title: MR-1 gene expression profiles of iron response

status: Public on Jan 13 2010

city: Oak Ridge

first: Yunfeng

last: Yang

address: 1 Bethel Valley Road

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Time-series transcriptional profiles of Shewanella oneidensis type strain MR-1 under iron depletion and repletion conditions. Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, temporal gene expression profiles were examined for iron depletion and repletion to delineate the iron response of S. oneidensis and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. In conclusion, we identified major biological pathways that were differentially expressed during iron depletion and repletion.

overall_design: Four biological replicates of S. oneidensis MR-1 cells were grown to the midlog phase (OD600 = 0.6). Samples were collected at time 0, and then at 1, 5, 10, 20, 40, and 60 min after adding 2,2'-dipyridyl to attain a final concentration of 160 uM. Thereafter, ferrous sulfate was added to final concentration of 200 uM, and cells were collected at 1, 5, 10, 20, 40, and 60 min.


title: Distribution of TrxG, RNA Pol II and associated histone marks in Sg4 cells

status: Public on Jan 08 2010

city: Piscataway

first: Yuri

middle: B

last: Schwartz

state: NJ

address: 604 Allison Rd

country: USA

institute: Rutgers University

type: Genome binding/occupancy profiling by genome tiling array

summary: PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac, H3K9ac in cultured Drosophila Sg4 cells by hybridization of ChIP products with tiling microarrays.

first: Tatyana

middle: G

last: Kahn

first: Vincenzo

last: Pirrotta


title: Distribution of PcG, TrxG, RNA Pol II and associated histone marks in ML-DmD23-c4 cells

summary: PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmD23-c4 cells by hybridization of ChIP products with tiling microarrays


title: Distribution of PcG, TrxG, RNA Pol II and associated histone marks in ML-DmBG3-c2 cells

summary: PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmBG3-c2 cells by hybridization of ChIP products with tiling microarrays.

first: Tatyna


title: Mycoplasma gallisepticum: Rlow vs. F

status: Public on Jan 07 2010

city: Storrs

first: Steven

middle: J.

last: Geary

state: CT

address: 61 N. Eagleville Rd

department: Pathobiology and Veterinary Science

institute: University of Connecticut

summary: Mycoplasma gallisepticum transcriptome comparison between in vitro grown cultures of strains Rlow and F utilizing oligo DNA microarrays.

overall_design: Two-condition experiment, Rlow vs. F strain cells.  Biological replicates: 3.  1 technical replicate per biological replicate which includes a dye swap.

middle: M

last: Szczepanek

middle: J


title: miRNA expression in C. elegans fem-2(b245ts) and fem-3(q20ts) mutants

city: Cambridge

first: Ezequiel

last: Alvarez-Saavedra

state: MA

address: 77 Massachusetts Avenue  Room 68-411

department: Biology

institute: MIT

summary: We compared animals that produce oocytes but no sperm fem-2(b245ts) to animals that produce sperm but no oocytes fem-3(q20ts). Using miRNA microarrays and we found that the mir-35-41 cluster genes were expressed to much greater extent in oogenesis than in spermatogenesis; furthermore, these miRNAs were the only C. elegans miRNAs that showed such differential germline expression.

overall_design: Total RNA was isolated from staged one day old adult populations.  The data were obtained from two biological replicates. Each oligonucleotide was printed four times. Data were scaled based on total array intensities (sum of the normalized spot intensities), and data for each sample and each gene were averaged.

first: H

middle: R

last: Horvitz


title: Genome-wide analysis of SATB1 target genes in human T helper cells: ChIP-chip

city: Turku

first: Helena

last: Ahlfors

address: Tykistökatu 6A

country: Finland

institute: Turku Centre for Biotechnology

summary: Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor induced by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. In this study, we investigated the role of SATB1 in T helper cell differentiation by performing ChIP-on-chip analysis of human cord blood CD4+ T cells cultured in Th1 and Th2 conditions. These results were combined with gene expression profiling results from human differentiating Th cells in which expression of SATB1 was downregulated by RNA interference (RNAi).Our results indicate that SATB1 regulates and is bound to sixty genes in primary human CD4+ T cells, including several IL-12 and/or IL-4 regulated factors, suggesting a role in the development or function of Th subtypes.

overall_design: Cross-linked chromatin obtained from human CD4+ T cells isolated from cord blood cultured in Th1 and Th2 conditions for 24 h was immunoprecipitated with anti-SATB1 antibody.

first: Sanjeev

last: Galande


title: Molecular profiling of temporal fossa arachnoid cysts

status: Public on Jan 06 2010

city: Bergen

first: Mads

last: Aarhus

address: Jonas Lies v 65

department: Center for Medical Genetics and Molecular Medicine

country: Norway

institute: Haukeland University Hospital

summary:
The gene expression signature of seven surgically removed intracranial temporal fossa arachnoid cysts was generated with two normal arachnoid membrane samples as control. Briefly, we used the Qiagen RNeasy minikit (QIAGEN GmbH Germany, Qiagen) to extract total RNA. After RNA quality and quantity assessment, we then constructed cDNA with RT-PCR reagents (Applied Biosystems, U.S). Gene expression microarray analysis was performed on the ABI 1700 Expression Array System (Applied Biosystems, U.S) using the Applied Biosystems Chemo luminescent RT-IVT Labeling Kit and Human Genome microarray (Applied Biosystems, U.S).
Signal intensities generated with the ABI 1700 Expression Array System (Applied Biosystems, U.S) were imported into the J-Express Pro 2.7 software (MolMine AS, Bergen, Norway), where inter-array quantile normalization was performed to minimize the effect of external variables into the data. All control spots and flagged spots were removed, leaving 33096 gene probes available for analysis. First, we performed an unsupervised hierarchical cluster analysis in which the group belonging of the samples was defined. Second, we used Significance Analysis of Microarrays (SAM) with 400 and 1000 permutations to compare AC and AM samples and generate gene lists of differentially expressed genes between these groups. With SAM the false discovery rate (FDR) of the gene lists was calculated. FDR returned the number of false positive genes present on the gene list. A measure of FDR is the Q value, which conveniently shows an estimation of the FDR in percent. In the current study only genes with a Q value <1.0 % were accepted as being differentially expressed.

