title: Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation (IMS v.1)

first: Naoyuki

last: Takahashi

state: Tokyo

summary:
In comparison with allogeneic hematopoietic stem cell transplantation using other sources, umbilical cord blood transplantation (UCBT) offers substantial clinical advantages including a lower incidence and severity of acute graft-versus-host disease (GVHD) despite the use of allogeneic UCB stem cells with more disparate HLA.  However, detailed pathophysiology of acute GVHD developed after UCBT has not yet been clarified.
Here, we examined the roles of inflammatory cells in the pathogenesis of acute GVHD following UCBT, by expression profiling of a total of 595 genes in each of 4 subsets (CD4+, CD8+, CD14+, and CD56+) of peripheral blood mononuclear cells (PBMCs), which were taken from 3 patients with hematologic malignancy, in whom acute GVHD had developed after UCBT.  We compared expression profiles measured during acute GVHD with those measured opon discharge (recovery phase), for each subset of PBMCs to identify immuno-regulatory genes which were assumed to be linked to the pathogenesis of acute GVHD.
Keywords: disease state analysis

overall_design:
Peripheral blood mononuclear cells (PBMCs) were taken from 3 patients with hematologic malignancy, in whom acute GVHD had developed after cord blood transplantation.  CD4+, CD8+, CD14+, and CD56+ cell subsets were isolated from the PBMCs of 2 patients, while only CD8+ and CD56+ cell subsets were isolated from the PBMCs of a patient.
PBMCs were taken twice - during acute GVHD phase and upon discharge (recovery phase), from each patient.  By using a custom-made fibrous oligonucleotide DNA microarray Genopal (Mitsubishi Rayon), we compared expression profiles of 595 unique genes measured during acute GVHD with those measured upon discharge (recovery phase), for each subset of PBMCs.

first: Noriharu

last: Sato

first: Tatsunobu

last: Fukushima

first: Satoshi

first: Arinobu

last: Tojo


title: Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth conditions

status: Public on Dec 13 2008

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

summary: S. typhimurium 14028 wt, hfq and smpB were harvested from log phase LB (LBlog); (2), stationary phase LB (LBstat); (3) 4h MgM medium pH 5.0 after resuspension of LB stat culture (MgMshock); and (4) log phase MgM medium pH5.0 after 100fold dilution of an LB stat culture (MgMDil). Total RNA was extracted, cDNA labeled and hybridized to a non-redundant Salmonella whole genome PCR product ORF array.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: S. typhimurium 14028 cells were harvested, on three separate days,  (1), after growth at 30°C to log phase in LB (LBlog); (2), after growth at 30°C to stationary phase in LB (LBstat); (3) after transfer of a stationary phase culture grown in LB into magnesium-deficient MgM medium [100 mM Tris-Cl, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 1 mM KH2PO4, 0.2% glycerol, 0.1% Casamino acids, 8uM MgCl2] pH 5.0 and growth for four more hours at 30°C (MgMshock); (4) after 100fold dilution of a stationary phase culture grown in LB into magnesium-deficient MgM medium pH5.0 and growth at 30°C to log phase (MgMDil). This procedure was performed on (A), wild type [WT] cells; (B), cells of an hfq- (STM4361) knockout mutant; and (C), cells of an smpB- (STM2688) knockout mutant, resulting in 36 samples total. Total RNA was extracted, cDNA labeled with Cy5-dCTP and hybridized versus Cy3-labeled 14028 gDNA to a non-redundant Salmonella whole genome PCR product ORF array.

first: Steffen

last: Porwollik

first: Hyunjin

last: Yoon

first: Fred

last: Heffron

first: Pui

last: Cheng


title: G. sulfurreducens growth with acetate as limiting electron donor versus fumarate as limiting electron acceptor

status: Public on Dec 09 2008

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary:
Microbially-mediated uranium bioremediation has been demonstrated in uranium contaminated aquifers when acetate was artificially supplied and growth of the natural population of Geobacteraceae was stimulated. In order to mimic the environmental response to acetate, steady-state cells of G. sulfureducens were cultured in chemostats under conditions of either 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor or 2) acetate was supplied in excess with fumarate as sole electron acceptor and limiting factor. In silico fluxome modeling and transcriptome analysis were used as tools for investigating the cell response to the acetate availability. For global gene expression profiling, a DNA microarray of the complete G. sulfurreducens genome was used. Statistically significant results were obtained from two-color, dye swap hybridizations produced from a total of three biological replicates. Eight technical replicates were tested from two of the biological replicates and six technical replicates were tested from the third biological replicate.
Major findings from this study are given as follows. The in silico model successfully predicted a higher TCA-cycle flux (ca. 2-fold) under acetate-excess conditions, suggesting that catabolism of acetate is favored with respect to anabolism, and thus more electrons are available for metal reduction. Transcriptome analyses offered a comprehensive picture of the regulation points subjected to the acetate availability. Under acetate-excess conditions, acetate transporters in the G. sulfurreducens genome were down-regulated. In addition the oxidation-related acetyl-CoA transferase was up-regulated approximately three-fold and the assimilatory-related acetate kinase was down-regulated approximately two-fold, respectively, indicating that the transcriptional regulation of acetate activation may be the key point for coping with the excess of acetate and increasing the TCA flux. The level of transcription for 10 c-type cytochromes was significantly increased in cells cultured with an excess of acetate. OmcS, an outer-membrane cytochrome which actively participates in electron transfer to Fe(III)-oxides and graphite electrodes from fuel cells, showed one of the highest fold increases in transcription. The integration of in silico modeling and genome-wide analysis shows for first time how G. sulffureducens adapts its metabolic flux and transcriptional network for optimizing the use of acetate as an electron donor for exocellular respiration instead of for use as a carbon source for biomass production.
Keywords: Geobacter, gene expression, acetate limitation, fumarate limitation

overall_design: RNA was extracted and used for hybridizations from three identically treated chemostat cultures (biological replicates) of Geobacter sulfurreducens DL1 at steady state. The two conditions tested were 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor and 2) acetate was supplied in excess with fumarate supplied as the sole electron acceptor and limiting factor. A two-color hybridization strategy was used to produce a total of twenty two technical replicates (hybridizations) from three biological replicates as follows. Eight technical replicates were completed from the two biological replicate of which four of the technical replicates were in the opposite or “flip dye” configuration and six technical replicates were produced from the third biological replicate of which three were “flip dyes” .

first: B

middle: A

last: Methé

first: A

last: Esteve-Núñez

first: R

last: Mahadevan

last: Glaven

first: D

middle: R

last: Lovley


title: Time course effect of A-factor addition

status: Public on Dec 04 2008

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

summary: Comparative hybridization of afsA deficient mutant versus afsA deficient mutant after A-factor addition

sample_organism: Streptomyces griseus subsp. griseus NBRC 13350

overall_design: 3 x dual channel slides, dye swap

first: Hirofumi

last: Hara

first: Sueharu

last: Horinouchi


title: Bead-based kinase phosphorylation profiling identifies SRC as a therapeutic target in glioblastoma

status: Public on Dec 05 2008

city: Cambridge

first: Jinyan

last: Du

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Institute

summary:
Here we describe a bead-based method capable of profiling tyrosine kinase phosphorylations in a multiplexed, high-throughput and low-cost manner. This approach allows for the discovery of tyrosine kinase-activating events, even when the DNA sequence is wild-type. In an effort to pilot the establishment of a tyrosine kinase activation catalog, we profiled tyrosine phosphorylation levels of 62 tyrosine kinases in 130 human cancer lines, and followed-up on the frequent SRC phosphorylation in glioblastoma.

Keywords: quantitative measurements of tyrosine phosphorylation levels on tyrosine kinases

overall_design: Total protein lysates were collected from 130 cancer cell lines. Tyrosine phosphorylation levels on 62 tyrosine kinases were measured with the bead assay.

first: Paula

last: Bernasconi

first: Karl

last: Clauser

first: DR

last: Mani

first: Stephen

middle: P

last: Finn

first: Rameen

last: Beroukhim

first: Melissa

last: Burns

first: Bina

last: Julian

first: Xiao

last: Peng

first: Haley

last: Hieronymous

first: Rebecca

middle: L

last: Maglathin

first: Timothy

last: Lewis

first: Linda

middle: M

last: Liau

first: Phioanh

last: Nghiemphu

first: Ingo

middle: K

last: Mellinghoff

first: David

middle: N

last: Louis

first: Massimo

last: Loda

first: Steven

last: Carr

first: Andrew

last: Kung

first: Todd

last: Golub


title: Identification of immune-related genes in tolerogenic dendritic cells

status: Public on Dec 08 2008

city: Jinan

first: Xiao-Lin

last: Zhang

state: Shandong Province

address: West Wen Hua Road 107

department: Department of Hematology

country: China

institute: Qilu Hospital, Shandong University

summary:
Comparison of gene expression data from induced-regulatory T cell treated- and untreated-DCs from patients with ITP.
Keywords: Regulatory T cell, dendritic cell

overall_design: This experiment consists of 10 arrays.The microarray slides were hybridized with RNA prepared from 5 biological replicate samples. As a measure of technical replication, each experiment also had a corresponding dye swap.

first: Xiao-lin

first: Jun

first: Jian-zhi

last: Sun

first: Ming

last: Hou


title: Suppression of LPS-induced IFNg and NO in splenocytes by select E2-regulated miRNA: A novel mechanism of immune mod.

