title: Sediment Extract Series River Rhine

city: Karlsruhe

first: Jens

last: Otte

address: Postfach 3640

department: Institute of Toxicology and Genetics

institute: Karlsruhe Institute of Technology

summary: The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerably extend be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism.

overall_design: Microarray analysis were performed with early life stages of zebrafish exposed to 2 sediment extracts from the Upper part of the River Rhine, Germany. The expression profile as then compared to the expression pattern of model toxicants, such as, 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, combining mechanism-specific bioassays as well as chemical analysis of the sediments to the gene expression data has contributed to a more comprehensive view on the hazard potential of the sediments.


title: Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.)

status: Public on Dec 17 2012

city: cankiri

first: mine

last: turktas

address: ballica campus

country: Turkey

institute: cankiri karatekin university

summary: We carried out genome wide transcriptome analyses in different organs and developmental stages of the olive tree using the NimbleGen Array oligonucleotide probe sets. Cluster analyses of the genes showed that samples collected from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing for O. europaea, as shown by the differential expressions of transcripts under different developmental phases and organs

platform_organism:
Populus trichocarpa
Olea europaea

overall_design: Six sample sets were prepared for array analyses: i) unripe fruit (UF); ii) ripe fruit (RF); iii) “on-year” mature leaf (November sample, ON-M); iv) “on-year” juvenile leaf (July sample, ON-J); v) “off-year” mature leaf (November samples, OFF-M); and vi) “off-year” juvenile leaf (July sample, OFF-J).

first: Mine

last: Turktas

first: Behcet

last: Inal

first: Sezer

last: Okay

first: Emine

middle: G

last: Erkilic

first: Ekrem

last: Dundar

first: Pilar

last: Hernandez

first: Gabriel

last: Dorado

first: Turgay

last: Unver


title: Gene expression profiling of fathead minnows (Pimephales promelas) following an acute exposure to pulp and paper mill effluents

status: Public on Dec 31 2012

city: Thunder Bay

first: Shannon

middle: L

last: Costigan

state: ON

address: 955 Oliver Rd

department: Biology

country: Canada

institute: Lakehead University

summary: We evaluated the possible mechanisms by which exposure to a sequentially treated pulp and paper mill effluent affects gene expression in the liver of male and female fathead minnows.

overall_design: Sexually mature fathead minnows were exposed to either river water, which served as our control (C), 10% untreated kraft effluent (UTK), 25% treated kraft effluent (TK) or 100% final effluent (CMO) from a multiprocess pulp and paper mill for 6 days.  A total of 4 treatments.  Each exposure aquarium consisted of a 42.1 L column that contained individual 5.3 L chambers.  Each chamber contained a FHM breeding pair.   A total of 3 biological replicates for male and female FHM per treatment were sent for microarray analysis resulting in a total of 24 arrays run as a reference design with a pooled sample of the 6 river water exposed fish serving as the reference sample..

first: Julieta

last: Werner

first: Jacob

middle: D

last: Ouellet

first: Lauren

last: Hill

first: R

last: Law


title: MicroRNAs as Regulators of the Immune Response during Allograft Rejection

status: Public on Dec 30 2012

city: Stanford

first: Liang

last: Wei

state: CA

address: 1201 Welch Rd MSLS P328

department: Surgery

country: USA

institute: Stanford University

summary: MicroRNAs are small non-coding RNA molecules that regulate the post-transcriptional expression of target genes. In addition to being involved in many biologic processes including development, cell differentiation, proliferation, and apoptosis, microRNAs are important regulators in innate and adaptive immune responses. Distinct sets of expressed miRNAs are found in different cell types and tissues and aberrant expression of microRNAs is associated with many disease states. MicroRNA expression was examined in a model of heterotopic heart transplantation by microarray analyses and a unique profile was detected in rejecting allogeneic transplants (BALB/C to C57BL/6) as compared to syngeneic transplants (C57BL/6 to C57BL/6). The microRNA miR-182 was significantly increased in rejecting cardiac allografts and in mononuclear cells that infiltrate the grafts. Forkhead Box (FOX) proteins are a family of important transcription factors and FOXO1 is a target of miR-182. As miR-182 increases after transplant, there is a concomitant post-transcriptional decrease in FOXO1 expression in heart allografts that is localized to both the cardiomyocytes and CD3+ T cells. The microRNA miR-182 is significantly increased in both PBMC and plasma during graft rejection suggesting potential as a biomarker of graft status. Our results identify microRNAs that may regulate alloimmune responses and graft outcomes.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: In total 14 microRNA microarrays data. For heart graft: each sample column corresponds to the expression profile of 3 pooled syngeneic or 3 pooled allogeneic heart grafts or 3 pooled normal heart.  For graft infiltrating lymphocytes (GILs): each sample column corresponds to the expression profile of 3 pooled syngeneic or 3 pooled allogeneic GILs or 3 pooled normal PBMC.

first: Mouer

last: Wang

first: Xiumei

last: Qu

first: Betty

last: Pham

first: Annelise

last: Mah

first: Xiaoxing

last: Xiong

first: Aleishia

last: Harris

first: Lori

last: Phillips

first: Karine

last: Piard-Ruster

first: Olivia

last: Martinez

first: Sheri

last: Krams


title: Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling

status: Public on Feb 06 2013

city: Madrid

first: José

middle: María

last: Izquierdo

state: Madrid

address: Campus de Cantoblanco

country: Spain

institute: CBM Severo Ochoa

summary:
Background: T-cell intracellular antigen (TIA) proteins function as regulators of cell homeostasis. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environmental stresses. Herein we identified a micro(mi)RNA signature associated to transiently TIA-depleted HeLa cells and analyzed the potential role of miRNAs combining genome-wide analysis data on mRNA and miRNA profiles.

Results: Using high-throughput miRNA expression profiling, transient depletion of TIA-proteins in HeLa cells was observed to promote significant and reproducible changes (>2-fold, FDR<0.0001) affecting to a pool of up-regulated miRNAs (miR-30b*, miR125a-3p, miR-193a-5p, miR-197_MM2, miR-203, miR-210, miR-371-5p, miR-373*, miR-483-5p, miR-492, miR-498, miR-503, miR-572, miR-586, miR-612, miR-615, miR-623, miR-625, miR-629, miR-638, miR-658, miR-663, miR-671, miR-769-3p and miR-744). Differential expression analysis of some miRNAs was validated by reverse transcription and real time PCR. By target prediction and combined analysis of the genome-wide expression profiles of the mRNAs and miRNAs identified in TIA-depleted HeLa cells, we detected concomitant connections between up-regulated miRNAs and putative and experimental targeted mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database analyses suggest that targeted mRNAs are related with biological processes associated to the regulation of DNA-dependent transcription, signal transduction and multicellular organismal development as well as with the enrichment of pathways in cancer, focal adhesion, regulation of actin cytoskeleton and MAPK and Wnt signalling pathways, respectively.

Conclusion: All this considered, these observations suggest that specific miRNAs could act as potential mediators of the epigenetic switch linking transcriptomic dynamics and cell phenotypes mediated by TIA proteins.

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

overall_design: The analysis includes two cell types. Three biological replicates were performed per cell type and they were compared by using three dual-channel microarray hybridizations.

first: Carmen

last: Sánchez-Jiménez

first: Isabel

last: Carrascoso

first: Juan

last: Barrero

middle: M


title: Identification of genes differentially expressed during the growth of Bambusa oldhamii

city: Taipei

first: Ai-Yu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Biochemical Science and Technology

country: Taiwan

institute: National Taiwan University

summary: To gain insights into the molecular mechanisms controlling bamboo growth, mRNA differential display was used to clone genes that are differentially expressed in various tissues of shoots at different growth stages, and their expression patterns were further validated by cDNA microarray. A number of genes and signaling pathways are proposed to have significant roles in controlling the elongation of the bamboo culm.

overall_design: Etiolated shoots (average height: 15 cm) that had not yet emerged from the ground and green shoots (average height: 100 cm) of Bambusa oldhamii were collected. The shoots were divided into three parts, the culm base, the middle and the top regions for RNA extraction and processing. The RNA from the middle region of the etiolated shoots was used as a reference in microarray comparisons.

first: Mong-Hsun

last: Tsai

first: Sheng-Hsiung

last: Yeh


title: Differential transcription of Geobacter sulfurreducens cells growing with Fe(III) oxide, Mn(IV) oxide or Fe(III) citrate provided as electron acceptor

status: Public on Dec 15 2012

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

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

overall_design: Refer to individual Series


title: Differential transcription of Geobacter sulfurreducens cells growing with Fe(III) oxide or Fe(III) citrate provided as electron acceptor [Fe]

summary:
Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport.  The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction.  Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens.
Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 μg) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturer’s instructions.