overall_design: A quantile normalized data set consisting of 33096 individual gene probes for each sample was subjected to Significance Analysis of Microarrays.

first: Per

last: Knappskog

first: Morten

last: Lund-Johansen

first: Christian

middle: A

last: Helland

first: Knut

last: Wester


title: DNA microarray analysis of CfMNPV genes

city: Guelph

first: Dan-Hui

state: Ontario

address: 488 Gordon Street

department: Dept. of Molecular and Cellular Biology

country: Canada

institute: University of Guelph

summary: Temporal expression profiles of all 146 ORFs, and their complements, of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) were determined by a modified oligonucleotide based two-channel DNA microarray. Total RNA was isolated at different times post infection from Cf203 insect cells infected with CfMNPV. The cDNA was synthesized, fluorescently labeled with Cy3, and co-hybridized to the microarray chips along with Cy5-labeled CfMNPV viral genomic DNA (vgDNA), which was used as an equimolar reference standard for each gene. From the microarray data, the temporal gene expression profiles could readily be classified into four clusters based on timing of expression. Transcription of some non-coding antisense strands of the CfMNPV genes was also detected, which provided novel insights into viral gene functions.

sample_organism: Choristoneura fumiferana multiple nucleopolyhedrovirus

first: Jondavid

last: de Jong

first: E

last: Nagy

first: Basil

last: Arif

first: Peter

last: Krell


title: Generic and specific adaptative response of S. pneumoniae to challenge with three distinct antimicrobial peptides

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: To investigate the response of S. pneumoniae to three distinct antimicrobial peptides (AMPs), i.e. bacitracin, nisin and LL-37, transcriptome analysis of challenged bacteria was performed. Only a limited number of genes was found to be up- or down-regulated in all cases. Several of these common highly induced genes were chosen for further analysis, i.e. SP0385-0387, SP0912-0913, SP0785-0787, SP1714-1715 and the blp cluster. Deletion of these genes in combination with MIC determinations showed that several putative transporters, i.e. SP0785-0787 and SP0912-0913, were indeed involved in resistance to lincomycin, LL-37 and to bacitracin, nisin, lincomycin, respectively. Mutation of blp-bacteriocin production and its immunity genes resulted in an increased of sensitivity to LL-37. Interestingly, a putative ABC transporter (SP1715) protected against bacitracin and Hoechst 33342, but confered sensitivity to LL-37. A GntR-like regulator, SP1714, was identified as a negative regulator of itself and two of the putative transporters. In conclusion, we show that resistance to three different AMPs in S. pneumoniae is mediated by several putative ABC transporters, some of which have not been associated with antimicrobial resistance in this organism before. In addition, a GntR-like regulator was identified, which regulates two of these transporters. Our findings extend the undertstanding of defense mechanisms of this important human pathogen against antimicrobial compounds and points toward novel proteins, i.e. putative ABC transporters, which can be used as targets for the development of new antimicrobials.

overall_design:
Experimental design. 1 ml aliquots of S. pneumoniae D39 were used to 100 ml THY medium, and were grown at 37°C until early logarithmic phase to an OD600 of ~0.25. Subsequently, cultures were split in two and exposed to either 0.7 μg/ml bacitracin, 0.1 μg/ml nisin or 4.5 μg/ml LL-37 (end concentrations) for 15 (early response) and 30 min (late response), respectively. These concentrations of AMPs were chosen, as they are able to just inhibit growth of S. pneumoniae D39 for approximately 10%. For each AMP, three replicates were performed.
RNA isolation, cDNA preparation and hybridization. RNA was isolated from 50 ml of three independent cultures exposed to either no AMPs or to each AMP. After centrifugation, pellets were frozen in liquid nitrogen and stored at -80°C. Subsequently, pellets were suspended in 500 μl of 10 mM Tris-HCl, 1 mM EDTA pH 8.0, after which 50 μl of 10% SDS, 500 μl of phenol:chloroform:isoamyloalcohol (24:24:1), 500 mg of glass beads (Sigma,75-150 μm), 175 μl of Macaloid solution (Bentone) were added. RNA was isolated with a High Pure RNA Isolation Kit (Roche). Subsequently, cDNA was obtained from 15-20 μg of total RNA and the labeling Cy3/Cy5-dCTPs of cDNA was performed with the CyScribe Post labeling kit (Amersham Biosciences). Hybridization was carried out at 45°C for 16 h in Ambion Slide hybridyzation buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC). Slides contained replicates of amplicons of 2.087 open reading frames (ORFs) of S. pneumoniae Tigr4 and 184 unique ORFs of S. pneumoniae R6. Amplicon sequences are available on the World Wide Web at molgen.biol.rug.nl. Slides were scanned using a GeneTac LSIV confocal laser scanner (Genomics Solutions).
Data analysis. ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD) was used to analyze the data. For the processing and normalization of the data the MicroPrep software was used as described previously (74,75). Genes with p < 0.0001 and with a differential expression greather than 1.5 or 2 – fold were considered significantly differentially expressed.

first: Joanna

last: Majchrzykiewicz

first: Oscar

middle: P

last: Kuipers

first: Jetta

last: Bijlsma


title: Xylella fastidiosa 9a5c: gomesin-treated cells vs. control

city: São Paulo

first: Paulo

middle: A.

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

summary: In the xylem vessels of susceptible hosts, such as citrus trees or grapevines, Xylella fastidiosa forms biofilm like-colonies that can block water transport, which appears to correlate to disease symptoms. Besides helping host colonization, bacterial biofilms play an important role in resistance against antimicrobial agents, for instance antimicrobial peptides (AMP). Here we show that gomesin, a potent AMP from a Brazilian tarantula spider, modulates X. fastidiosa gene expression profile upon 60 min treatment with a sublethal concentration. Data from DNA microarray hybridizations revealed that among the up-regulated coding sequences (CDS), some are related to biofilm production. In addition, we show that the biofilm formed by gomesin-treated bacteria is thicker than that formed by non-treated cells or cells exposed to streptomycin. We have also observed that treatment of X. fastidiosa with sublethal concentration of gomesin before inoculation in tobacco plants correlates with reduction in CVC symptoms, an effect possibly due to trapping of bacterial cells to fewer xylem vessels given the enhancement in biofilm production. Together, our results suggest that X. fastidiosa can selectively sense a sublethal concentration of gomesin modulating its gene expression to produce a stronger biofilm that may protect itself against the toxic effects of this AMP.

overall_design: Two-condition experiment, control (PW media) vs. gomesin-treated cells. Biological replicates: 5 control, 5 gomesin-treated, independently grown and harvested. Two replicates (left and right side of slide) per array. Total of 10 slides were hibridized, including dye-swap of and two self-self experiments.

first: Andréa

middle: C

last: Fogaça


title: Discovery of common Asian copy number variants using high-resolution array CGH

city: Seoul

first: Dongwan

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Genomic Medicine Institute, Seoul National University College of Medicine

type: Genome variation profiling by genome tiling array

summary:
Discovery of common Asian copy number variants using a novel integrated high-resolution array CGH and massively parallel DNA sequencing.