city: blacksburg

first: rujuan

last: dai

state: VA

address: 1410 price fork RD

department: CMMID

institute: virginia Tech

summary:
microRNA (miRNA), recently identified, non-coding, small RNA, are emerging as key regulators in homeostasis of the immune system.  Therefore, aberrant expression of miRNA may be linked to immune dysfunction, such as in chronic inflammation and autoimmunity.  In this study, we investigated the potential role of miRNA in estrogen-mediated regulation of innate immune responses, as indicated by upregulation of LPS-induced IFNg, inducible nitric oxide synthase (iNOS), and nitric oxide in splenic lymphocytes from estrogen-treated mice.  We found that miR-146a, a negative regulator of Toll-like receptor (TLR) signaling, was decreased in freshly-isolated splenic lymphocytes from estrogen-treated mice compared to placebo controls.  Increasing the activity of miR-146a significantly inhibited LPS-induced IFNg and iNOS expression in mouse splenic lymphocytes.  Further, miRNA microarray and Real-time RT-PCR analysis revealed that estrogen selectively upregulates/downregulates the expression of miRNA in mouse splenic lymphocytes.  miR-223, which is highly upregulated by estrogen, regulates LPS-induced IFNg, but not iNOS or nitric oxide in splenic lymphocytes. Inhibition of miR-223 activity decreased LPS-induced IFNg in splenic lymphocytes from estrogen-treated mice. Our data are the first demonstrating selective regulation of miRNA expression in immune cells by estrogen and are indicative of an important role of miRNA in estrogen-mediated immune regulation.
Keywords:  microRNAs, estrogen, splenic lymphocytes, TLR4 signaling, mouse

overall_design: Total RNAs were isolated from freshly-isolated splenic lymphocytes from 2 pairs of placebo-and estrogen-treated mice

first: Rujuan

last: Dai

last: Phillips

first: Yan

first: Deena

last: Khan

first: Oswald

last: Crasta

first: Ansar

last: Ahmed


title: Coordinated regulation of cell cycle transcripts by p53-inducible microRNAs, miR -192 and -215

status: Public on Dec 07 2008

city: Seattle

first: Sara

last: Georges

state: WA

address: 401 Terry Ave N

institute: Rosetta Inpharmatics, LLC

summary: Cell cycle arrest in response to DNA damage is an important anti-tumorigenic mechanism.  microRNAs (miRNAs) were shown recently to play key regulatory roles in cell cycle progression.  For example, miR-34a is induced in response to p53 activation and mediates G1 arrest by down-regulating multiple cell cycle-related transcripts.  Here we show that genotoxic stress promotes the p53-dependent up-regulation of the homologous miRNAs, miR -192 and miR-215.  Like miR-34a, activation of miR-192/215 induces cell cycle arrest suggesting that multiple microRNA families operate in the p53 network.  Furthermore, we define a downstream gene expression signature for miR-192/215 expression that includes a number of transcripts that regulate G1 and G2 checkpoints.  Of these transcripts, 18 transcripts are direct targets of miR-192/215 and the observed cell cycle arrest likely results from a cooperative effect among the modulations of these genes by the miRNAs.  Our results demonstrating a role for miR-192/215 in cell proliferation combined with recent observations that these miRNAs are under-expressed in primary cancers support the idea that miR-192 and miR-215 function as tumor-suppressors.

overall_design:
Description:  Transfection of siRNA luc, miR-192 or miR-215 into HCT116 Dicerex5, compared to mock-transfected cells, with mRNA expression profiled at 10h and 24h post-transfection.
Species: Human
Tissue: HCT116 Dicerex5 cell line (tissue of origin = human colorectal carcinoma); this cell line is hypomorphic for Dicer gene function.
Dye-swap: no
Negative control: siRNA luc
Replicates per each timepoint: no

first: Matthew

middle: C

last: Biery

first: Soo-yeon

last: Kim

first: Janell

last: Schelter

first: Jane

last: Guo

first: Aaron

last: Chang

first: Aimee

last: Jackson

first: Michael

middle: O

last: Carleton

first: Peter

middle: S

last: Linsley

first: Michele

last: Cleary

first: Nelson

last: Chau


title: Medicago truncatula seedlings grown two weeks in hydroponics media then carry out salt stress

status: Public on Dec 12 2008

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design:
6 samples of Medicago truncatula seedlings
grown two weeks in hydroponics media
200mM NaCl salt stress
material collect at 0, 1, 2, 5, 10, 24 hour after salt stress beginning
2 ug of total RNA was used to synthesize doublestranded cDNA


title: Maize grown under normal field conditions vs under 60% shade or under 2X density

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary: These experiments were to investigate changes in gene expression associated with maize competition for light when grown at double normal population density or under 60% shaded conditions as opposed to when maize is grown under normal field conditions.

overall_design: Three biological replicates (collected from separate field plots) comprised of pooled samples of 4 plants from each treatment were hybridized in a rolling circle dye swap hybridization screen.

last: Clay

first: Sharon

first: J.

last: Pullis

first: C.

last: Carlson

first: Stephanie

last: Hansen

first: G.

last: Reicks


title: Comparison between Saccharomyces cerevisiae HS 10, HS 34 and HS 12, HS 37

city: Leipzig

first: Franziska

last: Heine

address: Permoserstraße 15

department: Environmental Microbiology

country: Germany

institute: Helmholtz-Centre for Environmental Research - UFZ

summary:
Gene expression of different flocculent (HS 10 and HS 34) and powdery (HS 12 and HS 37) yeast strains compared to each other during exponential and stationary growth phase was analysed.
The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied.
6 µg of the total RNA per sample was used for each microarray experiments. The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences) was used to increase the Cy3 and Cy5 signals of microarray detection.
Each cDNA containing Biotin- and Fluorescein-nucleotides respectively was purified with a QIAquick PCR purification kit and suspended in 11 µl of the formamide containing hybridization buffer. The slides were hybridized at 42°C over night under a cover slip.
The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.
Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.
Keywords: sorted yeast cells

overall_design: Microarray experiments were realised with dye swap.

first: Frank

last: Stahl

first: Heike

last: Sträuber

first: Claudia

last: Wiacek

first: Dirk

last: Benndorf

first: Cornelia

last: Repenning

last: Schmidt

first: Thomas

last: Scheper

first: Martin

last: von Bergen

first: Hauke

last: Harms

first: Susann

last: Müller


title: Microarray analysis identifies candidate genes for key roles in coral development

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

country: Australia

institute: Australian National University

summary:
Background: Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development – when skeletogenesis is initiated, and symbionts are first acquired.
Methodology/ Principal Findings: Of approximately 5600 unique genes represented on the microarrays, 1084 were differentially expressed (P <0.05) in comparisons between four different stages of coral development, spanning key developmental transitions. Genes of likely relevance to the processes of settlement, metamorphosis, calcification and interaction with symbionts were characterised further and their spatial expression patterns investigated using whole-mount in situ hybridisation.
Conclusions/Significance: This study is the first large-scale investigation of developmental gene expression for any cnidarian, and has provided candidate genes for key roles in many aspects of coral biology, including calcification, metamorphosis and symbiont uptake. One surprising finding is that some of these genes have clear counterparts in higher animals but are not present in the closely-related sea anemone Nematostella. A second conclusion is that coral-specific processes (i.e. traits which distinguish corals from their close relatives) may be analogous to similar processes in distantly related organisms. This first large-scale application of microarray analysis demonstrates the potential of this approach for investigating many aspects of coral biology, including the effects of stress and disease.
Keywords: developmental

overall_design: Four developmental stages of Acropora millepora were compared - prawnchip, presettlement, postsettlement and adult.  Each was compared to every other 4 times; twice in one dye orientation and twice in the other (complete block design)

first: John

last: Maindonald

first: Stephen

last: Rudd

last: Hayward

first: Robert

last: Saint

middle: J

last: Miller

first: Eldon

middle: E

last: Ball


title: Gene expression profiles of HEK293 cells following induction of wild-type and mutated FOXP3

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: The forkhead DNA-binding protein FOXP3 is critical for the development and suppressive function of CD4+CD25+ regulatory T cells (TREG), which play a key role in maintaining self tolerance. Functionally, FOXP3 is capable of repressing transcription of cytokine genes regulated by the Nuclear Factor of Activated T cells (NFAT). Various mechanisms have been proposed by which FOXP3 mediates these effects. Using novel HEK cell lines that inducibly express either wild-type (WT) or mutant FOXP3, we have identified genome-wide expression patterns showing among other features that NFAT2 as an early target of FOXP3-mediated transcriptional repression.

overall_design: Six biological replicates of wild-type induced FOXP3 cell lines and six biological replicates of mutated FOXP3 cell line were studied.

