title: Mouse kidney cortex: control vs. low sodium diet + captopril treatment

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

department: Pediatrics

institute: University of Virginia

summary: miRNA profiling of mouse kidney cortex comparing control vs. low sodium diet + captopril treatment to induce renin expression.

overall_design: Two condition experiment: control vs treated; biological replicates: individual mice - 3 control, 3 treated. One replicate per array.

first: R

first: Silvia

last: Medrano

first: Maria

last: Monteagudo

middle: S

last: Sequeira-Lopez

first: Ellen


title: Mouse kidney arteriolar smooth muscle cells derived from the renin cell lineage: control vs. forskolin treatment to induce renin expression

status: Public on Feb 25 2012

country: USA

summary: miRNA profiling of mouse kidney arteriolar smooth muscle cells (aSMCs) of the renin lineage comparing control untreated cells with cells treated with forskolin to induce renin expression.

overall_design: Two condition experiment: control untreated aSMCs vs forskolin treated aSMCs; Biological replicates: control 3, treated 3; independently grown and harvested. One replicate per array.

middle: A

middle: C


title: SeqA Chip-chip analysis of E. coli MG1655 and derivatives

status: Public on Feb 22 2012

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

country: Germany

institute: Synmikro

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

summary: Chromosomes are composed of enormously long DNA molecules which must be distributed correctly as the cells grow and divide. In Escherichia coli the new DNA behind the replication forks is specifically bound by the SeqA protein. SeqA binds to GATC sequences which are methylated on the A of the old strand but not on the new strand. Binding lasts for a period of time until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemi-methylated DNA covered by SeqA follows the replication fork. We show that this is indeed the case by using global ChIP on Chip analysis and a newly developed method for methylation analysis. A comparison of rapid and slow growth conditions showed that in cells with multiple replication forks per chromosome, the old forks bind little SeqA. Analysis of strains with strong SeqA binding sites at different chromosomal loci supported this finding. The results indicate that a re-organization of the chromosome occurs at a timepoint when new forks have travelled about 20% and old forks about 75% of the way to the terminus. This timepoint coincides with the end of origin sequestration. It is so far not known what brings about the end of origin sequestration. Here we suggest that a reorganization event occurs resulting in both origin desequestration and loss of old replication forks from the SeqA structures.

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

overall_design: SeqA ChIP-Chip analysis of unsynchronized E. coli MG1655 and in cells synchronized regarding initiation of DNA replication; SeqA ChIP-Chip of Dam overproducing strain and SeqA4 mutant; SeqA ChIP-Chip of strains with chromosomal insertions of strong SeqA binding site. Methylation analysis of synchronized E. coli MG1655dnaC2 cells 0 and 15 min after initiation.

first: Kirsten

last: Skarstad


title: Prevention of bone marrow cell apoptosis and regulation of hematopoiesis by type I IFNs during systemic responses to pneumocystis (PC) lung infection

status: Public on Feb 20 2012

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary: IFrag-/- but not RAG-/- mice develop rapidly progressing bone marrow failure in response to PC lung infection. Changes contributing to accelerated bone marrow cell apoptosis in IFrag-/- mice appear to be initiated around day 7 post infection. To gain further insight into the mechanism underlying the induction of bone marrow failure in IFRag-/- but not RAG-/- mice in response to PC lung infection, IFRag and RAG mice were PC infected via intra-tracheal inocculation of 10e7 nuclei and bone marrow responses were assessed at day 0, and 7 post infection. One group of IFRag-/- mice also received anti-oxidants treatment with N-Acetyl cysteine in drinking water (100mg/ml) throughout the course of infection (IFRag-/- +NAC) as oxidative stress appeared to be a contributing factor.

overall_design: RT2 profiler PCR array, 5 conditions, 3 biological replicates

first: Nicole

last: Meissner

first: David

last: Taylor

first: Michelle

last: Wilkison

first: Jovanka

last: Voyich


title: TaqMan Peripheral blood mononuclear cell miRNA profiles of HIV-1-infected elite suppressors, viremic patients, and uninfected control donors

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: This study used TaqMan low-density arrays to identify and quantitate circulating cellular miRNAs during HIV-1 elite suppression, active HIV-1 replication, and uninfected status.

overall_design: Blood samples were from six uninfected controls, six HIV-1 elite suppressors with undetectable viral load, and six viremic HIV-1-infected patients.

first: Andria

middle: K

last: Watson

first: Joel

middle: N

last: Blankson

first: Janice

middle: E

last: Clements


title: Extended Primate aCGH

status: Public on Feb 24 2012

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
This set includes individuals from 10 different primate species whose genomic DNA was used in an array-based comparative genomic hybridization (aCGH)using human cDNA microarrays to detect gene copy number variation across 10 primate species.
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms.
Keywords: organism_part_comparison_design, array CGH

sample_organism:
Callithrix sp.
Macaca sp.
Papio hamadryas
Hylobates sp.
Homo sapiens
Lemur sp.

overall_design: Computed

first: Young

last: Kim

first: Laura

last: Dumas


title: Functions of the Mediator subunit Med31 in Candida albicans support a role in shaping species-specific gene expression.

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

summary: Mediator is an essential, evolutionarily conserved co-regulator of RNA polymerase II. Studies in model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe showed remarkably conserved roles for Mediator despite high species divergence, and thus whether Mediator contributed to establishment of species-specific gene expression programs within related fungal species remains an open question. Here we show that in the fungal pathogen Candida albicans, the Mediator middle domain subunit Med31 has a conserved role with non-pathogenic model yeasts in regulation of Ace2-dependent cytokinesis genes and stress responses, but also additional roles in the transcription of genes associated with virulence traits: genes related to filamentous growth and gene families expanded in pathogenic vs non-pathogenic yeasts, such as the ALS adhesins and the FGR6 family of filamentous growth regulators. Consistently, Med31 is required for two key virulence attributes of C. albicans: filamentous growth and biofilm formation. Unlike our data in C. albicans, no role for Med31 in adhesin expression has been reported in model yeasts. To show biological relevance for the control over adhesin gene expression, we demonstrate that ALS1 is a relevant Med31 target for development of biofilms. Collectively, our data supports a role for Med31 in shaping species-specific gene expression in related fungal species.

overall_design: Two-color experimental design comparing cells with a ∆med31 mutation with a control strain in which the MED31 gene was reintroduced. RNA from each replicate came from independent cultures.

first: Nathalie

last: Uwamahoro

first: Ana

last: Traven

first: Cecile

last: Beaurepaire


title: Affymetrix SNP array data for human skin keratinocytes

status: Public on Feb 28 2012

city: London

first: Emilios

last: Gemenetzidis

address: 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

summary: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from human skin keratinocytes derived from healthy donors, as well as from telomerase immortalised human skin keratinocytes (N/TERT), transduced with mock, EGFP, or EGFP-GLI2DeltaN transgenes to compare chromosomal ploidy status.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from human skin keratinocytes derived from healthy donors, as well as from telomerase immortalised human skin keratinocytes (N/TERT) to compare chromosomal ploidy status

first: Eleni

last: Pantazi

first: Tracy

last: Chaplin

first: Muy-Teck

last: Teh


title: Genomic anchors across the MHC of MRC5 cells upon treatment with IFN-gamma: Loop associated DNA vs Matrix associated DNA

status: Public on Feb 16 2012

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

summary: Identification of genomic anchors across the MHC in untreated MRC5 fibroblasts, and fibroblasts treated with IFN-gamma, using high resolution microarrays.

overall_design: Identification of genomic anchors using MRC5 fibroblasts, and fibroblasts treated with IFN-gamma: Loop associated DNA vs Matrix associated DNA, 2 biological replicates

first: Diego

last: Ottaviani

first: Elliott

last: Lever

first: Shihong

last: Mao

first: Rossitza

last: Christova

first: Babatunji

last: Ogunkolade

first: Tania

last: Jones

first: Jarek

last: Szary

first: Johan

last: Aarum

first: Muhammad

last: Mumin

first: Christopher

last: Pieri

first: Stephen

last: Krawetz


title: Molecular profiling of myeloid leukemia cell lines

last: Stanford Microarray Database

summary:
Cell lines.  The myeloid cell lines CMK, HEL, HL-60, K-562, KASUMI-1, KG-1, LAMA-84, M-07e, MONO-MAC-1, MV4-11, NB-4, OCI-AML2, OCI-AML5, SIG-M5, THP-1, and UT-7 were obtained from the DSMZ in Braunschweig, Germany (http://www.dsmz.de). The cell line ME-1 was kindly provided by Dr. Ikuya Sakai, Ehime University, Japan. Cell lines were cultured under standard conditions in RPMI 1640 containing 10% FCS, 2 mM L-glutamine, 100 units/ml penicillin and 100 units/ml streptomycin. For subsequent DNA and RNA isolation 1x107 cells of the respective cell lines were washed twice in phosphate-buffered saline, and stored as cell pellets at 800C. Gene expression profiling.  Gene expression profiling (GEP) was performed essentially as described using the previously described cDNA microarray platform (Bullinger et al., N Engl J Med 2004;350:1605-1616).
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

