates: 1-2 control.

first: Pamela

last: Ronald

first: Julia

last: Bailey-Serres

first: Takeshi

last: Fukao

first: Harkamal

last: Walia

first: Peijian

last: Cao

first: Young-Su

last: Seo


title: Genome-wide analysis of miRNA levels in colon cancer

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Analysis of miRNA levels found in tissue obtained from proficient mismatch repair (pMMR) TNM stage 2|3|4 colon tumor, deficient MMR (dMMR) colon tumor, and normal colon.

overall_design:
miRNA levels obtained from macrodissected colon tumors with > 70% H&E staining were compared with normal colon tissue. Additional comparisons based on mismatch repair status identified by loss of hMLH1 protein and microsattelite instability assay and TNM stage were carried out. This submission provides access to the data discussed in our paper.

The supplementary file 'GSE18392_non-normalized_data.txt' file contains non-normalized data for Samples GSM458618-GSM458762.


title: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula)

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

summary: A genomic overview of in vivo binding of a transcription factor Twist-like-1a/b in the ascidian early gastrula embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged Twist-like-1a/b. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Three independent experiments were performed to reduce experimental errors.

first: Yutaka

last: Satou


title: Causal Modeling Using Network Ensemble Simulations Predicts Novel Lipid Metabolism Genes

city: Bar Harbor

first: Gary

last: Churchill

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: We describe a simulation strategy for prediction of drug targets and functional analysis of genetically defined associations. This strategy utilizes Bayesian model averaging over a sample of parameterized networks to achieve robust predictions in light of uncertainty of the network structure. We illustrate the method with an analysis of liver gene expression, serum lipid profiles and body weight measured on 120 male mice from a mouse intercross population. An ensemble of 1024 networks, gave accurate predictions of animals that were not part of the training data and explained almost twice the variance compared to quantitative trait loci alone. Additional in silico experiments identified 38 transcripts that are predicted to impact serum lipid profiles and suggest that they play a role in controlling high density lipoprotein and free triglycerides plasma concentrations.

overall_design: Affymetrix MOE430A expression data were processed using a custom chip layout that masked probes with known SNPs between the parental mouse strains to minimize the discovery of erroneous cis-effects. Data were assessed using Affymetrix suggested quality control measures and all of the 120 arrays were found to be of high quality.  The custom chip layout was used to normalize the data using FARMS. A total of 1530 transcripts were identified as having sufficient variability to be informative and these were advanced to Bayesian network reconstruction.

first: Paul

middle: D

last: McDonagh

first: Karl

last: Runge

first: David

last: DeCaprio

first: Ioannis

last: Stylianou

first: Sharon

last: Tsaih

first: Bruce

last: Church

first: Iya

middle: G

last: Khalil