first: Troy

last: Torgerson

first: Anna

last: Genin

first: Chunxia

last: Chen

first: Mingce

last: Zhang

first: Bin

last: Zhou

first: Stephanie

last: Añover-Sombke

first: Mark

middle: B

first: Igor

last: Dozmorov

first: Elizabeth

last: Ocheltree

first: Petri

last: Kulmala

first: Michael

last: Centola

first: Hans

middle: D

last: Ochs

first: Andrew

last: Wells

first: Randy

middle: Q

last: Cron


title: human mesangial cell serum-treated for 6 h

city: Sao Paulo

first: Rodrigo

last: Tambellini

address: Rua Boticatu, 740

country: Brazil

institute: Federal university of Sao Paulo

summary:
Mesangial cells (MC) respond to various insults, such as hyperglycemia, with expressive phenotypic changes. Modifications in the patterns of MC proliferation, death, and the balance between matrix production and degradation affect directly glomerular function and ultimately lead to glomerulosclerosis. MC activation by growth factors (GF) has been demonstrated to be a trigger to changes in cell phenotype, and blockade of specific systems tend to attenuate glomerular damage. The identification of elements activated following GF stimulation of MC may facilitate the comprehension of the pathophysiology of glomerular diseases. By means of DNA microarray technology we identified that three inhibitors of DNA binding (ID1, ID3, and ID4) were among the most significantly regulated genes in serum-treated MC. We extended these studies and demonstrated that ID gene mRNA expression is markedly and rapidly affected by the pro-fibrotic cytokine TGF-beta1. Of interest, bone-morphogenetic proteins (BMPs), members of the TGF-beta superfamily with anti-fibrotic effects, also enhanced the expression of ID genes. Additional experiments indicate that these genes, classically described as dominant negative inhibitors of E-proteins, are regulated by TGF-beta1 and BMPs through distinct pathways and may act as immediate-early genes. Our results suggest that ID genes may play an active role in MC fate determination through undefined mechanisms.
Keywords: comparative gene regulation by serum treatment

overall_design: The GE HealthCare CodeLink Human UniSet I Bioarray system, containing 10 000 gene probes, was used to generate global transcription profiles of human Mesangial Cells. All reagents were provided in the CodeLink Expression Assay Kit (GE HEALTHCARE, Piscataway, NJ, USA), except where noted. cRNA synthesis was performed according to the manufacturer’s instructions from 10 µg of pooled total RNA, purified on RNeasy columns (QIAGEN GmbH, Hilden, Germany), and quantified by UV spectrophotometry. cRNA was fragmented by heating at 94°C for 20 min in the presence of magnesium and hybridized overnight at 37°C in an appropriate buffer to a CodeLink slide under continuous shaking in an Innova 4080 incubator (New Brunswick, Edison, USA) at 300 rpm. After the hybridization, arrays were washed in 0.75x TNT (1x TNT: 100 mM Tris-HCl pH 7.6, 150 mM NaCl, and 0.05% Tween 20) at 46°C for 1 h followed by incubation with streptavidin-Cy5 (GE HealthCare) at room temperature for 30 min in the dark. Arrays were then washed in 1x TNT twice for 5 min and rinsed in 0.05% Tween-20. The slides were dried by centrifugation and kept in the dark until scanning. Images were captured on an GenePix 4000B Scanner (AXON INSTRUMENTS, Arlington, TX) using CodeLink Expression Scanning Software and were analyzed using CodeLink Expression Analysis Software (GE HEALTHCARE). This software generates normalized intensity values for each gene in each microarray, using the overall mean intensity of the array as the normalization standard.

first: Alexandre

middle: H

last: Campos

first: Thiago

middle: T

last: Maciel


title: D. simulans vs. Sechellia adult bodies choice vs. no choice -DGRC Two Colour arrays with Dye Swapping

status: Public on Dec 03 2008

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

summary:
Here we show that Drosophila sechellia—a specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulans—has rapidly accumulated loss-of-function alleles and reduced gene expression at genes affecting olfaction, detoxification, and metabolism.
While D. sechellia increases expression of genes involved with oogenesis and fatty acid metabolism when on its host, many more genes show reduced expression in D. sechellia.  For several functionally related genes, this decrease in expression is associated with loss-of-function alleles.  The rapid accumulation of these alleles potentially affected D. sechellia’s initial adaptation to M. citrifolia, likely contributes to D. sechellia’s poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species.  Our results suggest that a subset of genes reduce or lose function as a consequence of host specialization, which may explain why, in general, specialist insects tend to shift to chemically similar hosts. Moreover, if the accumulation of non- or weakly functional genes in a specialist enhances the ecological isolation between it and other species, then this process may explain why specialists are speciose.

Keywords: comparative hybridization, gene expression

sample_organism:
Drosophila sechellia
Drosophila simulans

overall_design: 2 species (simulans and sechella) by choice vs no-choice treatment for octanoic & hexanoic acid blend

first: Corbin

last: Jones


title: Small RNAs from 4-week old seedling of Oryza sativa

city: Saint Louis

first: Xuefeng

address: One Brooking Dr.

department: Department of Computer Science and Engineering

type: Non-coding RNA profiling by high throughput sequencing

summary: In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing.

overall_design: Totally three sets of small RNAs, which were obtained under normal condition as well as salt and drought stress conditions

first: Ramanjulu

last: Sunkar

first: Jian-kang

last: Zhu

first: Weixiong

first: Yun

last: Zheng

first: Hailing

last: Jin


title: Campylobacter jejuni comparative genome: Control strain 11168 vs. strain NW

first: Linda

middle: S.

last: Mansfield

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

summary:
Gene content comparison of control C.j. strain 11168 which colonizes and causes disease in a murine model versus strain NW which colonizes but does not elicit disease symptomology in the mouse model.

Keywords: DNA/DNA comparison

overall_design: Two genome comparison of disease strain versus non disease strain of C.j., Biological replicates - 2, independently grown and harvested, Technical replicates 2, also independent, 3 ORF replicates per array.


title: DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tiling arrays to identify the consensus sequence for each transcription factor as a whole in the genome.

overall_design: Each protein was used for 2 independent replicates at a protein concentration of 40nM.  The second replicate is a dye-swap.  During analysis, regions of the genome had to be identified as bound in both replicates as well as the average of the two replicates to be considered true binding sites.

first: Gwenael

last: Badis

first: Esther

last: Chan

first: Harm

last: van Bakel

first: Lourdes

last: Pena-Castillo

first: Desiree

last: Tillo

first: Kyle

last: Tsui

first: Clayton

last: Carlson

first: Andrea

last: Gossett

last: Hasinoff

first: Christopher

last: Warren

first: Marinella

last: Gebbia

first: Shaheynoor

last: Talukder

first: Ally

last: Yang

first: Sanie

last: Mnaimneh

first: Dimitri

last: Terterov

first: David

last: Coburn

first: Ai

last: Yeo

first: Zhen

middle: X

first: Neil

last: Clarke

first: Aseem

middle: Z

last: Ansari

first: Corey

last: Nislow

first: Timothy

middle: R

last: Hughes


title: Gene expression profiling induced by overexpression and silencing of Ankrd2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
We have used a genomic approach based on microarray technology in order to identify the gene networks that are disturbed by Ankrd2 overexpression and silencing. We performed the experiments at the myoblast stage, because there Ankrd2 localizes in the nucleus where it may act as myogenic transcriptional regulator. The stable alteration of Ankrd2 expression level resulted in the modulation of different muscle differentiation-related genes belonging to functional classes having key roles in myogenesis (cell cycle regulation and apoptosis; skeletal muscle development and contraction; cell adhesion and cytoskeletal organization). The transcriptional profile of Ankrd2-overexpressing clones highlights a remarkable impairment of the myogenic differentiation program. In the same clones the alteration of genes regulating cell cycle and apoptosis shows that the Ankrd2 overexpression leads to raised C2C12 proliferation compromising the response to serum deprivation and then myotube formation. On the other side, in Ankrd2-silenced clones numerous genes promoting cell cycle arrest are found upregulated.
Keywords: gene-specific overexpression and silencing

overall_design: Gene expression profiling experiments have been performed using a mouse microarray platform containing a collection of 13,443 70mer oligonucleotide probes (Qiagen-Operon, version 1.1). Each oligonucleotide was spotted in two replicates on MICROMAX SuperChip I glass slides (Perkin-Elmer) using Biorobotics Microgrid II (Apogent Discoveries), supplied with 48 stealth micro pins.Total RNA was purified from two C2C12 Ankrd2-overexpressing (Ankrd2(+)clS9 and Ankrd2(+)clS12) and two –silencing clones (Ankrd2(-)clA9 and Ankrd2(-)clA10)and from C2C12 control cells at proliferating myoblasts stage. Competitive hybridization was done twice using different microarray slides in which each single sample and control RNA was labeled either with Cy3 or Cy5 fluorochromes (dye swapping procedure).Using this strategy we obtained four fluorescence intensity values for each probe in the platform. Fluorescence detection was carried out on a GSI Lumonics LITE dual confocal laser scanner (Perkin-Elmer) with ScanArray Microarray Analysis Software, and raw scanner images were analyzed with QuantArray software (Perkin-Elmer). Normalization of the expression levels was performed with MIDAW tool (Romualdi et al., 2005).

first: Camilla

last: Bean

first: Nicola

last: Facchinello

first: Michela

last: Salamon

first: Georgine

last: Faulkner


title: 5448 vs 5448R- in vivo 24h

status: Public on Dec 01 2008

city: Wollongong

first: Andrew

last: Hollands

state: NSW

address: Northfields Ave

department: School of Biological Sciences

institute: University of Wollongong

summary: Microarray analysis was performed on in vivo-derived RNA from the well characterized GAS strain 5448 and its derivative 5448R-, containing the mutated ropB allele from 5628.

overall_design: We followed a cyclic design that allowed us to compare every condition to each other at least twice, and guaranteed dye swapping to eliminate effects of non-specific binding. This study consists of 4 replicates of 5448 and 3 replicates of 5448R-.

first: Ramy

last: Aziz

first: Rita

last: Kansal

first: Malak

last: Kotb

first: Victor

last: Nizet

first: Mark

last: Walker


title: D. simulans vs. Sechellia adult heads choice vs. no choice -DGRC Two Colour arrays with Dye Swapping

first: Ian

last: Dworkin

first: Corbin

last: Jones


title: p53 regulates viral gene expression during infection with human cytomegalovirus

city: Moscow

first: Holger

last: Hannemann

state: ID

department: MMBB

institute: University of Idaho

summary:
Human cytomegalovirus (HCMV) is a common cause of morbidity and mortality in immunocompromised and immunosuppressed individuals. During infection, HCMV is known to employ host transcription factors to facilitate viral gene expression. To further understand the previously observed delayed viral replication and protein expression in p53 knockout cells, we conducted microarray analyses on p53+/+ and p53-/- immortalized fibroblast cell lines. At 12 hpi, applying the significance criteria defined above, no genes showed a significant difference in any of the comparisons. At 24 hpi, we found 19 genes to be significantly different in the THF versus p53-/- comparison and 14 genes to be significantly different in the HFF versus p53-/- comparison. Eleven genes were shared between HFF and THF cells when compared to p53-/- cells (UL30, UL54, UL63, UL65, UL69, UL75, UL110, UL122, IRL4, IRS1, TRS1, shown in bold in Table 1). Eight genes were unique in the THF versus p53-/- comparison (UL48, UL68, UL84, UL100, UL106, UL109, UL111, RL5A), and three genes in the HFF versus p53-/- cell comparison (UL14, UL16, US2). When comparing HFF and THF cells, only US2 showed a significant difference. The ratio (HFF versus p53-/- divided by THF versus p53-/-) of the expression levels of the eleven shared genes from the HFF versus p53-/- and THF versus p53-/- comparisons was an averaged 1.2, indicating that, with the exception of US2, these two cell lines behaved similarly with respect to p53-driven viral gene expression.