overall_design: RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix antisense-detecting arrays. The experimental condition (DL1 grown with Fe(III) oxide as acceptor) was labeled with cy5, the control condition (DL1 grown with Fe(III) citrate as acceptor) was labeled with cy3

first: Muktak

last: Aklujkar

first: Ching

last: Leang

first: Ludovic

last: Giloteaux


title: Transcription pattern in Normal (NL) and Down's Syndrome (DS) Astrocytes

status: Public on Dec 07 2012

city: Cordoba

first: Pablo

last: Helguera

state: Cordoba

address: Friuli 2434

country: Argentina

institute: INIMEC-CONICET

summary:
We performed a broad-spectrum microarray analysis using mRNA from 3 NL and 5 DS astrocyte cultures. The microarray output was validated for several genes To explore the relation
between gene expression and potential oxidative stress in DS samples, we also evaluated the transcription profile in NL astrocytes subjected to mild oxidative stress (50µM H2O2 for 24 hr).

overall_design: Samples of total mRNA from NL cultures non treated (NT), normal cultures treated with H2O2 (T), DS cultures NT and DS cultures T were included in the arrays.

middle: R

first: Jose

last: Rodriguez

first: Gustavo

middle: F

first: Jorge

last: Busciglio


title: miRNA expression profiling in tumor-associated BMDCs induced by mouse ovarian and colon tumor cells

status: Public on Dec 05 2012

city: Tianjin, P.R.China

first: Yang

last: Rongcun

address: 94 Weijin Road, Nankai District

department: School of medicine

country: China

institute: Nankai University

summary: miRNA expression profiling in tumor-associated BMDCs induced by tumor cells 1D8 or CT-26 in comparison with those cultured in medium.

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

overall_design: To prepare tumor-associated BMDCs(Bone Marrow-derived Dendritic Cells), murine BMDCs were co-cultured with 1D8 or CT-26 cells in a transwell plate in 1640 medium supplemented with 3% FCS and 1% penicillin and streptomycin for 24 hrs. Total RNAs were isolated using the TRIZOL® Reagent(Invitrogen) according to manufacturer’s instructions.The samples were labeled using the miRCURY™ Array Power labeling kit (Exiqon). miRNA array hybridization was performed, and unbound miRNA Labels were washed away. Microarrays were analyzed using GenePix 4000B scanner and GenePix Pro 6 software (Molecular Devices).

first: Rongcun

last: Yang


title: Differential transcription of Geobacter sulfurreducens cells growing with Mn(IV) oxide or Fe(III) citrate provided as electron acceptor [Mn]

overall_design: RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix antisense-detecting arrays. The experimental condition (DL1 grown with Mn(IV) oxide as acceptor) was labeled with cy5, the control condition (DL1 grown with Fe(III) citrate as acceptor) was labeled with cy3


title: miRNA profiling of breast cancer patients

status: Public on Dec 01 2012

city: Chicago

first: Ravand

last: Samaeekia

state: IL

department: Ben May Department of Cancer Research

institute: University of Chicago

summary: Chemotherapy resistance frequently drives tumor progression. However, the underlying molecular mechanisms are poorly characterized. Epithelial-to-mesenchymal transition (EMT) has been shown to correlate with therapy resistance, but the functional link and signaling pathways remain to be elucidated. We report here that miR-30c, a human breast tumor prognostic marker, plays a pivotal role in chemo-resistance by a direct targeting of the actintransporter TWF1, which promotes EMT. An IL-6 family member, IL-11 was identified as a secondary target of TWF1 in the miR-30c signaling pathway. Expression of miR-30c inversely correlated with IL-11 expression in clinical tumors and IL-11 correlated with relapse-free survival in breast cancer patients. Identification of a novel miRNA-mediated pathway that regulates chemo-resistance in breast cancer will facilitate the development of new management strategies.

overall_design: For the primary breast tumor and normal breast samples, both mRNAs (Agilent array data deposited in GSE22049) and miRNAs (Exiqon array data deposited here) profiles have been examined. Patient information include age, tumor subtype and outcome etc. When clustering samples and genes 152 of 757 miRNA passed the filtering criteria on variation across samples; standard deviation > 0.50. Hence, the upper 152 miRNAs in the expression matrix were used in the  two-way hierarchical clustering of genes. The matrix numbers are all log2(Hy3/Hy5) ratios, meaning sample/pool. The percentages above the matrix indicates the present call in each sample/slide. When calling of a particular miRNA failed on an array this is indicated as a blank in the row containing this miRNA and in the column corresponding to this array. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 2 or more of the 4 replicated measures of this miRNA were flagged 1 or 2 (i.e. the signal is below background) by the image analysis software. Further in the expression matrix all capture probes with Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated as a blank.

first: Chika

last: Nwachukwu

first: Huiping

last: Liu

first: Olufunmilayo

middle: I

last: Olopade


title: Comparative transcriptional analysis of Desulfovibrio G20 grown under syntrophic and respiratory condtions

status: Public on Nov 29 2012

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

summary: Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis in chemostats at a high growth rate of 0.047h-1

overall_design: 5 replicates of coculture and 3 replicates of sulfate-limited monoculture

first: Birte

last: Meyer

first: Jennifer

last: Kuehl

first: Adam

last: Deutschbauer

middle: P

last: Arkin

first: David

middle: A

last: Stahl


title: Rho and NusG suppress pervasive antisense transcription in Escherichia coli [tiling array].

status: Public on Nov 01 2012

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

department: Biochemistry

institute: UW-Madison

type: Expression profiling by genome tiling array

summary: Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global co-localization of the nucleoid-associated protein H-NS with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes.

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

overall_design: Tiling expression microarray experiments were performed in cells treated with 20 ug/ml bicyclomycin or cells deleted for nusG, or a partial deletion of nusA. Labeled cDNAs were hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 14 datasets.

first: Robert

last: Landick


title: Rho and NusG suppress pervasive antisense transcription in Escherichia coli [ChIP-chip].

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (RNAP; Beta subunit) in wild-type cells or cells deleted for hns, nusG, or a partial deletion of nusA. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 12 datasets.


title: Pseudomonas putida KT2440: Control vs. indole 1mM treated

status: Public on Oct 02 2012

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

summary: Transcriptional profiling of P. putida KT2440 cells comparing control untreated cells with 1 mM indole  treated cells

overall_design: Two-condition experiment, Control vs. treatment. Biological replicates: 2 control, 2 treated, independently grown and harvested


title: Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma

status: Public on Oct 09 2012

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

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

type: Genome variation profiling by genome tiling array

summary: Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2013.

overall_design: Genomic profiling of 78 lung carcinomas using 32K BAC aCGH microarrays.

first: Sofi

last: Isaksson

first: Anna

last: Karlsson

first: Mats

last: Jönsson

first: Leif

last: Johansson

first: Per

last: Botling

first: Patrick

last: Micke

first: Bo

last: Baldetorp

first: Maria

last: Planck


title: irs4 versus CAI-12

status: Public on Oct 06 2012

city: Pittsburgh

first: Hassan

last: Badrane

state: PA

address: 3550 Terrace Street, Scaife Hall, Room S875

department: Medicine

institute: University of Pittsburgh

summary: Comparison of expression profiling of irs4 null mutant versus isogenic strain (CAI-12) grown in blood (3 replicates)

overall_design: Two-condition experiment, irs4 null mutant versus CAI-12 wild-type. Biological replicates: 3 irs4 null mutant, 3 wild-type. Two replicates per array.

first: Corneilus

middle: J

last: Clancy

first: Ming-Hong

last: Nguyen

first: Suresh

middle: B

last: Raman

first: Shaoji

last: Cheng


status: Public on Nov 07 2012

city: Zurich

first: Michal

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

summary:
The transition between morula and blastocyst stage during preimplantation development represents the first differentiation event of embryogenesis. Morula cells undergo the first cellular specialization and produce two well-defined populations of cells, the trophoblast and the inner cell mass (ICM). Embryonic stem cells (ESCs) with unlimited self-renewal capacity are believed to represent the in vitro counterpart of the ICM. Both mouse and rat ESCs can be derived from the ICM cells, but their in vitro stability differs. In this study we performed a microarray analysis in which we compared the transcriptome of mouse and rat morula, blastocyst, and ICM. This cross-species comparison represents a good model for understanding the differences in derivation and cultivation of ESCs observed in the two species. In order to identify alternative regulation of important molecular mechanisms the investigation of differential gene expression between the two species was extended at the level of signaling pathways, gene families, and single selected genes of interest. Some of the genes differentially expressed between the two species are already known to be important factors in the maintenance of pluripotency in ESCs, like for example Sox2 or Stat3, or play a role in reprogramming somatic cells to pluripotency like c-Myc, Klf4 and p53 and therefore represent interesting candidates to further analyze in vitro in the rat ESCs. This is the first study investigating the gene expression changes during the transition from morula to blastocyst in the rat preimplantation development. Our data show that in the pluripotent pool of cells of the rat and mouse preimplantation embryo substantial differential regulation of genes is present, which might explain the difficulties observed for the derivation and culture of rat ESCs using mouse conditions
Casanova EA, Okoniewski MJ, Cinelli P. Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos.PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15.