overall_design: Using regression correlation

first: Lars

last: Bullinger


title: Transcriptional profiling of the host cutaneous response to Ixodes scapularis

status: Public on Feb 17 2012

city: Galveston

first: Dar

last: Heinze

state: Texas

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

summary:
Introduction: Ixodes scapularis ticks are hematophagous arthropods capable of transmitting many infectious agents to humans. The process of blood feeding is an extended and continuous interplay between tick and host responses. While this process has been studied extensively in vitro, no global understanding of the host response to ticks has emerged. To address this issue, we measured skin-specific expression of 233 discrete genes at 8 time points during primary and secondary infestations of mice with pathogen-free I. scapularis nymphs. Selected results were then validated at the mRNA and protein levels.
Results: Primary infestation was characterized by the late induction of an innate immune response. Lectin pattern recognition receptors, cytokines, and chemokines were upregulated consistent with increased neutrophil and macrophage migration. Gene ontology and pathway analyses of downregulated genes suggested inhibition of gene transcription and Th17 immunity. During the secondary infestation, additional genes were modulated suggesting a broader involvement of immune cells including CD8 and CD4 positive T lymphocytes. The cytokine response showed a mixed Th1/Th2 profile with a potential for T regulatory cell activity. Key gene ontology clusters observed during the secondary infestation were cell migration and activation. Matrix metalloproteinases were upregulated, apoptosis-related genes were differentially modulated, and immunoreceptor signaling molecules were upregulated. In contrast, transcripts related to mitogenic, WNT, Hedgehog, and stress pathways were downregulated.
Conclusions: Our results support a model of tick feeding where lectin pattern recognition receptors orchestrate an innate inflammatory response during primary infestation that primes a mixed Th1/Th2 response upon secondary exposure. Tick feeding inhibits gene transcription and Th17 immunity. Salivary molecules may also inhibit upregulation of mitogenic, WNT, Hedgehog, and stress pathways and enhance the activity of T regulatory cells, production of IL-10, and suppressors of cytokine signaling molecules (SOCS). This study provides the first comprehensive transcriptional analysis of the host response at the tick bite site and suggests both a potential model of the host cutaneous response and candidate genes for further description and investigation.

overall_design: Ear biopsies from BALB/cJ mice infested with Ixodes scapularis nymphs were assayed at 12, 48, 72, and 96 hours after infestation during a primary and secondary exposure. 3 mice were measured at each time point. Controls were 3 similarly housed but tick-free mice.

first: D

first: S

last: Wikel

first: F

last: Alarcon-Chaidez


title: The Rcs regulon in Erwinia amylovora

status: Public on Feb 18 2012

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. Besides amylovoran biosynthesis and regulatory genes, cell wall and cell envelope (membrane) as well as regulatory genes were the major components of the RcsBC regulon, including many novel genes. In addition, we have also demonstrated that transcripts of rcsA, rcsC and rcsD genes, but not rcsB gene, were up-regulated when grown in minimal medium or after infection of pear fruits compared to LB medium. Furthermore, a hidden Markov model (HMM) has predicted 60 genes with candidate RcsB binding site in the intergenic regions of the E. amylovora ATCC 49946 genome and 18 (28) of them were identified in the microarray assay. Based on our findings, a working model has been proposed to illustrate how the Rcs phosphorelay system regulates virulence gene expression in E. amylovora.

overall_design: A total of 12 samples were analyzed in two conditions: For in vitro condition (MBMA medium + 1% sorbitol), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates): For in vivo condition (on wounded immature pear fruits), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates).

first: Dongping

last: Wang

first: Youfu


title: Tiled Array Experiment of Murine Gammaherpesvirus 68 Transcripts Upon TPA-Stimulated Reactivation From Latency

city: Stony Brook

first: Laurie

last: Krug

state: NY

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

type: Expression profiling by genome tiling array

summary: Murine A20 B cells harboring latent MHV68 were treated with TPA and RNA expression was examined over a 24 hour timecourse experiment.

overall_design: Study includes 4 samples- an untreated sample and reactivation samples isolated at 6, 12, and 24 hours after treatment of a latent MHV68+ B cell line with TPA.

middle: T

first: Jizu

last: Zhi


title: miRNA profiling of double-positive thymocytes transduced with a retrovirus encoding Lin28a compared to untransduced controls

city: Bethesda

first: Stefan

middle: Adi

last: Muljo

address: 10 Center Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: We used the NanoString mouse nCounter miRNA expression platform to compare the miRNA expression in double-positive (DP) thymocytes that developed in the presence (GFP+) or absence (GFP-ve) of ectopic mLin28 expression.

overall_design: Transduced (GFP+) and untransduced (GFP-ve) CD4+ CD8+ CD3- thymocytes were FACS sorted and pooled from three recipients of hematopoietic stem and progenitor cells transduced with Lin28-RV six weeks post-reconstitution (bone marrow chimeric mice). Total RNA was extracted and used for sample preparation and hybridization per manufacturer's recommendations.

first: Joan

last: Yuan


title: Diagnosis of Parkinson's Disease Based on Disease-Specific Autoantibody Profiles

status: Public on Feb 27 2012

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Parkinson's Disease (PD) and Non-Demented Control (NDC) human sera were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators.

overall_design: In the study presented here, 29 PD and 40 NDC human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies.  Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant group prevelance were selected as biomarkers of disease.  Prediction classification analysis tested the diagnostic efficacy of the identified biomarkers; and differentiation of PD samples from other neurodegeneratively-diseased and non-neurodegeneratively-diseased controls (Alzheimer's disease, multiple sclerosis, and breast cancer) confirmed their specificity.

first: Eric

middle: P

first: Min

last: Han

first: Cassandra

last: DeMarshall


title: Bile-inducible membrane protein mediates the bile resistance phenotype of Bifidobacterium breve UCC2003

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Bbr_0838 from Bifidobacterium breve UCC2003 encodes a 683 residue membrane protein, that contains a permease domain displaying similarity to transporters belonging to the major facilitator superfamily, as well as a CBS (cystathionine beta synthase) domain. The high level of similarity to bile-efflux pumps from other bifidobacteria, suggests a significant role for Bbr_0838 in bile tolerance of B. breve UCC2003. Bbr_0838 transcription was shown to be monocistronic and strongly induced upon exposure to bile. Further analysis delineated the transcriptional start site and the minimal region required for promoter activity and bile regulation. Insertional inactivation of Bbr_0838 in B. breve UCC2003 resulted in a strain that exhibited reduced survival upon cholate exposure as compared to the parent strain, a phenotype that was reversed when a functional Bbr_0838 gene was introduced into UCC2003::838800. Transcriptome analysis of UCC2003::838800 grown in the presence or absence of bile demonstrated that transcription of Bbr_0832, which is predicted to encode a macrolide-efflux transporter gene, was significantly increased in the presence of bile, representing a likely compensatory mechanism for bile removal in the absence of Bbr_0838. This study represents the first in depth analysis of a bile-inducible locus in bifidobacteria, identifying a key gene relevant for bifidobacterial bile tolerance.

overall_design: In order to investigate differences in global gene expression upon growth or exposure of B. breve UCC2003-delta0838 to cholic acid compared to normal growing cells, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003-delta0838 cultures under normal conditions and cultures grown on or exposed to cholic acid. All experiments were performed in duplo and targets where confirmed with QRT-PCR. In addition transcriptome analyse was performed of B. breve UCC2003 compared to that of B. breve UCC2003-delta0838 both exposed to 0.1 % cholic acid. This was performed as a single experiment and targets were confirmed by QRT-PCR

first: Lorena

last: Ruiz

first: Mary

last: O'Connell-Motherway

first: Clara

last: de los Reyes-Gavilán

first: Abelardo

last: Margolles

first: Douwe

last: van Sinderen


title: Differentially expressed genes following injection with miR-1 mimics of the silkworm, Bombyx mori, during pupation

city: Beibei

first: GAO

last: Song

state: Chongqing

address: tiansheng road 2#

department: ISSB

country: China

institute: Southwest University

summary: The molting of insects is a complex biological progress which requires varies of genes to participate in the event. MicroRNAs are considered to be one of the key roles involved in development in many organisms. Microarray technology was employed to examine the expression profile of multiple genes after extrinsical up-regulation of miR-1 level by injection of miR-1 mimics in silkworm (Bombyx mori.L), which caused altered expression profile of numerous genes, especially those which involved in the processes of cuticle renewing and development. 814 genes were up-regulated and 636 were down-regulated after treated with miR-1 mimics, the rest 2961 detectable genes were considered to have no significant changes in expression level.

overall_design: Transcription profiling experiments, 3 pairs of samples (miR-1 injected and negative control) were analyzed. Dual-channel experiments, with control samples labeled by Cy5 and miR-1 injected samples labeled by Cy3. Fold change was calculated via comparing signal intensity of Cy3 vs Cy5. 3 biological replicates were performed.