Keywords: time course, virus, cytomegalo, hhv5, infection, p53

sample_organism:
Homo sapiens
Human herpesvirus 5 strain Towne

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: Each slide consisted of 4 arrays. Each array consisted of 305 control features, 1265 cellular gene features and 670 viral gene features. The study was performed on 6 slides (HFF-THF, HFF-p53-/-, THF-p53-/- at 12 and 24 hpi). 3 arrays per slide were hybridized with 3 biological replicates of labelled RNA, the 4th array was hybridized with an equimolar mixture of the 3 biological replicate samples. This array was used for control purposes only, and the results were not used for downstream calculations. Each slide was stripped and reprobed two times to provide 3 technical replicates of each sample. As our experiments concentrated on viral genes and their expression, cellular genes were not further analyzed in this study.

first: Kyle

last: Rosenke

first: John

last: O'Dowd

first: Elizabeth

middle: A

last: Fortunato


title: Transcriptional profile asm gene cluster of high Ansamitocin P3 producing mutants derived from A. pretiosum

city: Singapore

first: Peter

last: Nissom

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

summary:
This series of microarry is the study of the transcriptional profile asm gene clusster of high Ansamitocin P3 producing mutants derived from isolating rifampicin resistant mutants.  Background  The Actinomycete Actinosynnema pretiosum ssp. auranticum has commercial importance due to its production of ansamitocin P-3 (AP-3), a potent antitumor agent.  One method to improve the productivity of A. pretiosum is to genetically alter the regulation of ansamitocin biosynthesis by manipulating selected genes.  To identify potential targets for genetic engineering, the transcriptional profile of an A. pretiosum mutant with enhanced AP-3 yield was compared to the parental strain.  High-producing mutants were isolated from rifampicin-resistance screens using a plate-based bioassay. Transcriptional profiling of genes in the ansamitocin biosynthetic cluster was carried out using a custom-designed A. pretiosum microarray and verified with quantitative RT-PCR.    Results  Genes involved in the synthesis of the AP-3 precursor, 3-amino-5-hydroxybenzoic acid (AHBA), including asm43, asm45 and asm47, were significantly up-regulated (P-value<0.05) by more than two-fold in the high-producing mutant relative to the parental strain.  In addition, genes involved in polyketide synthesis (asmB and asmD), bicyclomycin resistance (asm35) and transcriptional regulation (asm29) were up-regulated, while the transcriptional repressor, asm2, was down-regulated.  Interestingly, the two AHBA synthase gene homologues, asm24 and asm43, had divergent expression profiles despite their strong sequence similarity and functional complementarities.  The rifampicin-resistance mutation associated with increased AP-3 production was mapped to the gene encoding RNA polymerase beta subunit, rpoB.  While distinct multiple mutations in RpoB were noted for each of the mutants sequenced, a common H436R mutation was identified in cluster I of rpoB in all four mutants sequenced.    Conclusions  The transcriptional analysis has provided useful insights into the mechanism underlying the increased AP-3 production in the high-producer mutant and expanded our understanding of the function and regulation of genes in the ansamitocin biosynthetic cluster.  In addition, the differentially expressed genes identified are potential targets for genetic manipulation; alternatively, they can be used in reporter-based selections to isolate mutants with greater AP-3 productivity.

Keywords: genetic modification, time course, boutique microarray, quantile normalization

overall_design: Microarray chip was hybdridized with cDNA obtained from samples vs sheared A. pretiosum gDNA. cDNA obtained from cultures of A. pretiosum (ATCC:31565) and r50D1 mutant were used. Cell pellets were harvested on days 2,4,6 and 8 of each culture.Three biological replicates were performed for each cell line with two technical replicates for each biological replicate:

first: Daniel

last: Ng

middle: M

middle: V

last: Wong


title: Profiling antibody function on antigen arrays

city: Budapest

first: József

last: Prechl

address: Pázmány Péter s. 1/C

department: Immunology Research Group

country: Hungary

institute: ELTE-MTA

summary:
Humoral immune responses are traditionally characterized by determining the presence and quality of antibodies specific for certain antigens. Arraying of large numbers of antigens allows the parallel measurement of antibodies, generating patterns called antibody profiles. Functional characterization of these antibodies could help draw an even more informative map of an immune response. To generate functional antibody profiles we simultaneously tested not only IgM, IgG and IgA binding to but also complement activation by a panel of endogenous and exogenous antigens printed as microarrays, using normal and autoimmune human sera. We show that complement activation by a particular antigen in a given individual cannot be predicted by the measurement of antigen specific antibodies, in spite of a general correlation between the amount of antigen-bound antibody and the deposited C3 fragments. This is due to both differences  in the isotypes that dominate in the recognition of an antigen and individual variations for a given isotype, resulting in altered complement activation potential. Thus, antigen  specific C3 deposition can be used as an additional parameter in immune response monitoring. This is exemplified by comparing the coordinates of antigens, used for the diagnosis of systemic lupus erythematosus, of normal and autoimmune serum samples in a two-dimensional space derived from C3 deposition and antibody binding. Since cleavage fragments of C3 mediate important immunological processes we propose that measurement of their deposition on antigen microarrays, in addition to antibody profiling, can provide useful functional signature about the tested serum.

Keywords: IgM immuneprofile, antigen array

overall_design: IgM, IgG, IgA and C3 binding in 30 human serum samples were examined using custom-made protein arrays

first: Krisztian

last: Papp

first: Péter

last: Végh


title: Microarray Analysis of Toxicogenomic Effects of Sodium Hypochlorite on Mycobacterium bovis BCG

city: ft. meade

first: Hyeung-Jin

last: Jang

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary:
In the present study, we employed Affymetrix Mycobacterium bovis BCG GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Mycobacterium bovis BCG to Sodium Hypochlorite, which involved initial growth inhibition and metabolism.

Keywords: Transcriptome study

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Sodium Hypochlorite. We calculated fold change as the ratio between the signal averages of three untreated (control) and three Sodium Hypochlorite-treated (experimental) cultures for 0, 10 and 20 min exposures.

first: Freshteh

last: Toghrol

first: William

last: Bentley


title: Gene expression profiling of maize anther and pollen ontogeny

city: Stanford

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Global gene expression profiles of seven stages representing 29 days of anther development are analyzed using a 44K oligonucleotide array querying ~80% of maize protein-coding genes.  Each anther stage expresses ~10,000 constitutive and ~10,000 or more transcripts restricted to one or a few stages.

Keywords: anther development, maize

overall_design: 4 replicates of 7 samples (6 anther stages plus mature pollen) were hybridized to a 44K Agilent array according to the A-optimal design recommended by Kerr and Churchill for 7 samples.

first: Jiong

last: Ma

first: Virginia

last: Walbot

first: David

last: Skibbe


title: Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

city: Eugene

first: Zachary

last: Lewis

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

type: Methylation profiling by genome tiling array

summary: Both RNAi-dependent and -independent mechanisms have been implicated in the establishment of heterochromatin domains, which may be stabilized by feedback loops involving chromatin proteins and modifications of histones and DNA.  Neurospora crassa sports features of heterochromatin found in higher eukaryotes, namely cytosine methylation (5mC), methylation of histone H3 lysine9 (H3K9me) and HETEROCHROMATIN PROTEIN-1 (HP1), and provides a model to investigate heterochromatin establishment and maintenance. We mapped the distribution of HP1, 5mC, H3K9me3 and H3K4me2 at 100bp-resolution and explored their interplay. HP1, H3K9me3 and DNA methylation were extensively colocalized and defined 44 heterochromatic domains on linkage group VII, all relics of repeat-induced point mutation (RIP).  Interestingly, the centromere was found in a striking ~350kb heterochromatic domain with no detectable H3K4me2.  5mC was not found in genes, in contrast to the situation in plants and animals.  H3K9me3 is required for HP1 localization and DNA methylation.  Here, we show that localization of H3K9me3 is independent of 5mC or HP1 at virtually all heterochromatin regions.  In addition, we observed complete restoration of DNA methylation patterns after depletion and reintroduction of the H3K9 methylation machinery, indicating that the signals for de novo heterochromatin formation lie upstream of H3K9 methylation.  These data show that A:T rich RIP’d DNA efficently directs methylation of H3K9, which in turn, directs methylation of associated cytosines.

overall_design: Immunoprecipitation experiments using antibodies to 5mC, H3K9me3, epitope-tagged HP1, and H3K4me2 were performed.  The immunoprecipitate fraction was labeled with Cy5 and the total input was labeled with Cy3.  Samples were hybridized to a N. crassa LGVII tiling path microarray.

first: Shinji

last: Honda

first: Tamir

middle: K

last: Khlafallah

first: Jennifer

last: Jeffress

first: Michael

last: Freitag

first: Fabio

last: Mohn

first: Dirk

last: Schubeler

first: Eric

middle: U

last: Selker


title: Listeria monocytogenes EGD and EGD-e

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

institute: Lehrstuhl für Mikrobiologie

summary:
Transcriptional profile after growth in MM (minimal medium (Premaratne et al. 2001) supplemented with 50 mM Glucose.