sample_organism:
Mus musculus
Rattus norvegicus

overall_design: We collected morula and blastocysts stage embryos from mouse and rat and, by immunosurgery, we isolated the ICM cells from the blastocysts. All the embryos and ICMs were pooled into two groups for every developmental stage. Pooling of embryos for RNA extraction in this study was chosen mainly because of the low amounts of RNA that can be isolated from preimplantation embryos, and in addition because of the heterogeneity of the cell populations present in the embryos. For the analysis we pooled a large number (n >100) of the independent isolated embryos to achieve a sufficient accuracy of biological pooling . Due to the difficulties to isolate a larger number of embryos from mice and rats, we performed the microarray study by using two replicate samples per developmental stage.

first: Elisa

last: Casanova

first: Paolo

last: Cinelli


title: σF regulon

city: Greifswald

first: Christian

last: Kohler

address: F.-L.-Jahnstrasse 15

department: Department of Microbiology

country: Germany

institute: EMAU

summary: The Alphaproteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metal in these sites. It has been reported that C. crescentus responds to chromium exposure by altering expression of a large number of genes. In this work, we showed that the ECF sigma factor SigF is one of the regulatory proteins involved in the control of this transcriptional response. Microarray experiments from cells under dichromate stress showed that SigF controls a small regulon consisting of seven genes. Promoter analyses revealed that a conserved SigF-dependent sequence is located upstream of all but one gene of this regulon. Surprisingly, sigF itself was not found to be strongly auto-regulated under dichromate exposure. Furthermore, we showed that the second gene (CC3252) in the sigF operon acts as a negative regulator of SigF function, as overexpression of this putative membrane protein abolishes the transcriptional activation of sigF and its regulon under dichromate stress. Additionally, we found that substitution of one or both the conserved cysteines in the protein encoded by CC3252 (C131 and C181) affects the ability of this protein in maintaining expression of SigF-dependent genes at basal levels. Interestingly, we showed that the activation of SigF is not caused by reactive oxygen species generated as a consequence of dichromate exposure. Therefore, dichromate most probably may lead to conformational changes in the putative anti-sigma factor CC3252, releasing SigF to bind RNA polymerase core and drive transcription of its regulon.

overall_design: Three replicates perfomed with independent biological samples

first: C

first: R

last: Lourenço

first: S

last: Gomes


title: Additional Routes to Staphylococcus aureus Daptomycin Resistance as Revealed by Comparative Genome Sequencing, Transcriptional Profiling, and Phenotypic Studies

status: Public on Oct 01 2012

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary: Daptomycin is an extensively used anti-staphylococcal agent due to the rise in methicillin-resistant Staphylococcus aureus. However, both laboratory-derived and clinical decreased susceptibility isolates have been described, but the mechanism(s) of resistance is poorly understood. To further understand daptomycin resistance, comparative genome sequencing, transcriptomics, ultrastructure ,and cell envelope studies were carried out on two relatively higher level (4 and 8 ug/ml-1) laboratory-derived daptomycin-resistant strains (strains CB1541 and CB1540 respectively) compared to their methicillin-resistant parent strain (CB1118;MW2). Genes altered in their expression common to both transcriptomes included some involved in glycine betaine accumulation, mscL, ure genes, femH, spa and smpB. However, the CB1541 transcriptome was further characterized by upregulation of various heat shock chaperone and protease genes, consistent with a mutation in clpP, and lytM and sceD. Both strains showed slow growth, and strongly decreased autolytic activity that appeared to be mainly due to decreased autolysin production. In contrast to previous common findings, we did not find any mutations in phospholipid biosynthesis genes, and it appears there are multiple pathways to and factors in daptomycin resistance.

overall_design: MHB cultures (biological replicates: N=3) were then grown to exponential phase (OD600=0.4). Dye-swapping was performed between samples.

first: Yang

last: Song


title: Zbtb16 Has a Role in Brown Adipocyte Bioenergetics

status: Public on Aug 31 2012

city: Seattle

first: Christopher

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: Study designed to identify genes that are induced in both BAT and skeletal muscle during acute adaptive thermogenesis in mouse using gene expression microarray.  Animal studies were performed under approved UCLA animal research protocols and according to guidelines established in the Guide for Care and Use of Laboratory Animals. C57BL/6J mice were maintained in 12-h light/dark conditions and fed a regular chow diet (Purina 50010, Lab Diet, USA). Cold exposure was performed as described. After euthanasia, tissues were collected and frozen until use.

overall_design: Total RNA was isolated from mouse tissues by extraction with TRIzol from either brown adipose tissue (BAT) or skeletal muscle (quadriceps) after exposure to cold (4 degrees C for 4 hours).  The mice were of the C57BL/6J strain and were maintained in 12-h light/dark conditions and fed a laboratory chow diet that consisted of 4.5% fat, 50% carbohydrate by weight (Lab Diet, Purina 50010).

first: Laurent

last: Vergnes


title: Transcriptional responses in Enchytraeus albidus (Oligochaeta): comparison between cadmium and zinc exposure and linkage to reproduction effects

status: Public on Jul 01 2012

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

summary: Metal ecotoxicity on soil organisms, e.g. in Enchytraeids (also known as potworms), has been addressed mainly by assessing effects on survival and reproduction but very little is known about the molecular underlying mechanisms of responses. The main purpose of the present study was to assess and compare the transcriptional responses of Enchytraeus albidus to an essential (zinc) and a non-essential metal (cadmium). Exposure was performed to two concentrations of known effect on reproduction (EC50, EC90) at three time periods (2, 4 and 8 days). Results showed that transcriptional responses were influenced by exposure duration but, independently of that, the mechanisms of response to Cd and Zn were consistently different. Both metals affected pathways related with the regulation of gene expression, calcium homeostasis and cellular respiration. Mechanisms of toxicity that were exclusively associated with Cd exposures were the inhibition of DNA repair and the impairment of ubiquitin-mediated proteolysis. The microarray for E. albidus was a useful tool to detect molecular pathways affected by metal exposures. Transcriptional responses strongly correlated with known mechanisms of Cd and Zn responses in other organisms, suggesting cross-species conserved mechanisms of action. It should be highlighted that we could not only retrieve mechanistic information, but also that genes responded within 2-8 days of exposure. This represents an additional advantage of using such molecular endpoints as a complement to the traditional, more time-consuming endpoints.

overall_design: Gene expression in E.albidus was measured at 2, 4, and 8 days after exposure to Cadmium and Zinc at 2 concentrations of effect on reprocduction (EC50 and EC90). Three biological replicates per exposure treatment in each time point and 4 biological replicates of control conditions were used.

middle: C

first: Wim

last: De Coen

first: Mónica

last: Amorim


title: Gene expression in liver, gill, hypothalamus, pituitary, and olfactory rosettes from Atlantic salmon parr and smolt

status: Public on Aug 20 2012

city: Kearneysville

first: Laura

last: Robertson

state: WV

address: 11649 Leetown Rd.

department: Leetown Science Center

institute: USGS

summary: To identify genes involved in the developmental process of Atlantic salmon smoltification, gene expression was compared between smolt and parr in tissues involved in osmoregulation  (gill), metabolism (liver), imprinting (olfactory rosettes) and neuroendocrine control (hypothalamus and pituitary).  Tissue samples were harvested from laboratory-reared parr and smolts on the same date.  Smolts were distinguished from parr by size and appearance; developmental status was confirmed by physiological assays.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Eight biological replicates (16 fish) balanced for sex and for dye were used in the liver, gill, olfactory rosette, and hypothalamus comparisons. Four male parr were compared to four male smolts and four female parr were compared to four female smolts; smolts were labeled with Alexa Fluor 555 on four arrays and with Alexa Fluor 647 on four arrays.   Six biological replicates (12 fish) were used for the pituitary comparison (two female and four male).