first: Song

last: Gao

first: Shiping

last: Liu

first: Lihui

first: Wei

first: Qingyou

last: Xia


title: NanoString miRNA profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors

first: Kenneth

last: Witwer

summary: This study used the NanoString nCounter hybridization system and nCounter miRNA expression assays to identify and quantitate circulating cellular miRNAs during HIV-1 elite suppression, active HIV-1 replication, and uninfected status.

overall_design: Blood samples were from eight uninfected controls, seven HIV-1 elite suppressors with undetectable viral load, and six viremic HIV-1-infected patients.

first: Andria

last: Watson

first: Joel

last: Blankson

first: Janice

last: Clements


title: Transcriptomics adaptation of porcine adipose- and bone marrow-derived stem cells during adipogenic and osteogenic differentiation

status: Public on Mar 01 2012

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

summary: Adipose-derived and bone-marrow-derived mesenchymal stem cells were collected from 3 pigs and cultivated in vitro up to 3 passages. At passage 3 cells were cultured to 80% confluence and induced to differentiate in adipose and bone. Cell were harvested at 0 day of differentiation (dd) or pre-differentiation, at 2, 7, and 21dd for RNA extraction. The RNA was used for a large microarray analysis using a specific pig oligo-array with >10,000 annotated genes. The main aim of the  microarray analysis was to directly compare the two transcriptomics adaptation of the two mesenchymal stem cells during osteogenic and adipogenic differentiation

overall_design: The mesenchymal stem cells were harvested at 0, 2, 7, and 21 day of differentiation (dd). A dye-swap reference design (reference =  mixture of RNA from several porcine tissues) was used.

first: Elisa

last: Monaco

first: Alecsandra

last: de Lima

first: Sandra

middle: L

last: Rodriguez-Zas

first: Walter

last: Hurley

first: Matthew

middle: B

last: Wheeler


title: Tiled Array Experiment of Murine Gammaherpesvirus 68 Transcripts In Newly Infected Fibroblasts

first: Laurie

last: Krug

summary: Murine NIH3T3 fibroblasts were infected with MHV68 and RNA expression was examined over an 18 hour timecourse experiment.

overall_design: Study includes 8 samples isolated at 0, 2, 4, 6, 8, 10, 12, and 18 hours after infection of NIH3T3 fibroblasts with murine gammaherpesvirus 68 at a multiplicity of infection of 10.0.

first: Jizu

last: Zhi


title: ChIP-chip of LeuO, H-NS and RNA Polymerase (RNAP) in Salmonella enterica serovar Typhimurium strain SL1344

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

summary: The LysR family transcription factor LeuO is believed to antagonize the global repressor H-NS. ChIP-on-chip analysis of LeuO, H-NS and RNAP binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between LeuO and H-NS regulated genes. Furthermore LeuO binding was associated with RNA polymerase recruitment, indicating a role for LeuO in activating transcription.

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

overall_design: Analysis of LeuO, H-NS and RNA Polymerase binding in Low-phosphate media (LPM)

first: Elena

last: Espinosa

first: Karsten

last: Hokamp

first: Josep

last: Casadesus

first: Charles

middle: J

last: Dorman


title: TaqMan Low Density Arrays on Glioma Stem-like Cell lines (GSC-1 to 11)

status: Public on Feb 15 2012

city: Poitiers

first: ulrich

last: cortes

address: 350 av. Jacques Coeur

country: France

institute: CHU Poitiers

summary: Determination of pluripotency and differentiation-related genes expression in GSC-1 to 11

overall_design: 11 GSCs lines and human ES (H1) cell line as reference

first: J

last: Chomel

first: L

last: Karayan-Tapon


title: Comparative analysis of stylar canal cells transcriptome in clementine mandarin (Citrus clementina)

city: Catania

first: Marco

last: Caruso

email: mcaruso@unict.it, slamalfa@unict.it

address: Via Valdisavoia 5

department: Dipartimento di Scienze delle Produzioni Agrarie e Alimentari

country: Italy

institute: University of Catania

summary: Compared to what is known in model species, reproductive biology in citrus is still poorly understood. Although in recent years several efforts have been made to study pollen-pistil interaction and self-incompatibility, little information is available about the molecular mechanisms regulating these processes. We performed microarray analysis for the identification of candidate genes involved in pollen-pistil interaction and self-incompatibility in clementine (Citrus clementina Hort. ex Tan.). The analysis was performed comparing the transcriptome of laser-microdissected stylar canal cells isolated from two clementine genotypes differing for self-incompatibility response (‘Comune’, self-incompatible; and ‘Monreal’, a self compatible mutation of ‘Comune’).

overall_design: Styles with stigmas, collected 24 hours after self pollination, were immediately snap-frozen in OCT embedding medium (Sakura Finetek, Zoeterwoude, Netherlands) in Peel-A-Way plastic embedding molds (Polysciences, Polysciences, Warrington, PA, USA). Transversal sections 10 µm thick at the upper part of the style were cut with a Leica CM1900 cryostat (Leica Microsystems, Germany) at -20°C. A Leica AS Laser Microdissection system (Leica Microsystems) was used for the isolation of stylar canals from transversal sections. Canals from the stigma were discarded to avoid contamination with pollen or pollen tubes. Three biological replicates were prepared for each genotype. Each biological replicate consisted of bulks of about 200 microdissected areas (composed of an average of 50 cells) coming from two different molds

first: Paz

last: Merelo

first: Gaetano

last: Distefano

first: Angela

middle: R

last: Lo Piero

first: Stefano

last: La Malfa

first: Manuel

last: Talon

first: Francisco

last: Tadeo

first: Alessandra

last: Gentile


title: Gene expression profiles of decidualized human endometrial stromal cells knockdown for HOXA10

status: Public on Feb 14 2012

city: Mumbai

first: Geeta

middle: Bhalchandra

last: Godbole

state: Maharashtra

address: Jehangir Merwanji Street, Parel

department: Molecular and Cellular Biology

country: India

institute: National Institute for Research in Reproductive Health

summary: The homeobox gene HOXA10 plays a key role in endometrial differentiation during embryogenesis and is abundantly expressed in the adult endometrium and decidual cells. In the adult endometrium the expression of HOXA10 is regulated by estrogen and progesterone and the levels are highest in the decidualized cells. We have shown that HOXA10 is required in the endometrial cells to maintain the decidual cell phenotype. In this study we aimed to determine the molecular mechanisms by which HOXA10 maintains the decidual phenotype and the other roles it might have in decidual physiology. In vitro decidualized human endometrial stromal cells were knocked down for HOXA10 using siRNA and gene expression profiles of the scrambled and HOXA10 siRNA transfected cells were compared at 24, 48 and 72 h post transfection. Several genes having multiple functions were found to be differentially expressed. We postulate that HOXA10 is required by the decidual cells to support immune cell differentiation, trophoblast invasion and cellular remodeling.

overall_design: In vitro decidualized priamry cultures of human endometrial strmal cells transfected with a siRNA againts HOXA10 or a scrambled siRNA. Cells harvested at 24, 48 and 72 h post transfection.  Dual channel hybridization with dye swap design in biological replicates

first: Debarshi

last: Chakrabarti

first: Muralidhara

last: Padigaru

first: Deepak

last: Modi


title: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array]

city: Chicago

first: Joseph

middle: M

last: Zullo

address: 929 E 57th Street

department: MGCB

institute: University of Chicago

summary:
These are the tiling array data for the experiments describing LADs on murine chromosomes 5, 12, and 15 by Dam-ID, as determined by LMNB and EMD Dam tagging and detection experiments
Supplemental Bed file contains GADA algorithm calls for genomic regions of chromosomes 5, 12 and 15 (-1= no lad, high confidence, 0=indeterminate, 1=LAD, high confidence)

overall_design: 2 experimental samples, both used the same 2 control CEL files (Dam_0519.CEL and Dam_0612.CEL provided at the foot of the Series record below). Also provided below are LMNA .CEL files. They were not processed as a comparison like for EMD and LMNB Samples in the scope of this study, but may be processed by users using the Tiling Array Software from Affy.


title: MicroRNA expression during somatic embryogenesis in Arabidopsis

status: Public on Feb 13 2012

city: Taian

first: Yubo

last: Liu

state: Shandong

address: Daizong Street 61#

department: Life Science

institute: Shandong Agricultural University

summary: The microarray test aims to find the miRNAs involved in somatic embryogenesis in Arabidopsis.  The plant microRNA array V2.0 (CapitalBio Corp., Beijing, China) contained 426 non-reduplicated plant miRNA probes, including 188 in Arabidopsis. Finally, 75 plant miRNAs expressed differentially, 36 increased and 39 decreased included.

overall_design: Two critical period samples of somatic embryogenesis were chosen for the microarray test: the edge of embryonic calli in embryonic callus-inducing medium (ECIM) for 14 days and the secondary somatic embryos protuberances in somatic embryo-inducing medium (SEIM) for 2 days (marked as “14D” and “J2D” accordingly) . Three chip were test in each sample.