Note: strain "EGD" has not been deposited at ATCC/NCTC. It is a derivative of the original Murray strain (Murray et al. 1926), obtained from S.H.E. Kaufmann. Strain "EGD-e" has been obtained from H. Hahn (Berlin) via T. Chakraborty (Gießen) and is deposited under ATTC BAA-679 and in the Pasteur culture collection.

Keywords: strain comparison

sample_organism:
Listeria monocytogenes
Listeria monocytogenes EGD-e

overall_design: A total of three independently isolated RNA samples from each strain were used for the analysis.

first: Sonja

last: Mertins

first: Biju

last: Joseph

first: Stefanie

last: Mueller-Altrock

first: Werner

last: Goebel


title: Circulating Cells in Coronary Collateral Artery Growth II

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

summary: In the present study, we performed transcriptome expression analyses in three independent peripheral blood-derived monocyte subpopulations from patients with chronic coronary occlusions (CTO) and tested for arteriogenesis. Whole-genome mRNA expression analyses were performed on these three monocyte subpopulations, namely: (1) unstimulated-, (2) 3 hours LPS-stimulated-, (3) monocyte-derived macrophages.  Whole-genome mRNA expression analysis amongst others confirmed increased expression of IFNbeta-regulated genes in patients with insufficient coronary collateralization (collateral flow index (CFI) ≤0.37 “nonresponders”), compared with patients having sufficient collateralization (CFI>0.37 “responders”).

overall_design:
Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation. Subsequently, monocytes were negatively isolated using immunomagnetic beads. Thereafter, from each patient the cells were divided into three separate pools that were separately treated: (1) untreated, (2) 3 hours LPS (10 ng/mL)-treated, and (3) differentiated into macrophages by 20 hours LPS (10 ng/mL) treatment.

Within each of these three cell populations the transcriptome profiles were divided into two patient groups, being the non-responders (CFI≤0.37) versus the responders (CFI>0.37). Both patient groups had been matched for age, sex, medication and other factors that influence collateral artery growth. The mRNA-derived probes were randomly hybridized to HumanRef-8 Expression v2 bead chip arrays (Illumina), followed by scanning and feature extraction (ServiceXS, Leiden, the Netherlands).

Sample number and barcodes of the three monocyte-derived cell populations:
(1) Unstimulated monocytes: N=9 nonresponding, N=10 responding patients, with barcodes GSM563265 to GSM563286.
(2) 3h LPS monocytes: N=10 nonresponders, N=10 responders, with barcodes GSM335353 to GSM335389.
(3) Macrophages: N=9 nonresponders, N=9 responders, with barcodes GSM563287 to GSM563304.

The raw data for Samples GSM335xxx are provided as individual supplementary files. The raw data for Samples GSM563xxx are provided in the supplementary file "GSE13290_raw_data.txt".

first: Anja

last: van der Laan

first: Stephan

last: Schirmer

first: Margreet

last: de Vries

first: Jasper

middle: J

last: Koning

middle: L

first: Joost

middle: O

last: Fledderus

first: Antonius

last: Bastiaansen

first: Josefien

last: Baggen

first: Karel

last: Koch

first: Jan

last: Baan Jr.

first: José

middle: P

last: Henriques

first: René

last: van der Schaaf

first: Marije

last: Vis

first: Reina

last: Mebius

first: Tineke

middle: C

last: van der Pouw Kraan

first: Paul

last: Quax

last: Piek

first: Anton

last: Horrevoets

first: Niels

last: van Royen


title: In vivo rabbit preimplantation development

city: JOUY EN JOSAS

first: Duranthon

last: Veronique

address: Domaine de Vilvert

department: Biologie du Développement et Reproduction

country: France

institute: INRA

summary:
Evaluation of the transcriptomic profile of the rabbit embryo along the preimplantation period during in vivo development. Three embryonic stages were used: four cell embryos (H32 post-coïtum);  morula (H58 pc) and blastocyst (H90 pc).

Keywords: time course rabbit embryo

overall_design: 18 samples


title: Activation by CcpA-FDP of two key determinants of pneumococcal virulence, capsule production and choline utilization.

city: Toulouse

first: Julien

last: Storai

address: 135 avenue de Rangueil

institute: CNRS

summary:
The kinetic behaviour of S. pneumoniae during vaccine production was studied using a dynamic systemic approach. Quantification of key intracellular glycolytic metabolites coupled to global transcriptomic analysis led to an improved knowledge of pneumococcal physiology. In controlled growth conditions, a direct correlation between the accumulation of key glycolytic intermediates and the expression of capsular polysaccharide genes (cps operon encoding the main pneumococcal antigen) was established. Interestingly, the same correlation was confirmed for the genes involved in the assimilation and the modification of choline, an indispensable nutritional requirement for both growth and virulence of S. pneumoniae. Such a correlation suggests a direct or indirect control of the expression of these genes by the global transcriptional regulator CcpA (catabolite control protein A) since putative cre sites upstream of the promoter were identified, even though the exact nature of this regulation remains to be confirmed. Preliminary results indicate that a ccpA mutation provokes a significant decrease in the expression of these genes. The global transcriptomic analysis coupled with motif research has revealed an extended CcpA regulon in S. pneumoniae including genes involved in diverse metabolic functions.
Keywords: Capsular polysaccharide industrial production

overall_design: One condition experiment examining the transcriptome between two growth phases of the same serotype (slide 1 to slide 4). Thus, cross analysis between the two serotypes during exponential growth was performed in order to complete the analysis

last: Storaï

first: Bernard

last: Martin

first: Chantal

last: Granadel

first: Marie-France

last: Planard

first: Jean-Pierre

last: Claverys

first: Nic

last: Lindley


title: Listeria monocytogenes EGD after growth BHI vs. LB vs. MM

first: Regina

last: Stoll

summary:
Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in BHI (brain-heart-infusion), LB (Luria Bertani broth) and MM (minimal medium (Premaratne et al. 2001)  (each supplemented with 50 mM Glucose).

Keywords: media comparison

overall_design: A total of three independently isolated RNA samples from each condition were used for the analysis.

first: Sonja

last: Mertins

first: Biju

last: Joseph

first: Stefanie

last: Mueller-Altrock

first: Werner

last: Goebel


title: miRNA Cancer Cell Line Profiles

city: X

first: Alex

middle: T.

last: Adai

state: X

address: X

department: Oncology Diagnostics

institute: Genentech

summary:
miRNA cancer cell line profiles
Keywords: cancer, cell lines

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: miRNA cancer cell line profiles with samples in either duplicate or triplicate.


title: Zebrafish Paired End DiTag libraries

first: Chia

middle: Lin

last: Wei

address: 60 Biopolis Street, #02-01, Genome

institute: Genome Institute Of Singapore

summary:
Used a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization.
Keywords: Paired End DiTags

overall_design: 5 zebrafish tissues examined.


title: Expression of EBV miRNAs in numerous EBV-positive cell lines

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

summary: EBV-positive cell lines were assayed for expression of EBV miRNAs.  The names of the miRNAs are from miRBase from Fall 2007.  Microarray probes are tandem complements of the mature miRNA sequence.  We assayed Burkitt's lymphoma (BL), Nasopharyngeal carcinoma, post-transplant lymphoproliferative disease (PTLD), primary effusion lymphoma, and lymphoblastoid cell lines.   We also assayed primary B cells that were infected with the B95-8 strain of EBV, which was found to express EBV miRNAs as early as 20 hours post infection.  We have found PTLD and BLs from HIV-positive donors both express EBV miRNAs.  These types of cell lines have not previously been found to express viral miRNAs.  We have found that cells that support type I and type II latency express only the BART miRNAs, whereas cells that support type III latency express BART and BHRF1 miRNAs.  Furthermore, BL cell lines that spontaneously lose EBV express levels of the viral miRNAs that are at least 5-fold lower than cell lines that do not lose EBV.

platform_organism:
Arabidopsis thaliana
Homo sapiens
human gammaherpesvirus 4

overall_design: In total, 48 samples have been assayed and included in this study.  EBV-negative control samples are not included in this data set, but raw and processed data may be requested from the contributors.  These EBV-negative cell lines include the Burkitt's lymphoma cell lines, BJAB and Akata-negative, the gastric carcinoma cell line, AGS, and uninfected primary B cells. Of the 48 samples, we have assayed 22 different EBV-positive cell lines and 4 different time points after infection of primary B cells with EBV.  Replicates of the majority of cell lines is included in this data set.  Replicates are from independent RNA isolations that were then hybridized to individual microarrays.