We attempted to discover common Asian copy number variants (CNVs) from the DNA of 30 Asian women (10 Korean, 10 CHB (HapMap), 10 JPT (HapMap)) using a custom-designed 24M-oligonucleotide Agilent platform (1.1M X 24 slides). The reference sample for aCGH was NA10851 (HapMap CEPH). In addition to the 30 women, 3 more individuals were analyzed as controls (AK1 (Kim, J.I. et al., 2009 Nature), NA12878 and NA19240).

overall_design: 33 test samples (30 Asian women, AK1, NA12878 and NA19240 (Cy5)); NA10851 as the reference sample (Cy3); and custom-designed 24M-probes Agilent Arrays were utilized.

first: Jeong-sun

last: Seo

first: Charles

last: Lee


title: RNA abundance in wild-type and rtt109 -/- Candida albicans, with and without peroxide stress

status: Public on Jan 04 2010

city: Worcester

first: Jessica

last: Lopes da Rosa-Spiegler

address: 364 Plantation street

institute: University of Massachusetts Medical School

summary: Candida albicans is a ubiquitous opportunistic pathogen that is the most prevalent cause of hospital-acquired fungal infections. In mammalian hosts, C. albicans is engulfed by phagocytes that attack the pathogen with DNA-damaging reactive oxygen species (ROS). Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 is important for yeast model organisms to survive DNA damage and maintain genome integrity. To assess the importance of Rtt109 for C. albicans pathogenicity, we deleted the predicted homologue of Rtt109 in the clinical C. albicans isolate, SC5314. C. albicans rtt109 -/- mutant cells lack acetylated H3K56 (H3K56ac) and are hypersensitive to genotoxic agents. Additionally, rtt109 -/- mutant cells constitutively display increased H2A S129 phosphorylation and elevated DNA repair gene expression, consistent with endogenous DNA damage.

overall_design: Four independent pairs of biological replicate samples were analyzed to compare RNA levels in wild-type and rtt109 -/- cells. Two experiments were performed: first, in unperturbed cells grown in YPD and second, in cells exposed to H2O2. To account for dye effects, two of the four samples for each experiment were analyzed using Cy3 labeling of the wild-type sample and Cy5 labeling of the mutant sample; the dyes were swapped for the other two biological replicates.

last: Lopes da Rosa

first: Victor

middle: L

last: Boyartchuk

first: Lihua

last: Zhu

first: Paul

middle: D

last: Kaufman


title: Multi-component epigenetic control of pro-invasive genes in cancer cells (ChIP-chip)

status: Public on Jan 05 2010

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix.

overall_design:
Microarray probes were designed using eArray software (Agilent). Unique DNA probes specific to 486 human genes from the high density (HD) ChIP Database (Agilent) were included in each microarray. Microarray, 8x15K format, slides were custom manufactured by Agilent. Additional hybridization control probes (universal control grid LA577) were included in the arrays (Agilent). Each individual probe in the microarray was replicated 3-10 times.

MCF7 vs.U251 cells

middle: V

first: Alex

middle: Y

last: Strongin


title: E.coli DH5alpha cells: reuterin-treated vs. untreated control cells

city: East Lansing

first: Laura

last: Schaefer

state: MI

address: 6144 Biomedical Physical Sciences

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Transcriptional profiling of E. coli DH5alpha cells comparing control untreated cells with cells exposed to sublethal concentrations of reuterin (3-hydroxypropionaldehyde).

overall_design: Two-condition experiment, reuterin-treated vs. untreated control E. coli DH5alpha cells. 5 biological replicate sets of reuterin-treated vs. untreated cells which were independently grown and harvested. Each array is probed with 1 replicate set.

first: Robert

last: Britton


title: Altered expression of microRNAs in the myocardium of rats with acute myocardial infarction

city: peking

first: bing

last: shi

address: NO 39 huayuan north road

department: department of cardiology

country: China

institute: peking university third hospital

summary: MicroRNAs are important cellular components and their dysfunctions are associated with various disease. Acute myocardial infarction (AMI) is one of the most serious cardiovascular diseases. Although several miRNAs have been reported to be associated with AMI, more novel miRNAs are needed to be investigated to ascertain if they are associated with AMI.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: SD rats (180-200g) was divided into sham-control group and two days group  after AMI, seven days group  after AMI, fourteen  days group after AMI, each group has six individual  animals   total RNA was taken from the border-zone myocardium , low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V2 biochip  representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.

first: Bing

last: Shi

first: Yanhong

last: Guo

first: Wei

last: Gao


title: Gene expression profilling of metastatic melanoma cell lines

status: Public on Jan 02 2010

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

summary: Melanoma can progress rapidly from a slow-growing surgically curable lesion to aggressive metastatic disease, with high mortality and poor response to current therapies. The mechanisms underlying melanoma progression and resistance to therapeutic agents are not well understood. There are few treatment options for melanoma once it has metastasized, and new biomarkers that aid diagnosis, predict clinical outcome, and suggest new therapies are required. This aim of this study was to invesigate  the molecular basis of melanoma biology and heterogeneity by defining genomic characteristics that correlated with tumour phenotype in a novel panel of 25 cell lines derived largely from New Zealand patients with metastatic melanoma.  The goals of this study were to (i) stratify melanoma cell lines by using global gene expression profiling ; (ii) correlate gene expression profiles with invasive potential; and (iii) identify new prognostic markers and therapeutic targets that might aid clinical cancer diagnosis and management.