first: Yinghua

last: Su

first: Xiansheng

last: Zhang


title: Expression of the RNA recognition motif protein RBP10 promotes a bloodstream-form transcript pattern in Trypanosoma brucei

status: Public on Feb 11 2012

city: Heidelberg

first: Martin

last: Wurst

address: INF 282

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

summary: In this study we investigate the function of RBP10, and present evidence that the presence of RBP10 is sufficient to induce the expression of mRNAs involved in bloodstream-form energy metabolism.

overall_design:
for BS RBP10 RNAi Samples: total of 6 slides, including 3 biological replicates and dyeswap
for RBP10 overexpression Samples: total of 5 slides, including 3 biological replicates and dyeswap

first: Beate

last: Seliger

first: Bhaskar

last: Jha

first: Cornelia

last: Klein

first: Rafael

last: Queiroz

first: Christine

last: Clayton


title: Global transcriptional profile at a higher fermentation temperature in S.avermitilis NRRL8165

status: Public on Feb 09 2012

city: shanghai

first: hang

last: wu

address: Huashan Road

institute: sjtu

summary: To explore the molecular mechanism of the positive thermoregulation on Jinggangmycin A biosynthesis, the transcriptomes of  S. hygroscopicus 5008 cultivated at 30℃ or 37℃ in liquid medium were compared by microarray analysis. Additionally, the transcriptomes of S. avermitilis NRRL8165 cultivated at the same conditions were analyzed in parallel to filter transcriptional changes common to Streptomyces genus.

overall_design: Global gene expression in NRRL8165 was measured at 30℃ or 37℃, respectively. Three independent experiments were performed at each condition.

first: Hang

last: Wu


title: Identification of DNA methylation differences correlated with transcriptional divergence between humans and chimpanzees in chromosomes 21 and 22

status: Public on Feb 02 2012

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

summary: While some studies have reported gene expression differences between humans and chimpanzees, the mechanisms underlying such changes remain poorly understood.  To address this issue, we examined, by MeDIP-chip, DNA methylation patterns of peripheral blood cells from age- and sex- matched human and chimpanzee individuals.  Our analysis identified some differentially methylated regions between the two species and suggests that changes in DNA methylation pattern are involved in the diversification of transcriptome during evolution.

sample_organism:
Pan troglodytes
Homo sapiens

overall_design:
Pooled genomic DNA of peripheral blood cells from four human or chimpanzee females were immunoprecipitated by anti-methylcytosine antibody (MeDIP) or fragmented (control), then subjected to Affymetrix microarray analysis.  Both the MeDIP and control data were obtained from three technical replicates.
The information about the human and chimpanzee individuals we used are as follows:

Human 1: female 27yo
Human 2: female 33yo
Human 3: female 35yo
Human 4: female 42yo
Chimp 1: female 27yo
Chimp 2: female 30yo
Chimp 3: female 31yo
Chimp 4: female 40yo

first: Kenji

last: Ichiyanagi


title: 050209-miRNA Melanoma miRNA microarray

status: Public on Feb 08 2012

city: Edinburgh

first: Yan

last: Xu

address: Crewe Road South

department: MRC

institute: The University of Edinburgh

summary: To identify improved molecular markers to support histological examination we used microarray analysis of formalin-fixed and paraffin-embedded samples from different stages of melanomagenesis to identify differentially expressed microRNAs.

overall_design: Total RNA were obtained from isolated 19 human cell lines and 52 FFPE  human samples. Cells include 2 immortalised melanocytes, 4 ovarian cancer cell lines and 13 melanoma cell lines. 61 FFPE samples include 11 benign naevi, 20 primary and 21 metastatic melanoma

first: Ewan

last: Brown

first: Thomas

last: Brenn

first: David

last: Melton


title: miRNA expression profiling in early stage breast cancer

city: Erlangen

first: Michael

middle: Georg

last: Schrauder

address: Universitätsstrasse 21-23

department: Gynecology

institute: University Hospital Erlangen

summary: MiRNA profiling from whole blood (EDTA) was used to identify a miRNA profile applicable for early stage breast cancer detection

overall_design: In the study presented here, a consecutively collected, well-defined cohort of 48 patients with early stage breast cancer (invasive ductal carcinoma) at diagnosis was compared with a cohort of 57 healthy individuals for known homo sapiens miRNAs (mirbase 15).


title: Genome-wide RNA Polymerase II binding signal in Arabidopsis thaliana

status: Public on Feb 10 2012

city: Charlottesville

first: xin

last: zhao

address: Department of Biology, 229 Gilmer Hall

department: Biology

institute: University of Virginia

summary: Several studies indicate that plant MIR genes are transcribed by RNA Pol II, similar to what is found in animals (Cai et al., 2004; Lee et al., 2004). By sequencing the 5' transcript ends Xie et al. (2005) mapped the transcription start sites (TSSs) for 52 MIR genes. This list was expanded upon through computational prediction of the core promoters (Zhou et al., 2007). In addition to the TATA box sequence motifs located upstream of the TSSs (Xie et al. 2005), Megraw et al. (2006) identified other transcription factor binding motifs in the promoter of Arabidopsis MIR genes. They showed that within the 800 nucleotides region upstream of TSSs, sequences resembling the binding sites for the transcription factors AtMYC2, ARF, SORLREP3, and LFY were overrepresented relative to protein-coding gene promoters and randomly sampled genomic sequences (Megraw et al. 2006).  While these previous studies are instrumental in establishing our working understanding of MIR gene transcription in plants, there are several major knowledge gaps that urgently need to be addressed. Binding of RNA Pol II to the identified MIR promoter regions has not been tested. Because expression of MIR genes does not involve translation, transcriptional control by RNA Pol II might be different from protein-coding genes. In addition, few of the predicted cis elements have been functionally tested. Futher, the number of annotated miRNA genes has since increased from 199 to 232 (miRBase release 17; Kozomara and Griffiths-Jones, 2011). None of the newly identified genes have been subject to examination for promoter and regulatory sequences. Compared to the previously known miRNAs, these genes have narrower phylogenetic distribution and exhibit weaker expression level and more prominent tissue-specific expression (Rajagopalan et al., 2006; Fahlgren et al. 2007; Yang et al., 2011). Based on these observations, it has been argued that continuous gene birth and death allows beneficial miRNAs to be maintained while deleterious ones avoided (Rajagopalan et al., 2006; Fahlgren et al. 2007; Chen and Rajewsky, 2007; Axtell and Bowman, 2008). Identification of the promoter regions of these MIR genes and their comparison to those of the conserved are highly desirable to fully elucidate miRNA based gene regulation. In the current study, we performed chromatin immunoprecipitation (ChIP)-chip for the Pol II complex using the Affymetrix 'At35b_MR_v04' array. We designed a computational approach using genome-wide RPol II binding patterns to identify the promoter region and transcription start site of pri-miRNAs that are actively transcribed.

overall_design: The wild-type plant used in this work was Arabidopsis thaliana ecotype Col-0. Arabidopsis seedlings were grown on 1× Murashige and Skoog medium (Sigma-Aldrich) agar plates containing 1% sucrose. Unless stated otherwise, the seedlings were incubated at 4°C for 2 to 4 d, after which they were exposed to continuous light conditions at 22°C for 4 d. The white light intensity was 170 μ mol m−2 s−1.Chromatin isolation was performed with 4-d-old whole seedlings grown under continuous white light according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 300 bp. Chromatin was immunoprecipitated, washed, reverse cross-linked, amplified, and hybridized according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. The antibody of anti-RNA polymerase II (sc-33754) from Santa Cruz was used, and a polyclonal HY5 antibody as described (Zhang et al., 2011) was used for normal chromatin immunoprecipitation. An aliquot of untreated sonicated chromatin was reverse cross-linked and used as a total input DNA control for microarray hybridization. An equal amount of sample without antibody was used as a mock control for ChIP-qPCR as well as the input DNA as positive control.  Four biological replicates were hybridized to tiling arrays.

first: Huiyong

first: Xin

last: Zhao

first: Lei

last: Li


title: Protein production by Aspergillus oryzae

status: Public on Feb 12 2012

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme  production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory  structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized  at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins,  and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving  industrial protein production.