middle: S

first: Stephen

last: McCormick


title: Enterococcus faecalis EfaR mutant transcriptome profile

status: Public on Jun 19 2012

city: Oeiras

first: Marta

middle: Coelho

last: Abrantes

address: Av. da República - EAN

institute: ITQB-UNL

summary: Metal ions are important cofactors of inumerous enzymes and can interfere in many biological processes. Manganese is a particularly relevant metal as it is also involved in protection from oxidative stress and several Mn-dependent regulators have been shown to have a role in bacterial pathogenicity. A putative DNA-binding motif, here called efa motif  was discovered in the promoter regions of genes previously shown to be differentially expressed in the presence of excess zinc, manganese and copper ions. This motif led to the finding and study of the genes putatively involved in the maintenance of manganese homeostasis in E. faecalis. In these genes is included the efaCBA operon, regulated by the Mn-dependent regulator EfaR. Other genes with this efa motif are shown to be regulated by EfaR. Regulation of these efa motif genes by EfaR is discussed as well as some clues on metal interaction with EfaR. Experiments mimicking conditions occurring on biological processes in the host showed that an EfaR plays an important role in biological processes crucial for E. faecalis colonization and virulence.

overall_design:
Comparison of the transcriptome profiles of Enterococcus faecalis strains VE14089 and VE14089 efaR::tet
2 condition experiment: E. faecalis VE14089 cells vs. E. faecalis VE14089 efaR::tet cells

first: Jan

last: Kok

first: Maria

last: de Fátima Lopes


title: Epigenetic regulation of receptive human endometrium through microRNAs

status: Public on Jun 23 2012

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

institute: iGenomix

summary: MicroRNAs (miRNAs) act as important epigenetic post-transcriptional regulators of gene expression. We aimed to gain more understanding to the complex gene expression regulation of endometrial receptivity by analysing miRNA signature of fertile human endometrium.

overall_design: We used Agilent miRNA arrays to define the miRNA expression pattern in receptive (LH+7, n = 3) vs. pre-receptive (LH<7, n = 4) endometrium from healthy fertile women.

first: Signe

last: Altmäe

first: Francisco

last: Esteban

last: Ruiz-Alonso

first: Anneli

last: Stavreus-Evers

last: Horcajadas

first: Andres

last: Salumets


title: mRNA expression analysis in mock and cgh-1(RNAi) animals

status: Public on Jun 18 2012

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary: To determine mRNA expression levels in mock and cgh-1(RNAi) animals, RNA was purified from young adult worms, using Trizol.

overall_design: A total of 6 samples was analyzed (triplicates of mock and cgh-1(RNAi) animals respectively)

first: Claudia

last: Scheckel

first: Stephane

last: Thiry

first: Jane

last: Wright

first: Rafal

last: Ciosk


title: mRNA expression analysis in wild-type, gld-1 and cgh-1 mutant animals

summary: To determine mRNA expression levels in wild-type, gld-1 (q485) mutant and cgh-1(tn691) mutant animals, RNA was purified from dissected gonads of young adult worms, using the PicoPur Kit.

overall_design: A total of 9 samples was analyzed (triplicates of wild-type, gld-1 mutant and cgh-1 mutant animals respectively)


title: Effect of nonylphenol on gene expression in Atlantic salmon liver, gill, hypothalamus, pituitary, and olfactory rosettes

status: Public on Jun 04 2012

last: Robertson

summary: Exposure to environmental contaminants like nonylphenol can disrupt smolt development and may be a contributing factor in salmon population declines.  We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of Atlantic salmon smolts treated with nonylphenol compared to control smolts.  Nonylphenol treatment was confirmed using physiological assays: nonylphenol-treatment significantly decreased gill Na+,K+-ATPase activity and plasma cortisol and T3 levels.

overall_design: Microarray analyses were used to compare expression in nonylphenol-injected fish with expression in vehicle-injected fish: eight arrays each for liver, gill, olfactory rosettes, hypothalamus, and pituitary tissues.  Total RNA was isolated from the tissues of eight nonylphenol-injected fish (six males and two females) and eight vehicle-injected fish (two males and six females) and reverse transcribed separately (not pooled); each slide represents a biological replicate.  For each tissue, the eight arrays were balanced for dye:  nonylphenol-injected fish were labeled with Alexa Fluor 555 and vehicle-injected fish were labeled with Alexa Fluor 647 on four slides, nonylphenol-injected fish were labeled with Alexa Fluor 647 and vehicle-injected fish were labeled with Alexa Fluor 555 on four slides.  Liver, gill, hypothalamus, pituitary, and olfactory rosette tissues were analyzed separately.

middle: D


title: Polysome profiling of wild-type and gld-1 mutant animals

summary: To determine the translational status of mRNAs in wild-type and gld-1 mutant animals, we analyzed total and polysomal RNA levels in both strains by tiling arrays

overall_design: A total of 16 samples was analyzed (quadruplicates of wild-type_total, wild-type_polysomal, gld-1_total, gld-1_polysomal RNA respectively)


title: Identification of GLD-1 target mRNAs

summary: To determine which mRNAs are bound by GLD-1 we performed GLD-1 and MYC (as a negative control) immunoprecipitation experiments on wildtype animals.

overall_design: A total of 6 samples was analyzed (triplicates of GLD-1 IPs and MYC IPs respectively)


title: GLD-1 mRNA regulation

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

overall_design: Refer to individual Series


title: Gene Expression Responses Linked to Reproduction Effect Concentrations (EC10,20,50,90) of Dimethoate, Atrazine and Carbendazim, in Enchytraeus albidus

status: Public on May 28 2012

first: Sara

last: Novais

summary:
Background: Molecular mechanisms of response to pesticides are scarce and information on such responses from soil invertebrates is almost inexistent. Enchytraeus albidus (Oligochaeta) is a standard soil ecotoxicology model species for which effects of many pesticides are known on survival, reproduction and avoidance behaviour. With the recent microarray development additional information can be retrieved on the molecular effects.
Methodology/Principal Findings: Experiments were performed to investigate the transcription responses of E. albidus when exposed to three pesticides – dimethoate (insecticide), atrazine (herbicide) and carbendazim (fungicide) – in a range of concentrations that inhibited reproduction by 10%, 20%, 50% and 90% (EC10, EC20, EC50 and EC90, respectively). The goal of this study was to further identify key biological processes affected by each compound and if dose-related. All three pesticides significantly affected biological processes like translation, regulation of the cell cycle or general response to stress. Intracellular signalling and microtubule-based movement were affected by dimethoate and carbendazim whereas atrazine affected lipid and steroid metabolism (also by dimethoate) or carbohydrate metabolism (also by carbendazim). Response to DNA damage/DNA repair was exclusively affected by carbendazim.
Conclusions: Changes in gene expression were significantly altered after 2 days of exposure in a dose-related manner. The mechanisms of response were comparable with the ones for mammals, suggesting across species conserved modes of action. The present results indicate the potential of using gene expression in risk assessment and the advantage as early markers.

overall_design: Gene expression in E.albidus was measured at 2 days after exposure to dimethoate, atrazine and carbendazim at 4 concentrations of effect on reprocduction (EC10, EC20, EC50 and EC90). Three biological replicates per treatment were used.

first: Wim

last: De Coen

last: Amorim


title: Detailed transcriptomics analysis of the effect of the PPARalpha agonist Wy14,643 on gene regulation in the murine heart

status: Public on Feb 21 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Fatty acids comprise the primary energy source for the heart and are mainly taken up via hydrolysis of circulating triglyceride-rich lipoproteins. While most of the fatty acids entering the cardiomyocyte are oxidized, a small portion is involved in altering gene transcription to modulate cardiometabolic functions. So far, no in vivo model has been developed enabling study of the transcriptional effects of specific fatty acids in the intact heart. In the present study, mice were given a single oral dose of synthetic triglycerides composed of one single fatty acid. Hearts were collected 6h thereafter and used for whole genome gene expression profiling. Experiments were conducted in wild-type and PPARα−/− mice to allow exploration of the specific contribution of PPARα. It was found that: 1) linolenic acid (C18:3) had the most pronounced effect on cardiac gene expression. 2) The largest similarity in gene regulation was observed between linoleic acid (C18:2) and C18:3. Large similarity was also observed between the synthetic PPARα agonist Wy14,643 and docosahexaenoic acid (C22:6). 3) Many genes were regulated by one particular treatment only. Genes regulated by one particular treatment showed large functional divergence. 4) The majority of genes responding to fatty acid treatment were regulated in a PPARα-dependent manner, emphasizing the importance of PPARα in mediating transcriptional regulation by fatty acids in the heart. 5) Several genes were robustly regulated by all or many of the fatty acids studied, mostly representing well-described targets of PPARs (e.g. Acot1, Angptl4, Ucp3). 6) Deletion and activation of PPARα had a major effect on expression of numerous genes involved in metabolism and immunity. Our analysis demonstrates the marked impact of dietary fatty acids on gene regulation in the heart via PPARα.

overall_design: To study the long term transcriptional effects of PPARα activation, wild type and PPARα−/− mice were fed a chow diet  (RMH-B diet Arie Block, Woerden, the Netherlands) containing 0.1% (w/w) of the specific PPARα agonist Wy14,643. After 5days hearts were collected and used for whole genome gene expression profiling.