overall_design: Two-colour spotted oligonucleotide microarrays were used to measure global gene expression in metastatic melanoma cell lines against a common universal reference. Biological replication was achieved by performing replicate arrays on a subset of randomly selected cell lines, in which the replicate total RNA samples were isolated from different vials of cells at different passage numbers, grown by different researchers, and often in different laboratories. Further, NZM01 and NZM02 were derived from different tumours from the same patient at different surgeries, and NZM07.2 and 07.4 were derived from the NZM07 cell line. The array hybridisations were peformed in three batches. Technical replication was achieved by using intra- and inter-batch replicates with different RNA samples from 6/25 of the cell lines: NZM04, 2 x batch 1, 1 x batch 2; NZM22, 2 x batch 1; NZM40, 1 x batch 1, 1 x batch 2; NZM06, 1 x batch 1, 1 x batch 3; NZM09, 1 x batch 1, 1 x batch 2; NZM15, 1 x batch 2, 1 x batch 3.


title: Profiling expression changes caused by a segmental aneuploid in maize meristem tissues

status: Public on Jan 01 2010

city: Saint Paul

first: Irina

last: Makarevitch

state: MN

address: 1536 Hewitt Ave

institute: Hamline University

summary:
Segmental aneuploidy refers to the relative excess or deficiency of specific chromosome regions.  This condition results in gene dosage imbalance and often causes severe phenotypic alterations in plants and animals.  The mechanisms by which gene dosage imbalance effects gene expression and phenotype are not completely clear.  The effects of aneuploidy on the transcriptome may depend on the types of cells analyzed and on the developmental stage.  We performed global gene expression profiling to determine the effects of segmental aneuploidy on gene expression levels in two different maize tissues and a detailed analysis of expression of 30 genes affected by aneuploidy in multiple maize tissues.
Multiple genes demonstrated qualitative changes in gene expression due to aneuploidy, when the gene became ectopically expressed or erroneously transcriptionally silenced in aneuploids relative to wild type plants.
Our data strongly suggested that quantitative changes in gene expression at developmental transition points caused by variation in gene copy number progressed through tissue development and resulted in stable qualitative changes in gene expression patterns.  Thus, aneuploidy in maize results in alterations of gene expression patterns that differ between tissues and developmental stages of maize seedlings.

overall_design: RNA was extracted from meristem tissues of 14 day-old maize seedlings segregating for segmental trisome of a short arm of chromosome 5.  There are three biological replicates of pooled wild-type siblings and three biological replicates of pooled DpDf plants. The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5. These plants are all in the B73 inbred genetic background.

first: Carolyn

last: Harris


title: Histone H1 binding is restricted by histone variant H3.3 (FAIRE)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary:
Linker histones are involved in the formation of higher-order chromatin structure. Although linker histones have been implicated in the regulation of specific genes, it still remains unclear what their principal binding determinants are and how their repressive function in vitro can be reconciled with presumed broad binding in vivo. We generated a full genome, high resolution binding map of linker histone H1 in Drosophila Kc cells, using DamID. H1 binds at similar levels across much of the genome, both in classical euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites of active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes. Rather, all regions with low binding of H1 show enrichment of the histone variant H3.3 which itself has been linked to high nucleosome turnover. Upon knockdown of H3.3, we find that H1 levels increase at sites previously not covered with H1 with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1 at genomic sites with high rates of histone turnover. This antagonism provides a mechanism to keep diverse genomic sites in an open chromatin conformation.
For this study, we generated DamID profiles of histone H1 and RpII18 and a FAIRE profile in Drosophila Kc167 cells. Additionally, we generated H1 profiles in cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Nucleosome positioning profiles were generated in untreated cells and cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Profiles of expression changes were generated for H3.3B RNAi and H3.3A and H3.3B RNAi.

overall_design: DamID experiments for H1 and RpII18 were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Formaldehyde-assisted isolation of regulatotry elements (FAIRE) was performed in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing over non-crosslinked genomic DNA. Nucleosome positioning profiles were made by hybridizing mononucleosomal DNA over MNase digested purified genomic DNA  on 380k NimbleGen arrays with 10 bp probe spacing. Expression profiles were made as H3.3 RNAi over white RNAi cohybridizations on spotted INDAC long oligo arrays. Every experiment was done in duplicate in the reverse dye orientation.

first: Ulrich

last: Braunschweig

first: Greg

last: Hogan

first: Ludo

last: Pagie


title: Vietnam Typhoid Study

city: Stanford

first: Lucinda

last: Thompson

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

institute: Stanford University

summary:
Patient Selection: Three hospitals were involved in the study: Dong Thap Provincial and An Giang Provincial hospitals, both located in the Mekong Delta Region of Vietnam where most of the Typhoid patients were admitted, and the Hospital for Tropical Diseases, Ho Chi Minh City, where the malarial patients were admitted. Infection status of each patient was determined by blood culture for the Typhoid patients and by microscopic examination of stained thick and thin peripheral-blood slides for the patients suspected of having Malaria. Patients with blood cultures positive for S. Typhi or S. enterica serovar Paratyphi A (S. Paratyphi A) (samples designated ST) or peripheral blood smears positive for Plasmodium falciparum or Plasmodium vivax (samples designated PF) were consented and enrolled in the study. A total of 28 S. Typhi positive patients and one S. Paratyphi A positive patient were enrolled in the first phase of the study and a further 9 S. Typhi and one S. Paratyphi A positive patient were enrolled in the second phase. Nine patients with Malaria caused by P. falciparum and one caused by P. vivax were enrolled. Sixteen uninfected healthy individuals (samples designated HC) were also enrolled in the study (one sample each). The Typhoid patients were randomly chosen to receive either Azithromycin or Gatifloxicin (20mg/kg/day for 7 days) antibiotics. Uncomplicated malaria patients were treated for 3 days with Artekin (dihydroartemisinin with piperaquine phosphate). Venous blood (2.5ml) was collected for total RNA extraction into PaxGene RNA collection tubes (Qiagen) at various times. The first sample (T1) was taken immediately on admission or entry into the study, then samples were collected, 3 (T3), 6-9 (T9 for Typhoid, T7 for Malaria), and 28-45 (T28) days following entry into the study and an average of 9 months (T9M) later. The PaxGene tubes were stored at 4degC until RNA was extracted as per the manufacturers instructions. Purified RNA was shipped on dry ice to Stanford University, CA for use in Microarray analyses. Microarrays: Experimental and reference samples (Human Universal RNA reference {Stratagene}) were amplified using the MessageAmp II aRNA Kit (Ambion) as per the manufacturer's instructions. Four micrograms amplified RNA was labeled through indirect incorporation of Cy5 (experimental) and Cy3 (reference) dyes (protocols can be found at http://cmgm.stanford.edu/pbrown/protocols/index.html). The labeled probes were then mixed and hybridized to Stanford Human cDNA arrays with 42 K features. Arrays were scanned using a Genepix 4000A laser scanner and data extracted with Genepix Pro Software version 5.1 (Axon Instruments). The data were then uploaded into the Stanford Microarray Database (SMD).
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Compound Based Treatment: Drugs used for treatment
Disease State: Malaria, Typhoid or Healthy Controls
Keywords: disease_state_design