Keywords: Two Aspergillus oryzae strains and two different carbon sources

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1

first: W

last: Vongsangnak

first: K

last: Hansen

first: J

last: Nielsen


title: Uterus and placenta gene expression at 10.5 days of pregnancies in control (B6 mice) and R3 IRCS mice

status: Public on Feb 01 2012

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

institute: INSERM

summary: R3 IRCS have a 6 Mb fragment of mouse chromosome 1 originating from Mus spretus; they display a increase rate of embryonic mortality

overall_design: Eight samples corresponding to two pools of three placentas, three uterus for the two strains (B6 and R3 IRCS) were hybridized on a four-quadrant Nimblegen expression array (two tissues x two types of mice x 2 duplicates)


title: Slf1p and Sro9p affinity isolations

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

summary: To identify RNAs specifically associated with Slf1p and Sro9p, cells expressing TAP-tagged Slf1, Sro9 or Fpr1 (negative control) were grown to mid-log phase in synthetic complete medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). from the extract (input) and from the affinity isolates was purified with the RNeasy Mini/ Micro Kit (Qiagen). RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.

overall_design: Set of arrays that are part of repeated experiments

first: Luca

last: Schenk


title: Daphnia magna exposed to narcotics and polar narcotics - methanol

city: Antwerpen

first: Nathalie

last: Dom

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

summary:
Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth).
 Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants.

overall_design: The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.

first: Ronny

last: Blust

first: Dries

last: Knapen


title: SLF1 overexpression versus control cells

summary: Measure the relative changes of gene expression upon GIS2 overexpression; BY4741 cells bearing plasmid pBG1805-Slf1 or control plasmid pBG1805 were grown in SC ura- gal  at 30 C for 6 or 24 hours. An overnight culture of cells was inoculated at an OD600 of 0.1 and further grown to an OD600 of 0.5- 0.7 in 60 ml SC Ura- Gal at 30 C. Cells were harvested by centrifugation, washed twice with 600 ul of ice-cold sterile water. 200 ul of cells were removed and RNA was isolated by hot phenol extraction for microarray analysis. 7.5 ug of total RNA derived from cells expressing the empty vector (pBG1805) or Slf1p (pBG1805_Slf1) were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized on yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices).

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.


title: Microarray profiling of monocytic differentiaion reveals miRNA-mRNA intrinsic correlation (miRNA)

city: Beijing

first: jing

last: wang

address: Tsinghu University

institute: Medical Systems Biology Research Center School of Medicine Tsinghua University

summary: Since the expression profile of miRNAs is specific in different tissues or under different physiological conditions, the correlations between miRNAs and mRNAs could vary under different biological circumstances. This is a study also used expression profiles of miRNA and mRNA during monocytic differentiation to explore the correlations between the expression levels of miRNAs and mRNA, either negative or positive.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: After treatment of TPA, U937 cells present functional differentiation markers as well as specific cell morphology, which were confirmed by flow cytometric analysis and Wright-Giemsa staining.Here we use a miRNA microarray (CapitalBio, Beijing, China) containing 509 well-characterized human, mouse and rat miRNAs and various controls to profile the expression levels of miRNA in normal U937 cells and differentiated U937 cells. Three independent biological experiments were performed, and for each differentiated and control sample, two hybridizations were performed by using a reversal fluorescent strategy.

first: Jing

last: Wang

first: Yuxiang

last: Zhou


title: Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus

status: Public on Jan 24 2012

city: Faro

first: Florbela

middle: A.

last: Vieira

address: Campus de Gambelas

country: Portugal

institute: CCMAR - UALG

summary:
Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the present manuscript the histological and molecular changes underlying skin and scale regeneration in fed and fasted sea bream (Sparus auratus) were studied using a microarray 3 and 7 days after scale removal to provide a comprehensive molecular understanding of the early stages of these processes.
Histological analysis of skin/scales revealed 3 days after scale removal re-epithelisation had occurred and the scale pocket had formed. In animals with scales removed, there was significant up-regulation of genes involved in cell cycle regulation, cell proliferation and adhesion, immune response and antioxidant activities. The expression profiles of the fasted animals centred on maintaining energy homeostasis. The utilisation of fasting as a treatment emphasised the competing whole animal physiological requirements with regard to barrier repair, infection control and energy homeostasis.

overall_design: Gene expression of sea bream (Sparus auratus) skin and scales was analysed in normal and treated animals. Three different treatments were applied: 1. scales removal at day 0 of the experiment; 2. unfed fish 7 days prior the start of the experiment; and 3. scales removal at day 0 of the experiment of unfed fish 7 days prior the start of the experiment. Fish were sampled at two different  days: day 3 and day 7 after scale removal. Five individuals from control and experimental groups were analysed for both sampling days (3 and 7), resulting in a total of 40 samples analysed by microarray.

middle: A

first: Silvia

last: Gregório

first: Serena

last: Ferraresso

first: Michael

last: Thorne

first: Rita

last: Costa

first: Massimo

last: Milan

last: Bargelloni

first: Melody

middle: S

last: Clark

first: Adelino

middle: V

last: Canario

first: Deborah

last: Power


title: The effect of kanamycin on Paenibacillus vortex

city: Kfar Yona

first: Dalit

last: Roth

address: Turmus 199

department: Microbiology

country: Israel

institute: Tel Aviv University

summary: Transcriptional profiling of the bacteria Paenibacillus vortex comparing control untreated cells with kanamycin treated cells after 18 hours of exposure. Goal was to determine the effect of the antibiotic kanamycin in concentration which affect the colony morphology on global bacteria gene expression.

overall_design: Two-condition experiment, control cells vs. kanamycin treated cells. Biological replicates: 2 control replicates, 2 treated replicates. Pooling of 5 technical replicates for each biological replicate.

first: Yael

last: Helman

first: Alexandra

last: Sirota-Madi

first: Leonid

last: Brodsky

first: Eshel

last: Ben-Jacob


title: Gene expression in three different chicken lines after Salmonella infection early in life

status: Public on Jan 29 2012

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

summary: Transcriptional profiling of jejunum infected with Salmonella in three different chicken lines early in life. Samples were taken at 8, 24 and 48 hours post infection. Salmonella was orally ingested at day zero (hatch).

overall_design: test sample vs. common RNA reference pool (all chickens from control and infected for all time points)

first: Arjan

last: Hoekman


title: Mycobacterium tuberculosis Growth After Aerobic Expression of the DosR Regulon

status: Public on Jan 31 2012

city: Seattle

first: Kyle

last: Minch

state: WA

address: 307 Westlake Ave N.

institute: Seattle BioMed

summary:
Investigation of whole genome gene expression of M. tuberculosis strain H37Rv:deltaRv3133c::pEXNF-3133c following ectopic expression of a plasmid-borne copy of wildtype Rv3133c compared the same strain with Rv3133c uninduced.
The M. tuberculosis H37Rv:deltaRv3133c was originally described in Mol Microbiol. 2003 May; 48(3): 833–843.

overall_design: A six chip experiment in which total RNA from H37Rv:deltaRv3133c::pEXNF-3133c was collected after 24 hours of treatment with chemical expression inducer or vehicle control.  Three separate cultures/biological replicates were interrogated for both induced and uninduced samples.  Labeled cDNA was hybridized to NimbleGen spotted oligo tiling arrays covering both strands of the M. tuberculosis genome at ~200 bp intervals between 60-mer probes.

first: Tige

last: Rustad

first: David

last: Sherman


title: Daphnia magna exposed to narcotics and polar narcotics - ethanol

first: Nathalie

last: Dom

first: Ronny

last: Blust

first: Dries

last: Knapen


title: Global analysis of the Staphylococcus aureus response to mupirocin

status: Public on Jan 23 2012

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary:
In the present study we analyzed the response of S. aureus to mupirocin, the drug of choice for nasal decolonization of S. aureus. Mupirocin selectively inhibits the bacterial isoleucyl-tRNA synthetase (IleRSs) leading to the accumulation of uncharged isoleucyl-tRNA and hence (p)ppGpp. The latter is a signal for the induction of the stringent response, an important global transcriptional and translational control mechanism that allows bacteria to adapt to nutritional deprivation.
To identify proteins with an altered synthesis pattern in response to mupirocin treatment we used the highly sensitive 2-dimensional gel electrophoresis technique in combination with mass spectrometry. Obtained results were complemented by DNA-microarray, Northern blot and metabolome analysis. Whereas expression of genes involved in nucleotide biosynthesis, DNA metabolism, energy metabolism and translation was significantly down-regulated, expression of the isoleucyl-tRNA synthetase, the branched chain amino acids pathway, genes with functions in oxidative stress resistance (ahpC, katA), putative roles in stress protection (SACOL1759, SACOL2131, SACOL0815) and transport processes was increased. Of particular interest were the differences in the transcription of genes encoding virulence associated regulators (i.e. arlRS, saeRS, sarA, sarR, sarS) as well as genes directly involved in the virulence of S. aureus (i.e. fnbA, epiE, epiG, seb).  In the present study we analyzed the response of S. aureus to mupirocin, the drug of choice for nasal decolonization of S. aureus. Mupirocin selectively inhibits the bacterial isoleucyl-tRNA synthetase (IleRSs) leading to the accumulation of uncharged isoleucyl-tRNA and hence (p)ppGpp. The latter is a signal for the induction of the stringent response, an important global transcriptional and translational control mechanism that allows bacteria to adapt to nutritional deprivation.

overall_design: In total four independent hybridization experiments with each representing a biological replicate including a control and a treated sample were carried out. To account for the dye bias two of the four replicates were dye swapped.

first: Swantje

last: Reiß

first: Jan

last: Pané-Farré

first: Patrice

last: François

first: Jacques

last: Schrenzel

first: Michael

last: Hecker

first: Susanne

last: Engelmann


title: transcriptomic analysis of wild type vs mpk3 mutants

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
au09-01_mpk
mpk
Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade.

overall_design: 2 dye-swap - wild type vs mutants

first: Concetta

last: Giuliani

first: Heribert

last: Hirt

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: wt-col0_flagellin

summary:
au09-01_mpk_flagellin - wt-col0_flagellin
Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. Flagellin is a protein present in the flagellum of almost all bacteria and triggers Innate Immunity in plants, mediated by a MAPK phosphorylation signal cascade. To better understand the changes occuring in wt-Col0 flagellin treatment at the gene expression level, we would like to perform a microarray transcriptomic analysis.

overall_design: 1 dye-swap - treated vs untreated comparison


title: MRNA expression data from human breast cancer cell lines after demethylation treatment.