first: Anastasia

last: Georgiadi

first: Mark

middle: V

last: Boekschoten

first: Michael

last: Muller

first: Sander

last: Kersten


title: RNA expression for ethanologenic Escherichia coli strain LY180 in the absence and presence of 15 mM furfural for 15 min

status: Public on Jan 10 2012

city: Gainesville

first: Xuan

last: Wang

state: Florida

address: Bldg. 981 Museum Road

department: Microbiology and Cell Science

institute: University of Florida

summary: The data explore the transcriptional response of strain LY180 to 15 mM furfural under anaerobic fermentation conditions. The expression differences of oxidoreductase in LY180 are described.

overall_design: Total RNA was prepared from cultures of LY180 immediately before and 15 min after addition of furfural to 15 mM. The NimbleGen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

first: Elliot

last: Miller

first: Lonnie

middle: O

last: Ingram


title: Transcriptome analysis of Newman delta2027

status: Public on Mar 09 2012

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: Intracellular small-molecule signaling has drawn increasing attention due to its importance in bacterial physiology and host-pathogen interactions. Here, we show that a new quinone-sensing transcriptional regulator, QsbR (quinone-stress sensing and bleomycin resistance regulator), is important for bacterial stress response and virulence in S. aureus. The mutant strain of qsbR exhibits dramatically reduced staphylococcal virulence in a murine abscess model of infection. Moreover, the qsbR mutant shows an accumulation of riboflavin and an increased resistance to quinone stress and bleomycin compared to the wild-type strain Newman. Microarray analysis confirmed that QsbR impacts the expression of genes that are involved in quinone stress response, bleomycin resistance, riboflavin biosynthesis, and pathogenesis. DNase-I footprinting and gel shift assays suggest that QsbR not only directly regulates transcription of genes involved in quinone detoxification and bleomycin resistance, but is also subject to autoregulation by binding to the palindromic consensus sequence GTATAN(5)TATAC in their promoter regions. This binding could be disrupted by quinone treatment in vitro. Mass spectrometric analysis showed that wild-type QsbR, but not QsbRC5S with Cys5 mutated to Ser, could be alkylated at Cys5 by quinone. Further mutagenesis studies revealed that Cys5 plays a key role in quinone sensing as substitution of Cys5 with Ser renders the bacterium more sensitive to quinone stress. Our results demonstrate that QsbR is a quinone-sensing regulator that dramatically impacts staphylococcal virulence and stress response.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Sample preparation for transcriptional analysis. For each strain, 2 clones were inoculated in TSB and collected from mid-log or stationary phase.  Appropriate volumes from each of the 2 cultures per strain were pooled and added to 2 volumes of RNAprotect reagent (Qiagen). Cultures were centrifuged and cell pellets were stored at 4 ºC until RNA extraction. During the experiment, OD600 and viable cfu per ml were monitored for each of the cultures. This procedure was repeated 2 independent times to generate 2 samples at each time point for each strain.

first: Marcus

last: Jones

first: Quanjiang

last: Ji

first: Fei

last: Sun

first: Taeok

last: Bae

first: Chuan

last: He


title: Human hepatocellular carcinoma: primary tumor vs.lung metastasis

status: Public on Jan 24 2012

city: Shanghai

first: Wei-Zhong

last: Wu

address: Fenglin Rd 180, Xuhui district

department: Zhongshan Hospital

institute: Fudan University

summary: microRNA exprssion profiling of HCC comparing primary tumor with lung metastasis. To explore differentially expressed microRNAs involved in process of HCC metastasis, and identify their biological functions.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition experiment, primary tumor specimens vs. lung metastasis specimens. Biological replicates: 3 primary tumor replicates, 3 lung metastatic replicates. One replicate per array.

first: Wei-zhong

first: Zhong-hua

last: Tao

first: Wei-wei

last: Li

first: Jin-liang

last: Wan


title: Gene expression analysis of hemizygous or heterozygous KIT exon 11 deletions NIH3T3 infected cells

status: Public on Jan 01 2012

city: GENEVE

first: Séverine

last: TABONE-EGLINGER

address: 1 rue Michel Servet

institute: Centre Médical Universitaire

summary: Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) of one sample of WT, D6, D54, WT/D6, WT/D54 and MIGR NIH3T3 cells, cultivated in the four different conditions (SCF+, SCF- and imatinib 1 or 5 µM), were used for the analysis of differential gene expression. Our aim was to choose the best candidate genes for low density array analysis. We first selected genes differentially expressed between WT and hemizygous samples grown in the SCF+ condition, whose fold change was superior or equal to 2 and whose expression for at least one of the sample was greater than 1.3 (commonly admitted threshold for low density arrays). We selected then 83 and 126 genes more that were differentially expressed between D6 and D54 cell lines (fold change ≥ 2; gene amplification > 1.3) in SCF+ or SCF- condition, respectively. Finally we obtained a list of 235 genes in which 94 were available for Taqman® low density array (Applied®).

overall_design: We have 6 samples per group: NIH3T3 MIGR (empty vector), NIH3T3 KIT wild-type (WT), NIH3T3 KIT del557-558 (D6), NIH3T3 KIT del564-581 (D54), NIH3T3 KIT WT/ KIT D6 and NIH3T3 KIT WT/KIT D54. All these samples were included in each of the 4 groups: culture medium without Stem Cell Factor (SCF-), culture medium with SCF (SCF+), culture medium with SCF and imatinib 1µM (STI 1µM), and culture medium with SCF and imatinib 5µM (STI 5µM). We analyzed each sample in one array.

last: Tabone-Eglinger

first: Jean-Baptiste

last: Bachet

first: Sophie

last: Dessaux

first: Anthony

last: Besse

first: Sabrina

last: Brahimi

first: Frédéric

last: Subra

first: Jean-François

last: Emile

first: Jean-Yves

last: Blay

first: Laurent

last: Alberti


title: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-CaUre2

city: Bethesda

first: Huei-Fung

last: Tsai

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

summary: [URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.

overall_design: Two groups (WT and ure2 mutants) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.


title: Gene expression of ovary and neural complex in adult Ciona intestinalis

status: Public on Nov 05 2011

city: Onnna, Kunigami

first: Takeshi

last: Kawashima

state: Okinawa

country: Japan

institute: Okinawa Institute of Science and Technology

summary: To compare with new Ciona intestinalis microarray NimbleGen 135k, we peformed gene expression analysis of GPL14686. Total RNAs from common samples with a part of NimbleGen's analysis are used for this analysis.

overall_design: Ovary and Neural Complex from adult Ciona intestinalis, duplicate, 2 time points during spawning

first: H

last: Matsumae

first: M

last: Hamada


title: PhyK, PhyR, σT and σU regulons

status: Public on Dec 21 2011

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

summary: The extracytoplasmic function sigma factor σT is the master regulator of general stress response in Caulobacter crescentus, and controls the expression of its paralogue σU. This work showed that PhyR and NepR act as positive and negative regulators, respectively, of σT expression and function. Biochemical data also indicated that NepR directly binds σT and the phosphorylated form of PhyR. We also demonstrated the essential role of the histidine kinase gene CC3474, here denominated phyK, for expression of σT-dependent genes and for resistance to stress conditions. Additionally, in vivo evidence of PhyK-dependent phosphorylation of PhyR is presented. This study also identified a conserved cysteine residue (C95) present in the periplasmic portion of PhyK that is crucial for the function of the protein. Furthermore, we showed that PhyK, PhyR and σT regulate the same set of genes and that σT is apparently responsible for the direct control of its complete regulon. In contrast, σU seems to have a very modest contribution for expression of a subset of σT-dependent genes. In conclusion, this work describes the mechanism involved in the control of general stress response in C. crescentus.

overall_design: Five experimetal procedures, each of them performed in three replicates. A total of fifteen independent biological samples were used

first: R

last: Lourenço

first: C

last: Kohler

first: S

middle: L

last: Gomes


title: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)

platform_organism:
Saccharomyces cerevisiae
Candida albicans
Nakaseomyces glabratus CBS 138


title: Expression data from mouse model of plaque regression

status: Public on Oct 01 2011

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

summary: Atherosclerosis is the leading underlying cause of death worldwide. We reported a mouse model of atherosclerosis regression that involves transplanting an atherosclerotic aortic arch into a normolipidemic mouse. There, emigration of plaque foam cells occurred in a CCR7 (dendritic cell migration factor) dependent manner.  It was obvious, though, that other pathways are likely to be involved in this process. We therefore performed microarrays on laser captured macrophages isolated from the progression and regression environments. This yielded two major findings. Firstly, genes associated with the contractile apparatus (such as actin and myosin) that are responsible for cellular movement were differentially up-regulated under regression conditions with members of the cadherin family (serves in adhesion functions) being significantly down-regulated. Secondly, the most highly up-regulated gene under regression was arginase I, a classical marker of the M2 alternative activated macrophage. Further examination revealed that regression was characterized by macrophages displaying other M2 markers such as CD163, C-lectin receptor, mannose receptor, and Fizz-1. In addition, we applied recently introduced local causal pathway discovery methods to our microarray data that revealed that genes such as vinculin and ApoCII may play a role in the pathophysiology of atherosclerosis regression. Ultimately, the insights gained from the regression model and the different modes of analyses should lead to new therapeutic targets against cardiovascular disease.