overall_design: Complex


title: Gene affected by deletion of 6S RNA in post-exponential phase

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary: Legionella pneumophila is a gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to test the hypothesis that sRNAs play a similar role in L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome.   A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which six were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed when the bacteria enter post exponential phase and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of σ70-containing RNAP. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA encoded by the ssrS gene positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA as well as many genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: The 70-mer microarray representing all annotated ORFs of L. pneumophila has been previously described (Charpentier et al., 2008). RNA was extracted from ssrS mutant strain and the wild-type strain grown to PE phase. gDNA was used as a reference channel on each slides. Labelling of samples, hybridization strategy and data acquisition were performed as described in the Methods section. Local background was removed from spot signal intensity and normalization was carried out by calculating the fraction over the total signal intensity in both channel as previously described (Faucher et al., 2006). Signal levels that were lower than background in experiments and controls were filtered out. A total of six cDNA to reference ratios were recorded for each time point. Statistical analysis between mutant and wild-type strain was performed using unpaired one-tailed student’s t-test. Genes were considered as differentially expressed if they demonstrated a ratio to control value of ±2-fold with a p < 0.001.

first: Gilgi

last: Friedlander

first: Jonathan

last: Livny

first: Hanah

last: Margalit

first: Howard

last: Shuman


title: Genetic markers of the immune response of Atlantic salmon (Salmo salar) to Infectious Salmon Anemia Virus (ISAV)

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

institute: Fisheries & Oceans Canada

summary: Infectious diseases among fish present an important economic burden for the aquaculture and fisheries industries around the world. For example, the infectious salmon anemia virus (ISAV) is known to infect farmed Atlantic salmon (Salmo salar), and results in millions of dollars of lost revenue to salmon farmers. Although improved management and husbandry practices over the last few years have minimized the losses and the number of outbreaks, the risk of new virulent isolates emerging is still a looming threat to the viability and sustainability of this industry. An understanding of the host-pathogen interactions at the molecular level during the course of an infection thus remains of strategic importance for the development of molecular tools and efficient vaccines capable of minimizing losses in the eventual case of a new outbreak.  Using a 32 k cDNA microarray platform (cGRASP), we have studied various signaling pathways and immune regulated genes, activated or repressed, in Atlantic salmon head-kidney during the course of an ISAV infection. Gene expressions were measured at 5 different time-points: 6h, 24h, 3d, 7d and 16d post infection to get an overall view of changes as they occurred in time. The earliest time points showed only a few differentially expressed genes in infected fish, relative to controls, although as time progressed, many additional genes involved in key defense pathways were up-regulated including MHC type I, beta-2 microglobulin, TRIM 25 and CC-chemokine 19. During the latest stage of the infection process, many genes related to oxygen transportation were under-expressed, which correlates well with the anemia observed prior to death in Atlantic salmon infected with virulent strains of ISAV.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon smolts from 2 families of Atlantic salmon were IP injected with either 0.1mL of 10e5 TCID50 mL-1 of virus or 0.1mL of sham solution (L15 culture medium) and divided equally in four 1000 L tanks: 2 duplicate tanks containing ISAV injected fish and 2 duplicate control tanks containing sham solution injected fish. Four fish per family were sampled immediately prior to injection. An additional two fish per family per tank (four fish per family total) were sampled at 6h, 24h, 3d, 7d and 16d post injection. Head-kidney was dissected from each fish and used for microarray analysis. ISAV infected Atlantic salmon were compared to non-infected Atlantic salmon for each time-point.

first: Mark

last: Laflamme

first: Nellie

last: Gagné


title: Microarray data from barley aleurone

city: Madison

first: Kegui

last: Chen

state: WI

address: 502 WALNUT STREET

department: Department of Agronomy

institute: University of Wisconsin

summary:
The phytohormone gibberellic acid (GA) is well known to promote seed germination in plants. One of its functions is to stimulate the production of hydrolytic enzymes in the aleurone and their secretion to the adjacent endosperm. The storage in the endosperm is thus degraded by these hydrolases into small molecules, which are utilized as nutrients for embryo growth to establish the young seedling. ABA in contrast plays antagonistic role to GA to keep seed in dormancy.
Cereal aleurone has been established as a model system to investigate giberrellin (GA) and abscisic acid (ABA) responses. Using Barley 1 GeneChip, we examined the mRNA accumulation of over 22 000 genes in barley aleurone treated with GA, ABA, GA plus ABA, and sln1 mutant.

overall_design: Barley aleurone tissues were separated from half-seed without embryo. Three independent RNA samples for each treatment including the control without any hormone were extracted and hybridized onto Affymetrix microarrays. We also did microarray in three replications for sln1 mutant aleurone without hormone treatment.

first: Li

last: Lin

first: Shulan

last: Tian

first: Charles

last: An


title: Microarray analysis of Chlorella Virus PBCV-1 Transcription during the viral lifecycle

status: Public on Jan 10 2010

city: Lincoln

first: James

last: Van Etten

state: NE

address: 4240 Fair Street

department: Plant Pathology

institute: University of Nebraska-Lincoln

summary: Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNA from poly A-containing RNA obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 (99%) of the arrayed PBCV-1 CDSs are expressed at some time in the virus life cycle in the laboratory; iii) 227 (62%) of the CDSs are expressed before virus DNA synthesis begins; iv) these 227 CDSs were grouped into two classes: 127 transcripts disappear prior to initiation of virus DNA synthesis (considered early) and 100 transcripts are still detected after virus DNA synthesis begins (considered early/late); v) 133 (36%) of the CDSs are expressed after virus DNA synthesis begins (considered late); vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor aphidicolin prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 lifecycle.

overall_design:
Time course analysis of chlorella virus PBCV-1:
cDNAs from poly A-containing RNAs isolated from cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against a reference sample on the microarrays.
Three independent biological replica, four technical replica of the genome per array.