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

institute: University of Bern

summary:
The contribution of aberrant DNA methylation and the downstream effects in tumorogenesis through silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations can be reversed, we investigated the effects of the epigenetic therapy in breast cancer cell lines.
We used microarrays to investigate the global gene expression profile after demethylation treatment with 5-aza-2’-deoxycytidine (DAC) in breast cancer cell lines and identified distinct classes of early and late systematic stable or transient effects of the treatment.

overall_design: Three selected breast cell lines including MDA-MB231 (a highly aggressive cell line), SKBR3 (a non-aggressive cell line) and HB2 (a breast epithelial cell line as control) were subject for RNA isolation before treatment, after treatment with DAC and at five point follow-ups (1st, 3rd, 5th, 7th and 10th passages) at “drug holiday” condition and hybridized on Affymetrix microarrays.

first: Frank

last: Staedtler

first: Martin

last: Schumacher

first: Nicole

last: Hartmann


title: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline

first: Nathalie

last: Dom

first: Ronny

last: Blust

first: Dries

last: Knapen


title: 5-aza-2'-cytidine and trichostatin A effect to gene expression of Epstein-Barr virus-transformed human lymphoblastoid cell lines (LCLs).

status: Public on Jan 27 2012

city: Kanazawa

first: Yo

last: Niida

state: Ishikawa

address: 13-1 Takaramachi

institute: Kanazawa Univ.

summary: Investigation of 5-aza-2'-cytidine and trichostatin A effect to gene expression of human LCLs. LCLs estabulished from patients with genetic dissease are commonly used for mRNA or protein analysis of disease related genes.  However, ofen times the gene of interset is not expressed in LCL. Epigenetic modification could be overcome this problem.

overall_design: Expression array study with total RNA extracted from normal male derived LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts variants.


title: Daphnia magna exposed to narcotics and polar narcotics - aniline


title: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline


title: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline


title: Whole Transcriptome Data from Embryonic Mouse Limb-Buds

city: Station 19

first: Denis

last: Duboule

state: Lausanne

address: SV 2843 (Bâtiment SV)

department: ISREC

institute: EPFL

summary: Limb development is a powerful model to investigate transcriptional complexity during differentiation and development, as tissue types appear at various stages, with unique transcriptional signatures. So far, most studies have used conventional expression arrays, which can identify only a predetermined set of cDNAs. However there is growing evidence that most of the non-coding part of the genome is transcribed as well. We took advantage of genomic tiling arrays, which cover most of the mouse genome, to look at limb transcriptomes in an unbiased manner, by identifying all genic- and intergenic transcripts. We selected three developmental stages (E11.5 ; E13.5 ; E15.5), covering a large period of limb organogenesis, during which the limb evolves from a mostly homogenous mesenchymal cell population to more specialized tissue types such as cartilage, bone, muscle and skin.

overall_design: Two biological replicates for each of three time points (E11.5, E13.5, E15.5).

first: Istvan

last: Gyurján

first: Bernhard

last: Sonderegger

first: Felix

last: Naef


title: MicroRNA expression profile in mouse bronchoalveolar stem cells (BASC)

status: Public on Jan 26 2012

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

summary: We performed miRNA and mRNA profiling in BASC cells and c-Myc depleted BASC cells. We built potential miRNA-mRNA interaction networks specific to c-Myc regulation in BASCs

overall_design: Replicated profilling for both BASC cells and c-Myc depleted BASC cells.

first: Dennis

last: Wigle


title: Expression analysis of Epstein-Barr virus–transformed human lymphoblastoid cell lines (LCLs) between male and female.

status: Public on Jan 20 2012

summary: Investigation of human X-linked imprinted gene. Comparing pooled RNA of lymphoblastoid cell lines from normal human male and female, identify the genes expressed with sex spesific manner.

overall_design: Expression array study with total RNA extracted from pooled male and female LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.


title: Daphnia magna exposed to narcotics and polar narcotics - isopropanol


title: Expression data from healthy postmenopausal women on 4 different types of hormone therapy, the RET study

status: Public on Jan 17 2012

city: Oslo

first: Anders

middle: Erik Astrup

last: Dahm

address: Kirkeveien 166

department: Hematology

country: Norway

institute: Oslo University Hospital

summary: Postmenopausal hormone therapy (HT) is associated with many diseases and conditions, but the underlying molecular mechanisms involved are incompletely understood. The aim of the current study was to investigate the effect of 4 types of HT on gene transcription. 24 women (6 women in 4 treatment groups) received 2 mg 17β-estradiol combined with 1 mg noresthisterone acetate (NETA), 1 mg 17β-estradiol combined with 0.5 mg NETA, tibolone, or raloxifene hydrochloride. RNA was isolated from whole blood before treatment (baseline) and after 6 weeks on treatment. The changes in mRNA from baseline to 6 weeks were assessed with a microarray chip.

overall_design: 4 treatment groups with 6 women in each group were blood sampled before treatment (baseline) and after 6 weeks on treatment, that is a total of 48 samples. The gene expression data at 6 weeks were compared to the expression data at baseline for each treatment.

first: Anette

last: Eilertsen

first: Jelle

last: Goeman

first: Ole

middle: K

last: Olstad

first: Reidun

last: Øvestebø

first: Peter

last: Kierulf

first: Marie-Christine

last: Mowinchel

first: Grethe

last: Skretting

first: Per

last: Sandset


title: Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity

status: Public on Jan 28 2012

city: Boston

first: Leila

last: Shokri

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Brigham and Women's Hospital and Harvard Medical School

summary: A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs having mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To better understand the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity.

overall_design: 10 Protein binding microarray (PBM) experiments of Drosophila transcription factors were performed. Briefly, the PBMs involved binding GST-tagged fly transcription factors to double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006 (PMID: 16998473). A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns. The array probe sequences on the custom array design used in this study were reported previously in Berger et al., Cell 2008 (PMID: 18585359) and are available via an academic research use license.  Here we provide the data transformed into median signal intensities (after normalization and detrending of the original array data) for all 32,896 8-base sequences, Z-scores for these intensities, and E-scores. E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots. 'Keep fraction' (kf) parameter setting of 0.9 was used to calculate E-scores. In general the E-scores are slightly more reproducible than Z-scores, but contain less information about relative binding affinity. Additional experimental details are found in Berger et al., Nature Biotechnology 2006 (PMID: 16998473), and the accompanying Supplementary information.

first: Brian

last: Busser

first: Savina

last: Jaeger

first: Stephen

last: Gisselbrecht

first: Anastasia

last: Vedenko

first: Aditi

last: Singhania

first: Michael

middle: F

last: Berger

first: Bo

last: Zhou

first: Martha

last: Bulyk

first: Alan

last: Michelson


title: beta-arrestin-2 deficiency effect on intestinal tumorigenesis in Apc-mutated mice

city: Montpellier

first: Caroline

last: Bonnans

address: 141 rue de la Cardonille

department: Oncology

institute: Functional Genomic Institute

summary: Amoung their pleiotropic functions, a role was recently assigned for b-arrestin scaffold proteins in tumor growth, angiogenesis and invasion. In order to elucidate the roles of b-arrestins in tumour developement in intestinal epithelium initiated by Apc mutation, we determined the effects of b-arrestin gene deletion on intestinal polypolis using ApcD14/+ mice, a relevant mouse model of human intestinal tumorigenesis.Here we show that unlike b-arrestin1, absence of b-arrestin2 dramatically decreased the number of spontaneously developping intestinal tumors in ApcD14/+ mice.The size of residual tumors was similarto that of controls, suggesting that their growth is b-arrestin2-independent. This result demonstrated a role for b-arrestin2 in the early development of a tumor subset. Gene expression profils analysis of ApcD14/+:Arrb2+/+ and ApcD14/+:Arrb2-/- tumors showed two distinct clusters among ApcD14/+:Arrb2+/+ tumors and one of them was statistically more correlated to ApcD14/+:Arrb2-/- tumors than to the other ApcD14/+:Arrb2+/+ cluster, eventhough a number of genes saw their expression affected in ApcD14/+:Arrb2-/- tumors only. Altogether, our data unravel an unexpected early diversity among intestinal tumors and a crucial role for b-arrestin2 in early tumor development in Apc-mutated mice.