overall_design: We performed microarrays on laser captured macrophages isolated from aortic arch from mouse in atherosclerosis progression and regression environments (C57Bl/6, ApoE -/-). Study was performed in two batches, with three treatment groups each: progression, regression and baseline. Profiled in the Merck/Agilent 3.0

first: Edward

last: Fisher


title: Microarray analysis in senescent chicken embryo fibroblast

status: Public on May 12 2011

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

summary: Transcriptional profiling of healthy chicken embryo fibroblast (CEF, P4) cells comparing senescent chicken embryo fibroblast (CEF, P18) cells. Goal was to identify differentially expressed genes comparing between healthy (P4) and senescent (P18) CEF cells.

overall_design: Two-condition experiment, healthy CEF (P4) vs. senescence CEF (P18). Biological replicates: 1 control CEF (P4) sample, 1 CEF (P18) experimental sample.

first: Lee

last: Jeong Yoon

first: Kong

last: Byung-Whi


title: Transcriptome analysis of hpl-2(tm1489) vs wild-type worms at mixed embryonic and third larval stages

status: Public on Nov 30 2011

city: Bern

first: Peter

last: Meister

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern

summary: Epigenetic factors guide cell fate decisions and can stabilize development by buffering environmental variation. HP1 proteins have a well-characterized role in heterochromatin packaging and gene regulation, while their function in organismal development is less well understood. Here we used genome-wide expression profiling to assess novel functions of the C. elegans HP1 homologue HPL-2 at specific developmental stages

overall_design: RNA was extracted from either mixed-stage embryos or from third larval stage worms for both wild-type N2 (Bristol) and hpl-2(tm1489) strains.

first: Sonia

last: Schott

first: Yu

last: Xiao

first: Cécile

last: Bedet

first: Sabine

last: Rohner

first: Selena

last: Bodennec

last: Molin

first: Florence

last: Solari

first: Susan

middle: M

last: Gasser

first: Francesca

last: Palladino


title: Global changes in Staphylococcus aureus gene expression in human blood provide insight into mechanisms of immune evasion and virulence

status: Public on Aug 26 2011

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Staphylococcus aureus is a leading cause of bloodstream infections worldwide.  In the United States, many of these infections are caused by a strain known as USA300.  Although progress has been made, our understanding of the S. aureus molecules that promote bacteremia and survival in human blood is incomplete.  To that end, we analyzed the USA300 transcriptome during culture in human blood, human serum, and trypticase soy broth (TSB), a standard laboratory culture media.  Notably, genes encoding several cytolytic toxins were up-regulated in human blood over time, and hlgA, hlgB, and hlgC (encoding gamma-hemolysin subunits HlgA, HlgB, and HlgC) were among the most highly up-regulated genes at all time points. Culture supernatants derived from a USA300 isogenic hlgABC-deletion strain (LACΔhlgABC) had significantly reduced capacity to form pores in human neutrophils and ultimately cause neutrophil lysis.  Compared with the wild-type USA300 strain (LAC), LACΔhlgABC had modestly reduced ability to cause mortality in a mouse bacteremia model.  On the other hand, wild-type and LACΔhlgABC strains caused virtually identical disease in a mouse skin infection model, and bacterial survival and neutrophil lysis after phagocytosis in vitro was similar between these strains.  Comparison of the cytolytic capacity of culture supernatants from wild-type and isogenic deletion strains lacking hlgABC, lukS/F-PV (encoding PVL), and/or lukDE revealed significant functional redundancy among two-component leukotoxins in vitro. These findings may explain in part the apparent limited contribution of any single two-component leukotoxin to USA300 immune evasion and virulence.

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: S. aureus strain USA300 transcriptome during culture in human blood, human serum, and trypticase soy broth (TSB): time course.

first: Natalia

last: Malachowa

first: Adeline

middle: R

last: Whitney

first: Scott

last: Kobayashi

first: Daniel

middle: E

first: Adam

last: Kennedy

first: Kevin

last: Braughton

first: Duncan

middle: W

last: Shabb

first: Binh

last: Diep

first: Henry

middle: F

last: Chambers

first: Michael

last: Otto

first: Frank

last: DeLeo


title: Gene expression profiling of in vitro matured bovine oocytes cultivated with or without cumulus cells.

status: Public on Aug 17 2011

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

country: France

institute: INRA

summary: Cumulus cells, surrounding the oocyte, play a key role in the acquisition of oocyte competence to be fertilized and to sustain early embryo development. Cumulus cells contribute to oocyte development by metabolizing energy substrates such as glutathione that may protect the oocyte from oxidative stress damages. The aim of our study was to compare transcriptomics profiles of cumulus enclosed (CEO) and cumulus denuded (CDO) oocytes after in vitro maturation.

overall_design: Global transcriptional profiling was performed using cumulus enclosed and cumulus denuded oocytes after in vitro maturation. Matured oocytes were obtained after 22h of maturation with (CEO) or without (CDO) cumulus cells and four replicates of 25 oocytes were collected for RNA extraction.  Gene expression analysis was performed by comparing CDO versus CEO oocytes that represents a total of 8 slides using a dye swap hybridisation protocol.

first: Sylvain

last: Auclair

first: Christine

last: Perreau

first: Pascal

last: Papillier

last: Marthey

first: Christelle

last: Hennequet-Antier

first: Rozenn

last: Dalbies-Tran

last: Uzbekova


title: Role of the accessory gene regulator agr in community-associated MRSA pathogenesis

status: Public on Mar 29 2011

first: Dan

last: Sturdevant

summary:
The success of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) as pathogens is due to a combination of antibiotic resistance with high virulence. However, evolution of the exceptional virulence potential of CA-MRSA is not understood. Our previous study indicated that differential gene expression contributes substantially to this process. Thus, we here investigated the role of the pivotal virulence gene regulatory system agr in the most prevalent CA-MRSA strain USA300. Using a mouse subcutaneous infection model, we show that agr is essential for the development of CA-MRSA skin infections, the most frequent manifestation of disease caused by CA-MRSA. Furthermore, genome-wide analysis of gene expression revealed significant differences in agr-dependent virulence gene regulation between CA-MRSA, HA-MRSA, and laboratory strains. Our findings demonstrate that agr functionality is critical for CA-MRSA disease and indicate that an adaptation of the agr regulon to optimize expression of a broad set of virulence determinants may have contributed to the evolution of exceptionally pronounced virulence of CA-MRSA strains.

Keywords: wild type vs mutant

overall_design: Wild type vs mutant agr strains.

first: Gordon

middle: Y

last: Cheung

first: Rong

last: Wang

first: Burhan

middle: A

last: Khan


title: Dose-dependent effects of dietary fat on development of obesity in relation to intestinal differential gene expression in C57BL/6J mice

status: Public on Apr 26 2011

first: Guido

last: Hooiveld

summary: Excessive intake of dietary fat is known to be a contributing factor in the development of obesity. In this study, we determined the dose-dependent effects of dietary fat on the development of this metabolic condition with a focus on changes in gene expression in the small intestine. C57BL/6J mice were fed diets with either 10, 20, 30 or 45 energy% (E%) derived from fat for four weeks (n=10 mice/diet). We found a significant higher weight gain in mice fed the 30E% and 45E% fat diet compared to mice on the control diet. These data indicate that the main shift towards an obese phenotype lies between a 20E% and 30E% dietary fat intake. Analysis of differential gene expression in the small intestine showed a fat-dose dependent gradient in differentially expressed genes, with the highest numbers in mice fed the 45E% fat diet. The main shift in fat-induced differential gene expression was found between the 30E% and 45E% fat diet. Furthermore, approximately 70% of the differentially expressed genes were regulated in a fat-dose dependent manner. Many of these genes were involved in lipid metabolism-related processes and were already differentially expressed on a 30E% fat diet. Taken together, we conclude that up to 20E% of dietary fat, the small intestine has an effective ‘buffer capacity’ for fat handling. From 30E% of dietary fat, a switch towards an obese phenotype is triggered. We further speculate that especially fat-dose dependently regulated lipid metabolism-related genes are involved in development of obesity.