first: Bill

last: Sugden

first: Srikumar

last: Sengupta

first: Malika

last: Kuzembayeva


title: Analysis of expression levels of genes on chromosome 19 in U937 cells expressing AML1/ETO

status: Public on Nov 28 2008

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

institute: European Institute of Oncology

type: Expression profiling by genome tiling array

summary:
Approximately 20% of Acute Myelogenous Leukemia (AML) cases carry the t(8;21) translocation, which involves the AML1 and ETO genes, and express the resulting AML1/ETO fusion protein that functions as a transcriptional repressor by recruiting NCoR/SMRT/HDAC complexes to DNA.
We used ChIP-chip to identify the determinants of AML1/ETO binding on a contiguous DNA region (chromosome 19). In order to correlate transcription factor binding to gene expression, we evaluated expression levels of genes localized on chromosome 19 by expression tiling.
Keywords: Gene expression

overall_design: A U937 cell line that conditionally expresses HA-tagged AML1/ETO under the control of the mouse metallothionine promoter (U937-A1E) (Alcalay et al., J.Clin.Invest, 2003,112, 1751-1761) was used. A cell line carrying the empty vector was used as control. Cell lines were treated for 8h with 100uM ZnSO4 to induce transgene expression in U937-A1E. For each of the U937 cell lines (AML1/ETO and Mt), three independent RNA extractions were performed, and an equal quantity of each of the three RNA preparations was then mixed to generate an RNA pool for each sample.


title: AML1/ETO, AML1, and HEB binding patterns on chromosme 19

summary:
Approximately 20% of Acute Myelogenous Leukemia (AML) cases carry the t(8;21) translocation, which involves the AML1 and ETO genes, and express the resulting AML1/ETO fusion protein that functions as a transcriptional repressor by recruiting NCoR/SMRT/HDAC complexes to DNA.
We used ChIP-chip to identify the determinants of AML1/ETO binding on a contiguous DNA region (chromosome 19). AML1/ETO binding regions are characterized by a specific sequence signature that includes the presence of the consensus binding sites for the AML1 and HEB transcription factors. We therefore assessed the binding patterns of AML1 and HEB on chromosome 19. A specific chromatin modification (tri-methylation of lysine 4 on histone 3 = 3MetK4) was also studied in U937 cells expressing AML1/ETO in order to correlate the identified binding profiles with active transcription sites.
Keywords: ChIP-chip

overall_design: A U937 cell line that conditionally expresses HA-tagged AML1/ETO under the control of the mouse metallothionine promoter (U937-A1E) (Alcalay et al., J.Clin.Invest, 2003,112, 1751-1761) was used. Cell lines were treated for 8h with 100uM ZnSO4 to induce transgene expression in U937-A1E. We performed ChIP using anti-HA,  anti-ETO, anti-AML1/RUNX1, anti-HEBor anti-3MetK4  antibodies. ChIP products were then PCR amplified, labeled with Cy3/Cy5 fluorescent dyes and hybridized to the NimbleGen custom made NGS_HG17_Chr.19Array. U937-Mt cells, which carry the empty vector, served as control (C) for non-specific antibody binding. Each sample identifier indicates Antibody_Cell line (example: HA_A1E = ChIP using anti HA antibody in U937-A1E cells; HA_C = ChIP using anti HA antibody in U937-Mt control cells)


title: Listeria monocytogenes EGDΔprfApPrfA and EGDΔprfApPrfA* compared to the wild type strain EGD

summary:
Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001) supplemented with 50 mM glucose, cellobiose or glycerol.

Keywords: prfA overexpressing strains

overall_design: A total of two independently isolated RNA samples from each condition were used for the analysis.


title: Ludwig Institute/UCSD ENCODE project August 2007 Release

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

summary:
	The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication.
Keywords: ChIP-chip ENCODE

overall_design:
ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K

first: Christopher

last: Glass

first: Michael

middle: G

last: Rosenfeld

first: Nicholas

last: Webster

first: Keith

last: Ching

first: Lindsey

last: Harp

first: Zhen

last: Ye

first: Rhona

last: Stuart

first: Sara

last: Calcar

first: Tae

middle: H

last: Kim

first: R

middle: D

last: Hawkins

first: Leah

last: Barrera

first: Roland

last: Luna

first: Kun

last: Wang


title: Xylella fastidiosa Study on different growth media

status: Public on Nov 27 2008

city: Berlin

first: Tiago

last: Lopes

address: Robert Rossle Strasse, 10

institute: Max-Delbruck Center for Molecular Medicine

summary: The arrays were hybridized against cDNAs labeled during reverse transcription reactions, which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE).

overall_design: A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The chips were spotted, hybridized, scanned and analyzed in our laboratory.


title: Heterologous Microarray Hybridization Between Vesicomyid Symbionts

city: Cambridge

first: Irene

last: Newton

state: MA

address: 16 Divinity Ave

department: OEB

institute: Harvard University

summary:
The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts.  These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content.

Keywords: comparative genomic hybridization

sample_organism:
Calyptogena magnifica symbiont
Calyptogena kilmeri gill symbiont
Calyptogena pacifica gill symbiont

platform_organism: Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)

overall_design: Microarrays were built off the Ruthia magnifica genome and two replicate hybridizations to this organism were used as a baseline for comparisons. Genomic DNA from two other vesicomyid symbionts (Calyptogena kilmeri and C. pacifica symbionts) was also hybridized to the array with three biological replicates for each sample.

first: Colleen

last: Cavanaugh


title: Photoperiod regulates genes encoding melanocortin 3 and serotonin receptors, and secretogranins expressed in the dmpARC of the Siberian hamster

status: Public on Nov 29 2008

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

summary: The mechanism(s) involved in the regulation of the seasonal-appropriate body weight of the Siberian hamster is currently unknown. We have identified photoperiodically regulated genes including VGF in a sub-region of the arcuate nucleus termed the dorsomedial posterior arcuate (dmpARC). Gene expression changes in this nucleus so far account for a significant number of those reported as photoperiodically regulated and are therefore likely to contribute to seasonal physiological responses of the hamsters. The present study was conducted to identify additional genes expressed in the dmpARC regulated by photoperiod that could be involved in regulating the activity of this nucleus with respect to seasonal physiology of the Siberian hamster. Using laser capture microdissection coupled with a microarray analysis and a candidate gene approach, we have identified in the dmpARC several photoperiodically regulated genes that are known to have roles in secretory and intracellular signaling pathways. These include secretogranin III (SgIII) and SgVI (secretory pathway), melanocortin 3 receptor (MC3-R) and serotonin (5-HT) receptors 2A and 7 (signaling pathway), all of which increase in expression in short photoperiod. The spatial relationship between receptor signaling and potential secretory pathways was investigated by dual in situ hybridization, which revealed that 5-HT2A and 5-HT7 receptors are expressed in neurons expressing VGF mRNA and that a sub-population (approximately 40%) of these neurons express MC3-R. These gene expression changes in dmpARC neurons may reflect the functional requirement of these neurons for seasonal physiology responses of the hamster

overall_design: Samples were taken from 10 individual animals, 5 of which had lived under a short day (SD) photoperiod, the other 5 under a long day (LD) photoperiod. Each hybridisation compared a LD sample (labelled with Cy5) with a SD sample (labelled with Cy3).

first: Kanishka

middle: N

last: Nilaweera

first: Gillian

first: Claus-Dieter

last: Mayer

first: Perry

last: Barrett

first: Zoe

middle: A

last: Archer

first: Peter

last: Morgan


title: Characterization of unique small RNA populations from rice grain

status: Public on Nov 24 2008

city: Saint Louis

middle: Elizabeth

last: Heisel

address: 800 North Lindbergh

department: Biotechnology

institute: Monsanto

summary: Small RNAs (~20 to 24 nucleotides) function as naturally occurring molecules critical in developmental pathways in plants and animals. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing.  Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the genome.  Hotspots here are defined as 1 kb regions within which small RNAs are significantly overproduced relative to the rest of the genome.  Hotspots were identified to facilitate characterization of different categories of small RNA regulatory elements.  Included in the hotspots, we found known members of 23 miRNA families representing 92 genes, one trans acting siRNA (ta-siRNA) gene, novel siRNA-generating coding genes and phased siRNA generating genes.   Interestingly, over 20% of the small RNA population in grain came from a single foldback structure, which generated eight phased 21-nt siRNAs.  This is reminiscent of a newly arising miRNA derived from duplication of progenitor genes.  Our results provide data identifying distinct populations of small RNAs, including phased small RNAs, in mature grain to facilitate characterization of small regulatory RNA expression in monocot species.

overall_design: In an attempt to gain a broader understanding of gene expression in rice grain, we characterized small RNA populations from Oryza sativa spp. japonica cv. Nipponbare utilizing a deep sequencing approach. Small RNA libraries were constructed from three pools of mature, dormant rice grain and three-week post germination seedlings utilizing RNA-adapter mediated ligation.  Each of the four libraries were independently sequenced using high-throughput pyrosequencing. We obtained a total of 679,146 sequences from the three rice grain libraries and 257,394 from one rice seedling library.

middle: E

first: Edwards

middle: M

last: Allen

first: Yuanji

last: Zhang

first: Liang

last: Guo

first: Jim

last: Roberts

first: Tracy

last: Reynolds

first: Xiao

last: Yang

first: David

last: Kovalic


title: Mapping of genome-wide action sites of topoisomerase IIbeta by a functional ChIP-chip technique (eTIP-tiling array)

city: Okayama

first: Mary Miyaji-Yamaguchi

state: Okayama

address: 2-5-1 Shikata-cho

department: Department of Neurogenomics

institute: Okayama University

summary: DNA topoisomerase II (topo II) catalyzes a strand passage reaction in that one duplex is passed through a transient brake in another. Completion of late stages of neuronal development depends on the presence of active isoform (topo IIbeta). We identified topo IIbeta action sites on 7 selected genomic regions (about 79 Mb in total), each containing at least one gene that is controlled by topo IIbeta in neuronal differentiation. We used a novel method, etoposide-mediated topoisomerase immunoprecipitation (eTIP), followed by identification of precipitated DNA fragments on genomic tiling arrays. These DNA fragments were first fractionated by concentrated salt prior to the array analysis. The 0.5 M NaCl-released fraction was analyzed as P2 and the salt-resistant fraction wad analyzed as P1.