Time course analysis of chlorella virus PBCV-1 gene expression in the presence of aphidicolin:
cDNAs from poly A-containing RNAs isolated from aphidicolin-treated cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against non-treated, infected samples from the same time points.
Three independent biological replica, four technical replica of the genome per array.

first: Giane

last: Yanai-Balser

first: Garry

last: Duncan

last: Eudy

first: David

last: Dunigan


city: Fort Worth

first: Jerry

last: Simecka

state: TX

address: 3500 Camp Bowie Blvd

department: Molecular Biology & Immunology

institute: UNT Health Science Center

summary:
Full title: Mouse Inflammatory Cytokines and Receptors Microarray-RNA profiling in lungs of WT, IFN-g-/- and IL-4-/- mice before and after Mycoplasma pulmonis infection
RNA profiling of inflammatory chemokines, cytokines and receptors in lungs of 4-6 week old wild-type, IFN-g-/- and IL-4-/- BALB/cJ mice
before and after 14-day Mycoplasma pulmonis infection

overall_design: RNA pooled from lungs of each group- Uninfected and Infected; Experiment performed twice. With 3 mice in each of the uninfected and infected groups in the first experiment and 4 mice in each group in the second experiment; comparison Mycoplasma infected  vs. uninfected mice within each strain of mice

first: Sheetal

last: Bodhankar


title: A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria

city: Auburn

last: Liles

state: AL

address: Rm 316, Rouse Life Sciences Building

department: Biological Sciences

institute: Auburn University

summary: Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction

overall_design: A ten chip study using PCR amplicons from cloned 16S rRNA genes and from diverse soil 16S rRNAs, with PCR primers specific to the Division Acidobacteria. Each chip measures the signal from 42,194 probes (in triplicate) targeting Acidobacteria division, subdivision, and subclades as well as other bacterial phyla. All samples except one (GSM464591) include 2.5 M betaine in the hybridization buffer. Pair files lost due to a computer crash.

first: Liles

last: Mark

first: Turkmen

last: Ozgur

first: Manske

last: Brian

first: Zhang

last: Mingzi

first: Rouillard

last: Jean-Marie

first: George

last: Isabelle

first: Balser

last: Teri

first: Billor

last: Nedret

first: Goodman

last: Robert M.


title: Comparative analysis of gene expression in retinal layers

city: Baltimore

first: Laszlo

last: Hackler

state: MD

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

summary: Purpose: The aim of this study was to give a comprehensive overview on spatial distribution of gene expression in the adult mouse retina and integrate this information into existing retinal gene expression databases.    Methods: Total RNA was collected by laser capture microdissection from the ganglion cell layer, inner nuclear layer, photoreceptors and the retinal pigmented epithelium of adult mice and was analyzed by oligonucleotide microarrays. The results were validated by quantitative real time PCR and in situ hybridization.    Results: The applied method resulted in good separation of cells of different retinal layers. The spatial distribution of gene expression was determined on a global scale in the retina and the RPE. Our results show good correlation with previously reported retinal gene expression and describe genes not yet characterized in the context of the retina.    Conclusions: The complexity of the vertebrate retina makes it necessary to determine not only temporal but spatial distributions of gene expression .Our work expands the already significant but still incomplete knowledge of retinal gene expression and hopefully facilitates functional characterization of key factors of retinal development and maintenance.

overall_design:
Laser capture microdissected regions of the adult mouse neuronal retina and retinal pigmented epithelium were subjected to microarray analysis. 5 conditions were investigated: ganglion cell layer (GCL,  3 biological replicates), innner nuclear layer (INL, 3 biological replicates), photoreceptor layer from Blk6 (PR-WT, 3 biological replicates) and NrlKO animals (PR-Nrl, 2 biological replicates) and retinal pigmented epithelium (RPE, 1 biological replicate). All samples are co-hybridized with a reference sample (retina). 2 or 3 technical replicates were used for each biological sample.
technical replicate - labeled-extract: GC1-1, GC1-2, GC1-3
technical replicate - labeled-extract: GC2-1, GC2-2, GC2-3
technical replicate - labeled-extract: GCpool-1, GCpool-2, GCpool-3
technical replicate - labeled-extract: INL1-1, INL1-2, INL1-3
technical replicate - labeled-extract: INL2-1, INL2-2, INL2-3
technical replicate - labeled-extract: INLpool-1, INLpool-2, INLpool-3
technical replicate - labeled-extract: PR-Nrl1-1, PR-Nrl1-2
technical replicate - labeled-extract: PR-Nrl2-1, PR-Nrl2-2, PR-Nrl2-3
technical replicate - labeled-extract: PR-WT1-1, PR-WT1-2, PR-WT1-3
technical replicate - labeled-extract: PR-WT2-1, PR-WT2-2, PR-WT2-3
technical replicate - labeled-extract: PR-WTpool-1, PR-WTpool-2, PR-WTpool-3
technical replicate - labeled-extract: RPE-1, RPE-2, RPE-3

first: Donald

last: Zack

first: Yanqin

last: Yang

first: Jiang

last: Qian


title: Transcriptional response of trematode-infected Biomphalaria glabrata during development of S. mansoni and E. paraensei

city: Albuquerque

first: Patrick

last: Hanington

state: NM

address: 1 University of New Mexico

department: Department of Biology, University of New Mexico

institute: Center for Evolutionary and Theoretical Immunology

summary:
Time series analysis of the transcriptional responses of Biomphalaria glabrata throughout the course of intramolluscan development of Schistosoma mansoni and Echinostoma paraensei.
Time series transcriptional profiling of Biompharlia glabrata comparing control uninfected M line B.glabrata with trematdoe infected groups.  The experimental groups are: Echinostoma paraensei infected and Schistoma mansoni infected at 12 hours(0.5day), 1 day, 2 days, 4 days, 8 days, 16 days adn 32 days post infection.