overall_design: 16 tumors from ApcD14/+:Arrb2+/+ mice and 13 tumors from ApcD14/+:Arrb2-/- mice

first: Maud

last: Falceliere

first: Christelle

last: Dantec

first: Jean-Pierre

last: Devignes

first: Julie

last: Pannequin

first: Dany

last: Severac

first: Emeric

last: Dubois

first: Frédéric

last: Bibeau

first: Virginie

last: Escriou

first: Philippe

last: Crespy

first: Laurent

last: Journot

last: Hollande

first: Dominique

last: Joubert


title: phytoplasma in plants vs. phytoplasma in insects (single hyb expts)

status: Public on Jan 16 2012

city: Bunkyo

first: Kenro

last: Oshima

state: Tokyo

institute: The University of Tokyo

summary: Transcriptional profiling of phytoplasma grown in plant (Chrysanthemum coronarium) and grown in insect (Macrosteles striifrons).

overall_design: Two-condition experiment, phytoplasma-infected plant and phytoplasma-infected insect. Biological replicates: 4 phytoplasma-infected plants and 4 phytoplasma-infected insects, independently grown and harvested. One replicate per array.

first: Oshima

last: Kenro

first: Namba

last: Shigetou


title: Subcutaneous and gonadal adipose tissue transcriptome differences in lean and obese female dogs

status: Public on Jan 15 2012

city: Urbana

first: Kelly

middle: Scott

last: Swanson

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary: Adipose, once considered an inert storage depot, is now known to be an active endocrine tissue involved in total body homeostasis and metabolism, which exerts effects on multiple systems including food intake, immune function, and blood glucose regulation.  Adipose tissue depots are known to have unique metabolic and gene expression profiles in vivo and when cultured in vitro.  Differences in adipose tissue depot function could be important in determining chronic disease risk.  Few comparisons of depot gene expression have been performed in the dog.  Utilizing microarray technology, our objective was to identify differentially expressed genes and enriched functional pathways between subcutaneous and gonadal adipose of lean and obese dogs.

overall_design: Subcutaneous and gonadal adipose tissue samples were collected from 9 intact female beagles (4 yr-old; 4 lean controls; 5 obese ad libitum-fed) after 24 wk of ad libitum feeding.

first: Ryan

middle: W

last: Grant


title: Phasevarion mediated random switching of gene expression in Helicobacter Pylori

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

country: Australia

institute: University of Queensland

summary: Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are subject to phase-variable expression (high-frequency reversible ON/OFF switching of gene expression). In Haemophilus influenzae, Neissera Meningtidis and Neisseria Gonorrhoeae, the random switching of the modA gene, associated with a phase variable type III restriction modification (R-M) system, controls expression of a phase-variable regulon of genes (a “phasevarion”), via differential methylation of the genome in the modA ON and OFF states. Phase variable type III R-M systems are also found in Helicobacter pylori, suggesting that phasevarions may also exist in this intriguing pathogen. Phylogenetic studies on the phase-variable type III modC gene revealed that there are 12 distinct alleles in H. pylori, which differ only in their DNA recognition domain, with the majority containing the C5 allele. Microarray analysis comparing the H. pylori wild-type P12modC5 ON strain to the P12(delta)modC5 mutant revealed that six genes were either up-regulated or down-regulated, some of which were virulence-associated. For example flaA, which encodes a flagella protein important in motility and hopG, which encodes an important outer membrane protein. This study, in conjunction with our previous work, indicates that phasevarions may be a common strategy used by host-adapted bacterial pathogens to randomly switch between “differentiated” cell types.

overall_design: Direct comparison of biological triplicates of wild type and mutant strains


title: Mycobacterium tuberculosis CDC1551 WT/sigI mutant

status: Public on Jan 30 2012

city: Baltimore

first: JongHee

last: Lee

state: MD

address: 1550 Orleans St. CRB2

department: Medicine

institute: Johns Hopkins Medical School

summary: Transcription profile of WT compare to sigma factor sigI deletion mutant at OD1 and OD2.

overall_design: This microarray is simple comparison of wild type strain of M. tuberculosis CDC1551 and its sigma factor gene deletion mutant (sigI) at OD1 and OD2, respectively.

first: William

last: Bishai


title: Effects of ad libitum feeding on canine skeletal muscle gene expression

summary: Skeletal muscle, as a large and insulin sensitive tissue, is an important contributor to metabolic homeostasis and energy expenditure.  Obese dogs exhibit skeletal muscle insulin resistance, but the causes of these changes are unclear.  Thus, we used canine microarrays to analyze gene expression profiles of skeletal muscle tissue collected from obese dogs, after 24 wk of ad libitum feeding.

overall_design: Skeletal muscle tissue samples were collected from 9 intact female beagles (4 yr-old; 4 control; 5 ad libitum) after 24 wk of ad libitum feeding.


title: Analysis of the Saccharomyces cerevisiae Pan-Genome Reveals a Pool of Copy Number Variants Distributed in Diverse Yeast Strains From Differing Industrial Environments.

city: Stanford

first: Barbara

last: Dunn

state: CA

institute: Stanford University

summary: We created a multi-species microarray platform, containing probes to the whole genomes of seven different Saccharomyces species, with very dense coverage (one probe every ~500 bp) of the S. cerevisiae genome, including non-S288c regions, mitochondrial and 2 micron circle genomes, plus probes at fairly dense coverage (one probe every ~2,100 bp) for each of the genomes of six other Saccharomyces species:  S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, S. kluyveri and S. castellii.  We performed array-Comparative Genomic Hybridization (aCGH) using this platform, examining 83 different Saccharomyces strains collected across a wide range of habitats; of these, 69 were widely used commercial S. cerevisiae wine strains, while the remaining 14 were from a wide range of other industrial and natural habitats.  Thus, we were able to sample much of the pan-genome space of the Saccharomyces genus.  We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains.  These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains.  To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole genome sequencing on nine of these strains.  These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design: Control arrays of the following types are included in the dataset:  (1) "Self-self" hybridizations (called "Self cntrl" in the dataset), where the reference DNA mix was labeled with either Cy3 or Cy5 (in separate reactions) and then mixed and hybridized. (2) Reference sub-pool hybridizations: the mix of 6 non-cerevisiae strains' DNA was labeled with Cy5, mixed with the final Reference pool (labeled in Cy3) and hybridized (called "OtherSppCompletePool" control) or the mix of 42 S. cerevisiae strains' DNA was labeled with Cy5, mixed with the final Reference pool (labeled in Cy3) and hybridized (called "Scer only ref pool") (3) Single Saccharomyces species hybridizations, where each of the 6 non-cerevisiae species, and also the S288c S. cerevisiae lab strain, was labeled with Cy5, mixed with the final Reference pool (labeled in Cy3) and hybridized (these arrays are called by the strain number followed by the species nickname).  Four separate replicates of the self-self hybridizations were performed, and duplicate arrays (done on different days using different DNA preparations) were performed for three of the wine strains: GSY2175, GSY2176 and GSY2196.


title: Physiological, biochemical and transcriptional analysis of onion bulbs during storage

city: Crawley

first: John

last: Hammond

address: 35 Stirling Highway

department: School of Plant Biology

institute: University of Western Australia

summary: Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses.

overall_design: Samples of RNA were prepared from onions of two cultivars, ‘Wellington’ (brown, long-storing) and ‘Sherpa’ (brown, average-storing), grown according to normal commercial practice at various physiological ages, viz, freshly harvested, cured, pre-sprouting and sprouting. Three biological replicates for each time (harvest, cured, before sprouting, sprouting), curing temperature (20, 28°C) and cultivar (Wellington, Sherpa) combination (n = 42).

middle: P

first: Katherine

last: Cools

first: Gemma

last: Chope

first: Andrew

last: Thompson

first: Leon

last: Terry


title: phytoplasma in plants vs. phytoplasma in insects (co-hybridizations)

overall_design: Two-condition experiment, phytoplasma-infected plant and phytoplasma-infected insect. Biological replicates: 6 phytoplasma-infected plants and 6 phytoplasma-infected insects, independently grown and harvested. One replicate per array.


title: Gene expression analysis of tumors from ApcD14/+ mice

first: Caroline

last: Bonnans

overall_design: 10 tumors from 2 different ApcD14 mice

first: Maud

last: Falceliere

first: Christelle

last: Dantec

first: Jean-Pierre

last: Devignes

first: Julie

last: Pannequin

first: Dany

last: Severac

first: Emeric

last: Dubois

first: Frédéric

last: Bibeau

first: Virginie

last: Escriou

first: Philippe

last: Crespy

last: Journot


title: Expression profile of ACC-overexpressed wild type yeast strain

status: Public on Jan 13 2012

city: Suwon-si

first: ga

middle: hee

last: shin

address: Gosaek-dong

country: South Korea

institute: Insilicogen

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of 1918 genes connected with lipid metabolism in yeast strain overexpressed of fatty acid biosynthesis gene

overall_design: In the study presented here, expression profiles of wild type and ACC-overexpressed wild type yeast strain were well-clustered by profiles- and gene similarities. It was analyzed the gene expression profile of ACC-overexpressing as compared with those of wild type. The expression levels between wild type(WT) and ACC-overexpressed wild type(ACC) were compared individually three times.