overall_design: The genomic DNA fractions from the immunoprecipitate (P1 or P2) were co-hybridized with a reference DNA isolated from the input of immunoprecipitation.

first: Kuniaki

last: Sano

first: Mary

last: Miyaji-Yamaguchi

first: K

last: Tsutsui

first: Ken


title: Rib bone growth

status: Public on Nov 23 2008

city: Grand Rapids

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary:
Rib bone growth in red deer stags - Abstract: In 'The Bone and Joint Decade' interest is focused on genetic factors causing bone disorders. Osteoporosis, attacking 10% of the population worldwide, is the most common metabolic bone disease, which is mimiced by several ovarectomised or genetically modified 'cascadeur' animal species, but none of them is able to remedy its pathologically porous bone tissue. Regeneration in skeletal elements is the curiosity of our newly investigated osteoporosis animal model, red deer (Cervus elaphus). The cyclic physiological osteoporosis in red deer stag is a consequence of the annual antler cycle. This phenomenon raises the possibility to explore new genes involved in regulating bone mineral density (BMD) and recovery of bone resorption on the basis of comparative genomics between deer and human. Here we compared the gene expression activities of osteoporotic and regenerating flying rib bone samples versus late autumn dwell control in red deer by heterologous microarray hybridization. Identified genes were tested on human femoral bone tissue from postmenopausal osteoporotic and non-osteoporotic patients. Expression data were evaluated by Principal Components Analysis and Discriminant Analysis.
Keywords: Gene Expression experiment

overall_design:
Approximately 2-3 g flying rib bone pieces in the entire cross section of bony rib were surgically removed from 3 anaesthetized [SBH-Ketamine (2.5 mg/kg live weight) combined with Xylazine (0.2 mg/kg live weight) i.m. injection] 6, 7 and 8 year old Cervus elaphus stags. (Cast antler pairs weighed 7-8 kg for each animal.) Removed rib pieces were extensively washed in PBS for eliminating blood and marrow contamination, than immediately frozen in liquid nitrogen. The time of tissue collections were (i) within the period of the active mineralization of antler, at the beginning of June when skeletal osteoporosis takes place, (ii) in the fitness improvement period with velvet shedding in late July, that is the 'regenerating time' and (iii) in the period of late autumn dwell at the end of November when in the skeleton the mineral mobilization and deposition are dynamically equilibrated (BMD is in steady state).

Each comparison performed on Platforms GPL4052 and GPL5352.


title: RNA-chip from MEF cells

city: Vienna

first: Florian

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

summary:
Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons.
Keywords: RNA-chip, chromosome 17 wide expression mapping

overall_design: mouse chromosome 17 wide expression mapping of transcribed genes by hybridization of ds cDNA in two independent MEF cell lines

first: Mathew

last: Sloane

first: Denise

last: Barlow


title: Chip-chip from MEF cells with H3ac, H4ac, H4K20me1, H3K27me3, H3K9me3, H4K20me3, H3K4me2, H3K4me3 and H3K9ac

summary:
Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons.
Keywords: Chip-chip, chromosome 17 wide unbiased mapping

overall_design: unbiased mapping of several histone modifications on chromosome 17 in two independent MEF cell lines


title: Comparison of gene expression after induction of DNA endonuclease in strains either containing a cut site or not

status: Public on Nov 21 2008

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

summary: Investigating the induction of the SOS response after the introduction of a single dsDNA break per genome by expressing the SceI endonuclease. The endonuclease is under the control of a xylose-inducible promoter.

overall_design: Grow cells from 2 strains (LAS210, which has an SceI cut site, and LAS195, which does not) in minimal arabinose and at T0 both strains get xylose to induce the endonuclease. In one strain the endonuclease does not produce cuts, however. Each set is done in triplicate.

first: Lyle

last: Simmon

first: Alexi

last: Goranov


title: Profiling 11,639 genes in PBMCs from 2 donors: U133 A 2.0 Custom CDF Version 9

city: Atlanta

first: Troy

last: Querec

state: GA

address: 954 Gatewood Rd

department: Emory Vaccine Rearch Center

institute: Emory University

summary:
The immune responses generated by YF-17D by profiling 11,639 genes in PBMCs from 2 donors cultured with YF-17D vaccine were accessed after 3 and 12 hours.

Keywords: time course, in vitro stimulaion

overall_design: PMBCs were isolated with citrate buffered cell preparation tubes (CPT) from 2 healthy donors who were not previously vaccinated with YF-17D.  Total RNA was either isolated directly from the freshly collected cells or after cell culture.  Cells were cultured for 3 and 12 hours in the presence or absence of YF-17D vaccine.

first: Querec

last: Troy

first: Akondy

last: Rama

first: Lee

last: Eva

first: Cao

last: Weiping

first: Nakaya

last: Helder

first: Teuwen

last: Dirk

first: Pirani

last: Ali

first: Gernert

last: Kim

first: Deng

last: Jiusheng

first: Marzolf

last: Bruz

first: Kennedy

last: Kathleen

first: Wu

last: Haiyan

first: Bennouna

last: Soumaya

first: Olouch

last: Herold

first: Miller

last: Joe

first: Vencio

last: Ricardo

first: Mulligan

last: Mark

first: Aderem

last: Alan

first: Ahmed

last: Rafi

first: Pulendran

last: Bali


title: Comparison of gene expression after induction of DNA endonuclease

first: Alan

last: Grossman

summary: Investigating the induction of the SOS response after the introduction of a single dsDNA break per genome by expressing an endonuclease. The endonuclease is under the control of a xylose-inducible promoter.

overall_design: Grow cells in minimal arabinose and at T0 split the culture. One set gets xylose to induce the endonuclease and the other does not. Each set is done in triplicate.

first: Lyle

last: Simmons

first: Alexi

last: Goranov


title: Technical Analysis of Fundulus heteroclitus cDNA Microarrays, experiment A

city: Miami

first: Cinda

last: Scott

state: FL

address: 4600 Rickenbacker Cswy

department: Marine Biology and Fisheries

institute: University of Miami

summary: In the teleost fish Fundulus heteroclitus there is extensive variation in gene expression among individuals within and between populations.  Accurate measures of the variation in mRNA expression using microarrays can be confounded by technical variation, which includes variation in RNA isolation procedures, day of hybridization and methods used to amplify and dye label RNA for hybridization.  In this manuscript we analyze the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations demonstrating that for a wide-range of mRNA concentrations the fluorescent signal is a linear function of the amount of mRNA.  Additionally, the separate isolation, labeling or hybridization of RNA does not add significant amounts of variation in microarray measures of gene expression.  However, single or double rounds of amplification for labeling do have small but significant affects on 10% of genes, but this source of technical variation is easy to avoid.  To examine both technical and stochastic biological variation, mRNA expression was measured from the same five individuals over a six-week time course.  There were few, if any, meaningful differences in gene expression among time points.  Thus, microarray measures using standard laboratory procedures can be precise and quantitative and are not subject to significant random biological noise.

overall_design:
mRNA expression was measured using microarrays where each array had four spatially separated replicates per gene.  The 384 F. heteroclitus cDNA microarrays were printed using 55 control genes and 329 cDNAs which encode essential proteins for cellular metabolism.
To test for the relationship between fluorescence and the quantity of RNA, five concentrations of fluorescently labeled RNA were used: 1.2 to 700 pmol of Cy3 or Cy5.
A 15 µl hybridization using the 384 cDNA array corresponds to 0.09 to 47 µM of Cy dye.  Cy5 dye labeled RNA was used at concentrations 18% less than Cy3 because the Cy5 dye is a more efficient fluorophore (greater fluorescence per photon) than the Cy3 dye.  The average of eight fluorescence values for each gene was normalized to the original concentration of RNA added.

first: Douglas

last: Crawford

first: Danielle

last: McDonald

first: Jeff

last: VanWye


title: Profiling 20,077 genes in 25 vaccine recipients: U133 Plus 2.0, Custom CDF Version 9

first: Troy

last: Querec

summary:
The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs.  The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs.

Keywords: time course

overall_design: This study is a combination of 2 separate YF-17D vaccination trials.  Trial 1 has 15 subjects, and Trial 2 has 10 subjects.   The two trials occurred 1 year apart and used different lots of the vaccine.  Enrolled volunteers were healthy, aged 18 to 45, and signed a written informed consent form. Potential volunteers were excluded from participating in the study if they were pregnant, or if they had been vaccinated previously with YF-17D. Blood samples were taken pre-vaccinaion to serve as a reference point for each individual, and post-vaccination samples were taken a days 1, 3, 7, and 21 after YF-17D vaccination.  All subjects received YF-17D.  Blood samples for microarray analysis were collected either in blue and black topped citrate buffered cell preparation tubes (CPT).  Following PMBC isolation from CPT, 2 x 106 cells were lysed in 1 ml of TRIzol and stored at -80?C (Cat# 15596-026; Invitrogen Life Technologies).  After all time points were collected for a subject, the samples were thawed, and the RNA isolation proceeded according to the manufacturer’s protocol.

first: Querec

last: Troy

first: Akondy

last: Rama

first: Lee

last: Eva

first: Cao

last: Weiping

first: Nakaya

last: Helder

first: Teuwen

last: Dirk

first: Pirani

last: Ali

first: Gernert

last: Kim

first: Deng

last: Jiusheng

first: Marzolf

last: Bruz

first: Kennedy

last: Kathleen


title: Technical Analysis of Fundulus heteroclitus cDNA Microarrays, experiment B

summary:
Analysis of the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations. In addition, we measured expression for differences in RNA labeling and for the day on which RNA is prepared.