overall_design:
Samples: control and two trematode infected B.glabrata in a time series: 0.5, 1, 2, 4, 8, 16 and 32 days post exposure were analyzed in triplicate
Stress and immune response

first: Cheng

last: Lun

first: Coen

last: Adema

first: Eric

middle: S

last: Loker


title: Adult C. elegans: Control daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

city: POHANG

first: SEUNG-JAE

last: LEE

state: GYEONGBUK

address: SAN 31 HYOJA-DONG, NAM-GU

department: LIFE SCEICNE

institute: POHANG UNIVERSITY OF SCIENCE AND TECHNOLOGY

summary: Transcriptional profiling of adult C. elegans comparing daf-16(-); daf-2(-) animals with adult daf-2(-) animals.

overall_design: Two-condition experiment, daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi. Biological replicates: 8 daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi, independently grown and harvested. One replicate per array.

first: Seung-Jae

last: Lee

first: Coleen

middle: T

last: Murphy

first: Cynthia

last: Kenyon


title: Adult C. elegans: Control OP50 culture vs. OP50 + 2% glucose culture

summary: Transcriptional profiling of adult C. elegans comparing normally cultured control animals with adult animals that were cultured on diet supplemented with 2% D-glucose.

overall_design: Two-condition experiment, control animals vs. 2% glucose-fed animals. Biological replicates: 6 control vs. glucose-fed animals, independently grown and harvested. One replicate per array.


title: Lactate Stress in L. plantarum WCFS1

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: Cultures were grown untill an optical density of 1.0. Cells were subsequently stressed with 2000 mM Na-lactate and samples were taken in time (15, 30, and 60 minutes).

overall_design: Samples were hybridized against a reference sample taken at t=0, just before addition of lactate. Biological duplicate was performed.

first: Marc

last: Stevens

first: Douwe

last: Molenaar

last: Keerebezem


title: Detection of predicted small RNA of Legionella pneumophila

first: Sebastien

last: Faucher

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: A microarray was designed for the detection of 101 predicted sRNAs by using OligiWiz version 2.1.3 (Nielsen et al., 2003, Wernersson & Nielsen, 2005). The prokaryotic setting was used to design 50-mers probes located, when possible, at the 3’ end of the predicted genes. Probes for 10 negative controls, representing 10 genes of the L. pneumophila Paris plasmid, were also designed. Probes (Illumina) were dissolved in 50% DMSO to a final concentration of 30 uM and printed in triplicate on UltraGAPS coated glass slides (Corning) using a PerkinElmer SpotArray microarray printer. Fifteen micrograms of total RNA was labelled during cDNA synthesis using Superscript II reverse transcriptase (Invitrogen) and amino-allyl dUTP (Sigma). Bacterial genomic DNA was used as the reference channel on each slide to allow comparison of each time point and different samples (Talaat et al., 2002). Five micrograms of genomic DNA (gDNA) was labelled with amino-allyl dUTP by using Klenow fragment and random primers (Invitrogen) at 37 °C for 18 h. DNA was subsequently coupled to the succinimidyl ester fluorescent dye AlexaFluor 546 (for cDNA) or Alexa Fluor 647 (for gDNA) (Invitrogen) following manufacturer’s protocols. Hybridization and data acquisition were performed as previously described (Hovel-Miner et al., 2009).Very low density array, like the sRNA microarray used here, cannot be normalised with common procedure like total intensity or lowess. Local background was removed from spot signal intensity and the noise signal was estimated by recording the average signal intensity of 10 negative controls printed on the chip. Normalisation of signal intensity was carried out by calculating the fold increase over the noise signal value. Correlation of replicates using this normalisation procedure was ≥ 0.95.

first: Gilgi

last: Friedlander

first: Jonathan

last: Livny

first: Hanah

last: Margalit

first: Howard

last: Shuman


title: Anaerobic carbon-limited retentostat cultivation of Lactobacillus plantarum WCFS1

summary: Lactobacillus plantarum WCFS1 was grown under anaerobic carbon-limited conditions in a chemostat with complete biomass retention (retentostat). In this cultivation system, the biomass concentration progressively increases while the dilution rate is kept constant, resulting in decreased specific susbtrate availibility, and hence, a progressive decrease in the specific growth rate. During the progressive transition from growth to virtually no growth, the global changes occurring at the level of metabolism and gene expression were studied using a genome-scale metabolic model and DNA microarrays.

overall_design: Four different time-points are compared, corresponding to 4 different specific growth rates, and hence, 4 different ratios of energy used for maintenance and growth. The samples taken at the start of retentostat cultivation serves as a a reference sample, to which the three other samples (taken after 3 days, 17 days, and 31 days under retentostat conditions) are compared. No biological replicates: all samples were taken from the same retentostat fermentation.

first: Philippe

last: Goffin

first: Bert

last: van de Bunt

first: Marco

last: Giovane

first: Bas

last: Teusink

first: Jeroen

last: Hugenholtz


title: Somatic Mutation Screen of Clear Cell RCC I

city: Grand Rapids

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary:
Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/.