first: GaHee

last: Shin


title: Major differences in gene expression profiles revealed in day-25 trophoblast but not embryonic discs from cattle clones

city: Champaign

first: Robin

middle: Edward

last: Everts

address: 1201 West Gregory Drive

department: Animal Sciences

institute: UIUC

summary:
To better understand the problems associated with cloning, gene expression profiling of AI- and SCNT-derived bovine (day 25 of pregnancy) fetuses was performed.  The embryonic disc and the extraembryonic tissues for each fetus were analyzed separately using a bovine oligoarray. Clustering of all the expression profiles showed clustering by tissue, but no separation of AI vs. SCNT samples was observed.  Statistical analysis using a mixed model revealed 188 differentially expressed genes between the extraembryonic tissues and 10 differentially expressed genes between the embryonic discs of AI- and SCNT-derived fetuses.  Between the tissue types >9,000 genes showed differential expression, of which 2,127 that showed >=2-fold difference in expression.  The data generated in the current experiment clearly shows that the main problem with SCNT pregnancies is related to abnormal gene expression in the extraembryonic tissues.
Keywords: nuclear transfer

overall_design: Ref design with dye swap

middle: E


title: Normal human osteoblasts and SKBR3 mono and coculture

status: Public on Jan 06 2012

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented malignant epithelial cell compartments (SKBR3) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Tatiparthi

last: Reddy


title: Normal human osteoblasts and HMEC mono and coculture

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented healthy epithelial cell compartments (HMEC - human mammary epithelial cell) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.


title: Role of SPI-1 Secreted Effectors, SipA, SopABDE2, in Acute Bovine Response to Salmonella enterica Serovar Typhimurium

status: Public on Jan 10 2012

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary: Salmonella enterica Serovar Typhimurium (S. Typhimurium) causes enterocolitis in humans and calves characterized by diarrhea and polymorphonuclear cell (PMN) influx to the intestinal mucosa.  The Salmonella Type III Secretion System encoded at Pathogenicity Island I (SPI-1) translocates the Salmonella effector proteins SipA, SopA, SopB, SopD, and SopE2 into the host epithelial cell cytoplasm. These five effector proteins act in concert to induce fluid secretion and transcription of C-X-C chemokines, which serve to recruit PMNs to the intestine. While the individual molecular interactions of these Salmonella proteins with cultured host cells have been extensively characterized, their combined role in the generation of fluid secretion and inflammation is less well understood.  A bovine ligated ileal loop model was used in conjunction with a custom bovine microarray to determine intestinal response to acute S. Typhimurium infection in the calf.  Gene expression responses to both wild type S. Typhimurium a delta sipA, sopABDE2 mutant were measured at seven times during the initial 12 hours of infection.   Microarray analysis confirmed increased expression of genes encoding proteins previously associated with immune response to Salmonella spp. infection.  Gene expression changes were mapped to molecular interaction pathways and changes in expression of mechanistic genes, which are defined as perturbed genes identified by Bayesian genetic network modeling, were strongly involved in the mechanisms of the host immune response.  In addition to correctly identifying known effects of wild type S. Typhimurium on host (bovine) gene expression, Bayesian genetic network modeling identified novel effects of S. Typhimurium on several molecular interaction pathways.  Novel effects impacted gene regulation in the following pathways: adipocytokine signaling, insulin signaling, complement and coagulation cascades, axon guidance, gap junction, neuroactive ligand-receptor interaction, long-term depression, long-term potentiation,  melanogenesis, and natural killer cell mediated cytotoxicity.  Known effects were observed in the following pathways: regulation of actin cytoskeleton, apoptosis, cytokine-cytokine receptor interaction, cell adhesion molecules (CAMs), MAPK signaling, calcium signaling, Jak-STAT signaling, leukocyte transendothelial migration, adherens junction, tight junction, and ECM-receptor interactions, phosphatidylinositol signaling system, and antigen processing and presentation.  Quantitative real-time PCR was used to verify the expression of some of these mechanistic genes.

overall_design: Microarrays were used to examine the transcriptional profiles of bovine intestinal epithelia infected with wild type Salmonella enterica serotype Typhimurium (control and wild type or delta sipA sopABDE2 mutant infected) across seven time points (15 min, 30 min, 1, 2, 4, 8, and 12 hours).  Experiments were performed in quadruplicate (bovine ligated ileal loops surgeries were performed with four calves), generateing a total of 84 arrays.

first: Sara

middle: D

last: Lawhon

first: Sangeeta

last: Khare

first: Carlos

last: Rossetti

first: Cristi

middle: L

last: Galindo

first: Sarah

last: Luciano

first: Josely

last: Figueiredo

first: Jairo

last: Nunes

first: Tamara

last: Gull

first: George

last: Davidson

first: Kenneth

last: Drake

first: Harold

middle: R

last: Garner

first: Harris

last: Lewin

first: Andreas

middle: J

last: Bäumler

first: L

middle: G


title: Comparative genomic hybridization of hiPSC stem cell lines.

status: Public on Jan 07 2012

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

type: Genome variation profiling by genome tiling array

summary: The Purpose of this series of experiments is to identify copy number variations, duplications, and deletions in human induced pluripotent stem (hiPSC) cell lines.

overall_design: Genomic DNA of different human induced pluripotent stem cell lines are extracted and hybridized to NimbleGen CGH microarray, using genomic DNA of hESC H1 or H9 as common reference. Difference between different stem cell lines will be revealed.

first: Karen

last: Montgomery


title: Differential functional effects of EGF along the human fetal intestine

status: Public on Jan 11 2012

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

summary: Transcriptional profiling of small and large intestinal explants cultured in the absence or in the presence of EGF (50 ng/mL).

overall_design: Two-condition experiment, control intestinal explants vs EGF intestinal explants

first: Eric

last: Tremblay

first: Emanuela

last: Ferretti

first: Babakissa

last: Corentin

first: Ernest

last: Seidman

first: Daniel

last: Ménard


title: Local adaptation of a fungal pathogen introduced into a soil community

status: Public on Jan 04 2012

city: College Park

first: Monica

last: Pava-Ripoll

address: 4112 Plant Sciencies Bldg

department: Entomology

institute: University of Maryland

summary: Identifying the genetic basis for natural selection is a fundamental research goal, and particularly significant for soil fungi because of their central role in ecosystem functioning. Here, we identify rapid evolutionary processes in the plant root colonizing insect pathogen Metarhizium robertsii. While adapting to a new soil community, expression of TATA box containing cell wall and stress response genes evolved at an accelerated rate, whereas virulence determinants, transposons and chromosome structure were unaltered. The survival of diversified field isolates was increased, confirming that the mutations were adaptive, and we further show that large populations of Metarhizium are principally maintained by associations with plant roots rather than insect populations. These results provide a mechanistic basis for understanding mutational and selective effects on soil microbes.

overall_design: A loop design was used to compare differential gene expression between the original input strain Metarhizium robertsii ARSEF 2575 (designated as Control) and 5 field strains (designated as Re01, Re02, Re03, Re04 and Re05). The control samples contained samples of input strain Mr2575 were compared to themselves to establish a base-line for natural variation in gene expression and standardize the data and confirm there were no technical issues with the design. These design generated seven-condition experiment: Control vs. Control (five biological replicates, no dye swapping), Control vs. Re01 (three biological replicates, dye swapping), Re01 vs.Re02 (three biological replicates, dye swapping), Re02 vs. Re03 (three biological replicates, dye swapping), Re03 vs. Re04 (three biological replicates, dye swapping), Re04 vs. Re05 (three biological replicates, dye swapping) and Re05 vs. Control (three biological replicates, no dye swapping). Biological replicates were independently grown and harvested. Three replicates per array (in-slide replicates). Dye-swap was performed as specified in parenthesis.

first: Sibao

last: Wang

first: Tammatha

last: O'Brian

first: Raymond

last: St. Leger


title: Chip-chip from Mouse MEFs cells for H3K36me3, Srsf1, Psip1(A300-847 antibody).

status: Public on Jan 01 2012

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary:
The p52 isoform of Psip1/Ledgf links histone H3K36 methylation and the regulation of alternative splicing.
Chromatin immunoprecipitation (ChIP) of Psip1 together with H3K36me3 and Srsf1 and by ChIP-on-chip analysis demonstrated that  H3K36me3, Psip1 and SRSF1 enrichment correlates on the gene bodies

overall_design: Array design includes 2 dye swap replicates for Srsf1 and Psip1-/- samples, and single arrays for PSIP and H3K36me3 samples

first: Pradeepa

middle: M

last: Marulasiddappa

first: Wendy

middle: A

last: Bickmore


title: Identification of reference genes for quantitative Real-Time PCR in Bifidobacterium bifidum PRL2010 based on transcriptome analysis

status: Public on Jan 05 2012

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

summary: In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by micro array technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., lag-, exponential and stationary phase. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes, which resulted expressed in all phases. A proportion of the latter genes were further investigated as potential reference genes by Quantitative Real Time PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, encompassing cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic and osmotic) and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria.

overall_design: Transcriptional profiling of B.bifidum PRL2010 at different growth phases (lag phase, early exponential phase, late exponential phase, early stationary phase).