Keywords: Gene expression

overall_design: Two-condition experiment, number of rounds of RNA amplification and the day on which it was prepared.  Four replicates per gene per array.

first: M


title: Gene expression quantitative trait loci (eQTL) study using the HB3×Dd2 genetic cross progeny of P. falciparum

status: Public on Nov 20 2008

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

summary:
The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of parasite drug resistance. To clarify the role of transcriptional variation as a source of stain-specific diversity in the most deadly malaria species and to find genetic loci that dictate variations in gene expression, we examined genome-wide expression level polymorphisms (ELPs) in a genetic cross between phenotypically distinct parasite clones. Significant variation in gene expression is observed through direct co-hybridizations of RNA from different P. falciparum clones. Nearly 18% of genes were regulated by a significant eQTL. The genetic determinants of most of these ELPs resided in hotspots that are physically distant from their targets. The most prominent regulatory locus, influencing 269 transcripts, coincided with a Chromosome 5 amplification event carrying the drug resistance gene, pfmdr1, and 13 other genes. Drug selection pressure in the Dd2 parental clone lineage led not only to a copy number change in the pfmdr1 gene but also to increased copies of putative neighboring regulatory factors that, in turn, broadly influence the transcriptional network. Previously unrecognized transcriptional variation, controlled by polymorphic regulatory genes and possibly master regulators within large copy number variants, contributes to sweeping phenotypic evolution in drug-resistant malaria parasites.

Keywords: Segregation patterns of gene expression levels.

overall_design: A total of 36 test parasite samples (Dd2, HB3, and progeny) from a single time point in the parasite life cycle (18 hours post RBC invasion) were co-hybridized to a common reference HB3 sample, each a single replicate.

first: Joseph

last: Gonzales

first: Pradipsinh

middle: K

last: Rathod

middle: T


title: Examination of growth mode dependent replication dynamics and expression levels for Vibrio parahaemolyticus RIMD2210633.

city: Suita

first: Kaori

last: Izutsu

state: Osaka

address: 1-1 Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka University

type:
Expression profiling by array
Genome variation profiling by array

summary:
Replication of bacterial chromosomes increases the copy numbers of genes located near the origin of replication relative to genes located near the terminus. Such differential gene dosage is variable and depends on several factors including replication rate, generation time and chromosome size. For vibrios, a diverse family of fast growing marine living gammaproteobacteria, gene dosage effects may be particularly important as they harbour their genome within two differently sized chromosomes. In this series of experiments, gene dosage at the genomic level and its influence on the expression level has been examined in V. parahaemolyticus. For the genomic analyses, gene copy numbers for bacteria in mid-logarithmic phase grown in rich media (Luria-Bertani containing 3% (w/v) NaCl) at two temperatures (37°C or 20°C) or in minimal media (M9 containing 3% (w/v) NaCl and 0.4% (w/v) glucose) were compared against gene copy numbers for non-replicating cells. For expression analyses, cDNA derived from bacteria in mid-logarithmic phase grown in rich broth at two temperatures (37°C or 20°C) or in minimal media were compared against gDNA from non-replicating cells. Also, cDNA derived from early (OD600=0.2) or mid-logarithmic phase bacteria (OD600=0.5) in rich broth at 37°C,  were compared against cDNA derived from mid-logarithmic cells in minimal media (OD600=0.5) or cDNA from early stationary phase rich broth cells (OD600=3.0).
Keywords: Comparative genomic and/or cDNA hybridization

sample_organism:
Vibrio parahaemolyticus
Vibrio parahaemolyticus RIMD 2210633

overall_design: Samples of genomic DNA and/or cDNA were labeled with Cy3 and Cy5 and cohybridized on six single arrays.

first: R

last: Dryselius

first: K

first: T

last: Iida


title: SIRT1 and H1AcK26 promoter-association in mouse ES cells changes upon oxidative stress

status: Public on Nov 26 2008

city: Boston

first: Philipp

last: Oberdoerffer

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

type: Genome binding/occupancy profiling by array

summary:
Association of the (histone) deacetylase SIRT1 with promoters was assessed to determine putative SIRT1-regulated genes. Based on the observation that the SIRT1 yeast ortholog Sir2 redistributes across the yeast genome in repsonse to genotoxic stress and double strand breaks (DSBs), we investigated the impact of oxidative stress on the chromatin binding pattern of SIRT1. Oxidative stress causes a major change in SIRT1 binding that is accompanied by an inverse H1K26 acetylation pattern. H1K26 was shown to be a direct target for deacetylation by SIRT1.

Keywords: ChIP-chip, stress response

overall_design: ES cells were left untreated or treated with 2 mM H2O2 for 1 hour. Both samples were subjected to ChIP against SIRT1, H1AcK26 or rabbit Ig (one IP per treatment and Ab). Input DNA was labeled with Cy3, IP DNA with Cy5, enrichment over input is reported as 2log.

first: David

last: Sinclair


title: Gene expression change in natural allotetraploid, A.suecica

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

summary: Arabidopsis is a suitable system for testing the hypothesis that duplicate genes accelerate evolution of expression diversity among species diverged from shared whole genome duplications (WGDs) and recurrent events of WGD. In Arabidopsis, at least 9 species split after WGD of the common ancestor and new allotetraploids were formed in nature and can be resynthesized between closely related species. Using genomic and gene expression microarrays, we detected WGD duplicate and single-copy genes preserved in A.thaliana and A.arenosa in addition to change of gene expression levels among those species. We found that even conserved duplicate genes show higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors’ duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. This results show that WGD duplicate genes provide expression variegation in response to recurring polyploidy as well as among species diverged from common WGD. Duplicate genes related to external stresses tended to be differentially expressed in allopolyploids and among their progenitors. Moreover, multiple-copy duplicate genes are likely to change expression between species and in the resynthesized and natural allotetraploids. Compared to single-copy genes, duplicate genes are less likely to be methylated in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. Our results suggest that highly retained duplicate genes are important source for developing species specific expression level and novel expression regulation to adapt to environmental changes including subsequent polyploidy.

sample_organism:
Arabidopsis thaliana
Arabidopsis arenosa
Arabidopsis suecica

overall_design:
Microarray data was obtained using a comparison between mRNA from A. suecica and an artificial mRNA mix of two parents. Total 8 hybridization intensity pairs were obtained. two dye swap experiments and four replications of them using different plant populations (biological replications). In one biological replication, 500 ng of mRNA each from about 12 A.suecica plants and from artificial mix of more than 12 A.thaliana plants and 12 A.arenosa plants were used for the labeling reacting using Cy3- or Cy5-dCTP (Amersham Biosciences). For each biological replication, the Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization experiment, and then an equal amount of RNA samples was reversely labeled for another hybridization experiment (dye-swap experiment). Four biological replications were performed. Eventually, 8 replicated measurements were obtained per probe feature. We applied a linear model to exclude technical variation by arrays and dyes and biological variation by different plant populations. The linear model is
Log (Yigkl) = µ + Gi + Tj + Ak + Dl + (G*T)ij + (G*A)ik + (G*D)il + (G*T*D)ijl + ɛijkl
Where Y represents raw intensity after background level is subtracted; G, T, A, and D are main sources of variation from gene (G), treatment (plant species, T), array (A) and dye (D); i = 1,…, 31818; j = 1, 2; k = 1, 2, 3, 4;l = 1,2; µ represents the overall mean. The interaction terms, G*T, G*A, G*D, and G*T*D mean gene-by-species, gene-by-array, gene-by-dye and gene-by-species-by-dye. ɛijkl represents random error.
To test difference of mRNA expression between A.suecica and mid-parent value (MPV), t-tests were employed for individual genes (pergene-variance).
The null hypothesis, H0: TA.suecica + (G*T)i,A.suecica = TMPV + (G*T)i,MPV  was examined by p-value. Overall type I error rate of multiple testing was controlled to be below 0.05 employing the false discovery rate of Benjamini and Hotchberg.

first: Eun-Deok

first: Z

middle: J

last: Chen


title: Genomic hybridization of Col, Van and reciprocal hybrids

status: Public on Nov 18 2008

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

type: Genome variation profiling by genome tiling array

summary:
Genomic DNA of Col, Van and reciprocal hybrids,  bioprime random labeling, and hybridization to AtTILE1 forward array.
Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.

overall_design: Each genotype has four replicates, Single chanel. Total four genotypes (Col, Van, Van female x Col male, Col female x Van male). Total 16 samples.


title: Human ES cells reveal recurrent genomic instability at 20q11.21

status: Public on Nov 19 2008

city: Evry cedex

first: Anselme

middle: Louis

last: Perrier

address: 5 rue desbrueres

department: I-Stem, AFM

institute: INSERM/UEVE UMR 861,

summary: By analyzing five human embryonic stem (hES) cell lines over long-term culture, we detected a recurrent genomic instability in the human genome. An amplification of 2.5–4.6 Mb at 20q11.21, encompassing about 23 genes in common, appeared in four cell lines of different origins. This amplification, which has been associated with oncogenic transformation, may provide a selective advantage to hES cells in culture

overall_design:
Array-based comparative genomic hybridization, was performed on genomic DNA samples from different human embryonic stem cell lines, all cultured in our laboratory under the same conditions.

VUB05-HD is an hES cell line carrying the Huntingtin mutant gene
H1, H9, SA01, and VUB01 are various hES cell lines

GSM341552 and GSM341553: SNP analysis
GSM341589 to GSM341669: CGH analysis

first: Nathalie

last: Lefort

first: Maxime

last: Feyeux

first: Cécile

last: Bas

first: Olivier

last: Feraud

first: Annelise

last: Bennaceur-Griscelli

first: Gérard

last: Tachdjian

first: Marc

last: Peschanski

middle: L