overall_design: The proximal, middle, and distal parts of the intestine of mice fed 10, 20, 30, or 45E% dietary fat were analyzed. 10 replicates each.

first: Nicole

middle: J

last: de Wit

first: Mark

last: Boekschoten

first: Eva-Maria

last: Bachmair

first: Philip

last: de Groot

first: Isabel

last: Rubio-Aliaga

first: Daniel

last: Hannelore

last: Müller


title: Expression of time series data of spawning  with light/dark conditions for mature adult Ciona intestinalis

status: Public on Nov 01 2011

first: Takeshi

last: Kawashima

summary: Investigation of gene expression during spawning in ovary and neural complex in Ciona intestinalis.

overall_design: 2 chips of 135k 12plex NimbleGen arrays.

first: Hiromi

last: Matsumae

first: Mayuko

last: Hamada

first: Nori

last: Satoh


title: embryo 0h reference tiling array

status: Public on Nov 18 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3172
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (early embryo); Developmental Stage: Mixed stage of embryos 20dC; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue reference (early embryo)

first: Bob

last: Waterston

first: David

last: Miller

last: Gerstein

first: Mike

last: Wilson

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: embryo PVC neurons tiling array

summary:
modENCODE_submission_2500
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC2015 (engineered, target gene glr-1 tagged by dsRed); Tissue: PVC neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: ynIs40[flp-11::GFP];hdIs32[glr-1::DsRed2]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NC2015 (engineered, target gene glr-1 tagged by dsRed); temperature 25; Developmental Stage Mixed stage of embryos 20dC; Tissue PVC neurons (embryonic)


title: sciP array data

status: Public on Dec 01 2010

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

summary: Progression through the Caulobacter cell cycle is driven by the master regulator CtrA, an essential two-component signaling protein that regulates the expression of nearly 100 genes. CtrA is abundant throughout the cell cycle except immediately prior to DNA replication. However, the expression of CtrA-activated genes is generally restricted to S-phase. We identify the conserved protein SciP (small CtrA inhibitory protein) and show that it accumulates during G1 where it inhibits CtrA from activating target genes. The depletion of SciP from G1 cells leads to the inappropriate induction of CtrA-activated genes and, consequently, a disruption of the cell cycle. Conversely, the ectopic synthesis of SciP is sufficient to inhibit CtrA-dependent transcription, also disrupting the cell cycle. SciP binds directly to CtrA without affecting stability or phosphorylation; instead SciP likely prevents CtrA from recruiting RNA polymerase. CtrA is thus tightly regulated by a protein-protein interaction which is critical to cell cycle progression.

overall_design:
For the sciP depletion studies, the sciP depletion strain was grown to mid-exponential phase in rich media supplemented with xylose, synchronized, and swarmer cells released into either glucose or xylose.  Following one cell cycle, swarmers were again isolated from the two conditions and compared directly on arrays.  This was done in duplicate.

For the sciP overexpression studies, a wild type strain harboring the plasmid pJS14-Pxyl-sciP was grown to mid-exponential phase and xylose added for 2 hours.  A strain harboring an empty vector was treated identically.  The two populations were compared directly on arrays.  This was done in duplicate.

first: Kasia

middle: G

last: Gora

middle: T


title: Expression profile analysis of C. elegans intermediate sized non-coding transcriptome

status: Public on Oct 01 2010

city: Beijing

first: Yunfei

last: Wang

address: Chaoyang District, Datun Road, No. 15

institute: Institute of Biophysics, Chinsese Academy of Sciences

type: Non-coding RNA profiling by genome tiling array

summary: We detected 32230 transfrags by Tiling array Analysis Software, of which 5866 were transfrags with unknown function (TUF). These TUFs exhibited distinct chromosome location, expression and conservation  patterns.

overall_design: Six developmental and two conditional stages of C. elegans 70~500nt transcriptome. L1~L4, mature adult (MA), male (ML), dauer (DU), heat shocked (HS). GSM591423_CB2007199-L4-1.CEL is Ce25b_MF, GPL5634 is Ce25b_MR, CEL file is okay using GPL5634's cdf.

first: Jingjing

last: Chen


title: Gene expression in adipose, liver and skeletal muscle of mice fed a diet with c9, t11 conjugated linoleic acid enriched beef

status: Public on Oct 19 2010

city: Dublin

first: Helen

last: Roche

state: Belfield

address: UCD Conway Institute of Biomolecular and Biomedical Research

country: Ireland

institute: University College Dublin

summary: Conjugated Linoleic Acid (CLA) is a collective term for the positional and geometric isomers of linoleic acid. In recent years CLA has been reported to have anti-carcinogenic, anti-obesity, anti-inflammatory and anti-artherogenic effects.  The aim of this study was to determine the effects of a natural high-CLA enriched beef source on three primary insulin responsive tissues: adipose, liver and skeletal muscle.

overall_design: ob/ob mice were assigned to one of two diets: a control beef diet, low in c9, t11-CLA (control diet) or a c9, t11-CLA enriched beef diet. After a 28 day feeding trial, RNA was extracted from adipose, liver and skeletal muscle tissue and hybridized to Affymetrix microarrays.


title: Expression profiling of ccRCC samples treated with anti-VEGF therapies reveals distinct markers

status: Public on Jan 07 2011

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Metastatic renal cell carcinoma (mRCC) patients treated with anti-vascular endothelial growth factor (VEGF) therapies demonstrate promising outcomes but not all patients benefit. Factors that predict response remain to be elucidated. Nephrectomy material from 37 patients with mRCC receiving bevacizumab 6 erlotinib was used for protein and gene expression assessment. Protein lysates were subjected to reverse-phase protein array profiling. RNA extracts were used to carry out gene expression microarray-based profiling. Normalized protein and gene expression data were correlated with overall survival (OS) and progression-free survival (PFS) using univariate Cox hazard model and linear regression. Immunoblotting was carried out to validate the results. High protein levels of AMP-activated protein kinase and low levels of cyclin B1 (CCNB1) were associated with longer OS and PFS. Further validation revealed reduced expression and activation of phosphoinositide 3-kinase (PI3K) pathway components and cell cycle factors in patients with prolonged survival after therapy. Gene expression analysis revealed up-regulation of PI3K- and cell cycle-related pathways in patients with shorter PFS. The OS and PFS of bevacizumab 6 erlotinib-treated patients with renal cell carcinoma were associated with changes in expression of protein and gene expression markers related to PI3K pathway and cell cycle signaling.

overall_design:
Expression profiling of ccRCC samples post-treatment (bevacizumab plus erlotinib, or bevacizumab alone).
Note: sample 'Jonasch_R06_Tumor_3-27-08_CMM' was not used in the publication (PMID: 20089566).


title: Embryo pharyngeal muscle tiling array

status: Public on Aug 24 2010

summary:
modENCODE_submission_2548
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1293 (engineered, target gene myo-2 tagged by GFP); Tissue: pharyngeal muscle; Developmental Stage: Mixed stage of embryos 20dC; Genotype: ccIs9753[myo-2::GFP]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NC1293 (engineered, target gene myo-2 tagged by GFP); temperature 25; Developmental Stage Mixed stage of embryos 20dC; Tissue pharyngeal muscle

first: Mark


title: Pacific salmon gill samples: fate tracking in river, sampled in ocean

status: Public on Dec 31 2010

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

summary: The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues.  Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster.  A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested.  At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish.  Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus.  These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series is of gill expression profiles from the study of fish sampled and tagged in the ocean and tracked as they entered the river system and swam towards the spawning grounds.

overall_design: Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

first: Louise

last: Donnison

first: Kristi

last: Miller-Saunders


title: Genome-Wide Expression Profiling of cultured B-CLL cells

status: Public on Sep 21 2010

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

summary: Increased survival of primary B-CLL cells cultured in high cell density: Evidence for activation of pathways also induced by stromal cells.

overall_design: Expression profiles of B-CLL cells before and after three different survival-inducing culture conditions: (1) stromal cell coculture [HCo], (2) stromal cell conditioned medium [CM], (3) high cell density cultures [CD]. Controls without survival-inducing culture conditions are included [0]. Peripheral blood samples were obtained from B-CLL patients.

first: Angela

last: Schulz

first: Stephan

last: Stilgenbauer

first: Hartmut

last: Doehner

first: Peter

last: Lichter

first: Martina

last: Seiffert


title: Genome-wide identification of DAF-12 binding sites in Caenorhabditis elegans

status: Public on Apr 05 2011

city: Pittsburgh

first: Alfred

last: Fisher

address: 3471 5th Ave., Suite 500

institute: University of Pittsburgh

summary:
DAF-12 is involved in development, dauer formation, and aging in Caenorhabditis elegans. To understand how DAF-12 is involved in these biologic processes, we performed chIP-chip using a DAF-12:TAP transgene and an anti-DAF-12 antibody. We identified 1175 genomic binding sites which were located within 5 kb of 3179 genes. These genes include known DAF-12 target genes as well as new genes involved in developmental timing, microRNA function, and stress resistance.
The supplemental BED file contains all 1175 genomic binding sites described in our work.

overall_design: DAF-12:TAP transgenic worms with chIP performed using an anti-DAF-12 antibody compared to input chromatin and chIP performed using the daf-12(rh61rh411) null mutant.

first: Daniel

last: Hochbaum

first: Yue

last: Zhang

first: Carsten

last: Stuckenholz

last: Labhart

first: Vassili

last: Alexiadis

first: René

last: Martin

first: Hans-Joachim

last: Knölker


title: Embryo BAG neurons tiling array

first: DCC

last: modENCODE

summary:
modENCODE_submission_2499
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: MT17370 (engineered, target gene gcy-33 tagged by GFP); Tissue: BAG neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: nIs242[gcy-33::GFP];lin-15(n765); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain MT17370 (engineered, target gene gcy-33 tagged by GFP); temperature 25; Developmental Stage Mixed stage of embryos 20dC; Tissue BAG neurons (embryonic)

first: Bob

last: Waterston

first: David

last: Miller

first: Mark

last: Gerstein

first: Mike

last: Wilson

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: Global genetic robustness of the alternative splicing machinery in C. elegans

status: Public on Jan 01 2011

city: Haren(GN)

first: Yang

last: Li

address: Kerklaan 30

institute: Groningen Bioinformatics Center

summary: Alternative splicing is considered a major mechanism for creating multicellular diversity from a limited repertoire of genes. Different isoforms can be produced at the same time in the same cell type and their ratios can be the same or different between divergent genotypes. Here, we studied genetic variation in alternative splicing patterns in a large recombinant inbred population of C. elegans, using whole-genome tiling arrays. This experiment allowed us to detect heritable differences in gene expression with exquisite sensitivity and resolution, and we detected 435 genes with substantial heritable variation for at least one exon. Nonetheless, we find only a very small number of examples of heritable variation in alternative splicing (22 transcripts), and most of these genes co-localize with the associated genomic loci. This is in striking contrast to earlier observations in humans, which showed much less genetic robustness.

overall_design: C. elegans recombinant inbred lines were generated and genotyped as described in (Li et al. 2006). mRNA was isolated from 60 RILs reared under standard condition and hybridized to Affymetrix 1.0 C. elegans tiling arrays. The hybridization was done by ServiceXS (Leiden, The Netherlands).

first: Rainer

last: Breitling

first: L

middle: B

last: Snoek

first: K

last: van der Velde

first: Morris

last: Swertz

first: Joost

last: Riksen

first: Ritsert

middle: C

last: Jansen

first: Jan

last: Kammenga


title: Pacific salmon gill samples: fate tracking in river

first: Paul

last: Pavlidis

summary: The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues.  Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster.  A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested.  At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish.  Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus.  These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds.

first: Louise

last: Donnison

first: Kristi

last: Miller-Saunders


title: Clostridium difficile strain 630 against various strains from different hosts

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

summary: Clostridium difficile is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human C. difficile infection has markedly increased. In this study, we evaluated the genomic content of 73 C. difficile strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from C. difficile strains 630 and QCD-32g58. The sequenced genome of C. difficile strain 630 was used as a reference to define a candidate core genome of C. difficile and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining C. difficile. Absent or divergent genes in the tested strains were distributed across the entire C. difficile 630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among C. difficile strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for C. difficile.investigated by determining changes in transcript profiles when aerobic steady-state cultures were depleted of air.

overall_design:
Dye-swap experiments with genomic DNA of tested and reference strains

8383cy3.gpr- Cy3 – test, Cy5 – reference
8384cy3.gpr- Cy3 – test, Cy5 – reference
8384cy5.gpr- Cy3 – reference, Cy5 – test
8385cy3.gpr- Cy3 – test, Cy5 – reference
8385cy5.gpr- Cy3 – reference, Cy5 – test
8386cy3.gpr- Cy3 – test, Cy5 – reference
8525cy3.gpr- Cy3 – test, Cy5 – reference
8525cy5.gpr- Cy3 – reference, Cy5 – test
8527cy5.gpr- Cy3 – reference, Cy5 – test
8529cy5.gpr- Cy3 – reference, Cy5 – test
8531cy3.gpr- Cy3 – test, Cy5 – reference
8531cy5.gpr- Cy3 – reference, Cy5 – test
8533cy3.gpr- Cy3 – test, Cy5 – reference
8533cy5.gpr- Cy3 – reference, Cy5 – test
8596cy3.gpr- Cy3 – test, Cy5 – reference
8596cy5.gpr- Cy3 – reference, Cy5 – test
8694cy3.gpr- Cy3 – test, Cy5 – reference
8694cy5.gpr- Cy3 – reference, Cy5 – test

2 GPR files per Sample record except for 4 Sample records (GSM480414, GSM480417, GSM480419, and GSM480420) which have 1 GPR file each
4 GPR file for those Sample records are lost

first: Joy

last: Scaria

first: Yung-Fu

last: Chang


title: Transcriptional profile in low to high-level macrolide resistant C. jejuni strain selected from NCTC 11168

status: Public on Dec 28 2010

city: Ames

first: Haihong

last: Hao

state: IA

address: 1600 Christensen Drive

institute: Iowa State University

summary:
Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggeted that development of macrolide resistance in campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, multiple series of macrolide-resistant C. jejuni mutants were selected in vitro by stepwise exposure of C. jejuni NCTC11168 to increasing concentrations of erythromycin and tylosin. A set of the selected resistance were subjected to microarray and the the global transcriptional profile was analyzed. In this sery, DNA microarray was used to compare the gene expression profiles of  macrolide resistant strains (68E1, 68E8 and 68E64) with its parent wild-type strain NCTC11168.
The assay identified a small number of genes that showed significant changes (q-value<0.1)  in expression in the low-level macrolide resistant strain 68E1, while a large number of gene showing significant changes in intermedia-level resistant stran 68E8 and high-level resistant strain 68 E64. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protienand putative aminotransferase, while the majority of the down-regulated genes  are involved in electron transport,lipoprotein, heat shock protein and unknown function proteins. These findings suggest that there is not much change in low-level macrolide resistant C. jejuni strain. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni.
Keywords: macrolide resistant C. jejuni selected from NCTC 11168 step-wise selection.

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni. Four hybridizations were performed each with independently extracted samples of either macrolide susceptible C. jejuni NCTC11168 cDNA samples or macrolide resistant C.jejuni cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus, there were four biological replicates of each sample.

first: Zonghui

last: Yuan

first: Qijing

last: Zhang


title: Rainbow trout red blood cells (RBCs): Control vs Heat shock, repeated samples from individuals

city: Ottawa

first: Johanne

last: Lewis

state: ON

address: 30 Marie Curie

department: Biology

institute: University of Ottawa

summary: The retention of a nucleus in the mature state of fish red blood cells (RBCs), and the ability to easily collect and manipulate blood in non-terminal experiments, makes it an ideal tissue on which to study the cellular stress response in fish. Through the use of the cGRASP 16K salmonid microarray, we are currently investigating differences in RBC global gene transcription in fish held under control conditions (12C) and exposed to heat stress (one hour at 25C followed by recovery at 12C). Repeated blood sampling (via a dorsal aorta cannula) enables us to examine the individual stress response over time. Samples were taken pre-heat stress (representing individual control) and at 4 and 24 hours post heat stress (representing early and late transcriptional regulation). A total of ~3000 features had significant signal when hybridized with RBC RNA derived targets and cannulation did not have a significant effect on RBC mRNA expression at the investigated time points. Genes involved in the stress response, immune response, and apoptosis were among those showing the highest dysregulation during both early and late transcriptional regulation. Additionally, genes related to the differentiation and development of blood cells were upregulated at the twenty-four hour time point. This study enables a broader understanding of the mechanisms underpinning the stress response in fish and the discovery of novel genes that are regulated in a stress specific manner. Moreover, salmonid transcripts that are consistently dysregulated in blood in response to heat stress are potential candidates of non-lethal biomarkers of exposure to this particular stressor.

overall_design: Two condition experiment, control (11C) and heat stressed fish (one hour at 25C followed by return to 11C). Six fish in each treatment. 3 repeated samples taken from each individual at time 0, 4 hours post heat stress and 24 hours. Common reference design used, with all experimental samples (control or heat stress) combined with reference pool RBC RNA on each array.

first: Tiago

last: Hori

first: Matthew

last: Rise

first: Patrick

last: Walsh

first: Suzanne

last: Currie