These samples were run at a different facility than VARI - scmmlab.com

overall_design:
Correlating gene expression profiling with mutational status
To access mutation information in these samples please query the COSMIC database with the IDs listed in GSE17895_Cancer_Genome_Project_ID.txt.gz. (http://www.sanger.ac.uk/genetics/CGP/cosmic/)


title: citrate vs nitrate Reducing cultures

summary: The effect of nitrate reduction (anaerobic cultivation in the presence of heme, vitamin K2 and nitrate) was compared with anaerobic cultivation supplemented with citrate (Lactobacillus plantarum). The medium was chemically defined medium with mannitol as main carbon source

overall_design:
Two-condition experiment, nitrate vs citrate reducing cells. Biological replicates: 4 nitrate reducing cultures, 4 citrate reducing cultures, independently grown and harvested. Two slides were used, each slide contained 8 Arrays.
Citrate reducing cultures are called reactor 1-4, Nitrate reducing cultures are called reactor A-D

first: Rob

last: Brooijmans


title: Escherichia coli colony biofilms: Interior vs. Exterior

city: SHEFFIELD

first: Joe

last: Latimer

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary: Transcriptional profiling of Escherichia coli in the biofilm mode of growth.  A comparison of the transcriptional profiles of the biofilm interior and perimeter.

overall_design: Four replicates each composed of mRNA from three separately-grown biofilms.  Biofilms were grown on nylon membranes placed on nutrient agar.

first: Robert

last: Poole


title: Transcriptional profiling across adult Anopheles gambiae age

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

institute: University of Oxford

summary: Whole genome transcription was quantified in adult female and male Anopheles gambiae atdifferent ages; 0 (0-24 h), 10, 20 and 30 days post-eclosion. The objective of the experiment was to identify genes with significant age-dependent transcription.

overall_design: One-colour gene expression arrays were run in duplicate on both male and female RNA samples at the following ages;  0 (0-24 h), 10, 20 and 30 days post-eclosion.

first: Peter

last: Cook


title: Human GI tract samples of Lactobacillus plantarum 299v

first: Michiel

last: Wels

summary: The indigenous human gut microbiota is a major contributor to the human superorganism with established roles in modulating nutritional status, immunity, and systemic health including diabetes and obesity. The complexity of the gut microbiota consisting of over 1012 residents and approximately 1000 species has thus far eluded systematic analyses of the precise effects of individual microbial residents on human health. In contrast, health benefits have been shown upon ingestion of certain so-called probiotic Lactobacillus strains in food products and nutritional supplements, thereby providing a unique opportunity to study the global responses of a gut-adapted microorganism in the human gut and to identify the molecular mechanisms underlying microbial modulation of intestinal physiology, which might involve alterations in the intestinal physico-chemical environment, modifications in the gut microbiota, and/or direct interaction with mucosal epithelia and immune cells. Here we show by transcriptome analysis using DNA microarrays that the established probiotic bacterium, L. plantarum 299v, adapts its metabolic capacity in the human digestive tract for carbohydrate acquisition and expression of exo-polysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a gut-adapted commensal microorganism in the human gut. Comparisons of the transcript profiles to those obtained for L. plantarum WCFS1 in germ-free mice revealed conserved L. plantarum responses indicative of a core transcriptome expressed in the mammalian gut and provide new molecular targets for determining microbial-host interactions affecting human health.

overall_design: Hybridization of the samples against a common reference of gDNA isolated from L. plantarum 299v

first: Maria

last: Marco

first: Maaike

last: de Vries

first: Douwe

last: Molenaar

last: Mangell

first: Siv

last: Ahrne

first: Willem

last: de Vos

first: Elaine

middle: E

last: Vaughan

last: Kleerebezem


title: Rescue of alpha-synuclein toxicity in a yeast model of Parkinson's disease

city: Cambridge

first: Linhui

middle: Julie

last: Su

address: 9 Cambridge Center

institute: Whitehead Institite for Biomedical Research

summary: Cellular toxicities of alpha-synuclein manifest through multiple pathways, including mitochondrial dysfunction and the inhibition of vesicle trafficking. Several defects can be ameliorated by small molecule suppressors that antagonize toxicity in model systems ranging from yeast to neurons. Connections between these distinct pathologies may be central to Parkinson Disease and to therapeutic strategies.  First, yeast cultures with 1 or 2 copies of human alpha-synuclein were profiled during a time series of 0 to 6 hours.  Second, to investigate any potential rescue of alpha-synuclein toxicity, one of a series of six compounds: compound 1 ((4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one); compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one); compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one); was introduced and the expression profile assayed at 4 hours.

overall_design:
For the time series, at each time point (0, 2, 4, 6 hours) three yeast samples (2-copy alpha-synuclein; 1-copy alpha-synuclein; empty vector control) were each prepared and hybridized in all three combinations (2-copy vs control; 1-copy vs control; 2-copy vs 1-copy) for that time point.

For the drug treatment, three yeast samples were grown each with 2-copy alpha-synuclein or an empty vector control, with or without one of six compounds: compound 1 ((4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one); compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one); compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone); compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one).  2-color hybridization compared (a) 2-copy vs 2-copy+compound, (b) vector vs vector+compound, or (c) 2-copy+compound vs vector+compound.

first: Esti

last: Yeger-Lotem

first: George

middle: W

last: Bell


title: Ethanol stress response in Lactobacillus plantarum WCFS1

summary: Transcriptome profiles of control Lactobacillus plantarum WCFS1 cells were compared with 8% ethanol adapted cells and with 10 min or 30 min 8% ethanol shocked cells.

overall_design: A continuous culture was performed in duplicate on medium containing ehtanol (tE). A shock experiment was performed in duplicate in which ethanol was added to a batch culture immediately after t0 (=control). The culture was sampled at time=0 (t0), time =10 min (t1) and time=30 min (t2).

first: Hermien

last: van de Veen

first: Beatriz

last: Rojo-Bezares

first: Roger

last: Bongers

first: Marcel

last: Tempelaars

first: Tjakko

last: Abee


title: Transcriptional analysis of the Neisseria gonorrhoeae Fur regulon

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

summary:
In Neisseria gonorrhoeae, Fur (ferric uptake regulator) protein regulates iron homeostasis gene expression through binding to conserved sequences in promoters of iron-responsive genes. We have expanded the gonococcal Fur regulon using a custom microarray to monitor iron-responsive gene expression throughout the growth curve combined with a genome-wide in silico analysis to predict Fur boxes (FB), and in vivo FuRTA assays to detect genes able to bind Fur.

Keywords: time course: (1hr ,2hr, 3hr, 4hr)

platform_organism:
Neisseria gonorrhoeae
Neisseria meningitidis

overall_design: The effect of iron on global gene expression was determined over a 4-h time period by comparing the RNA profile of the organism grown in iron-deplete conditions to growth in iron-replete conditions.

first: Tom

last: Ducey

first: Jeremy

last: Zaitshik

first: Joshua

last: Orvis

first: David

last: Dyer


title: MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO)

city: baltimore

first: chris

last: cheadle

address: 5200 Eastern Ave

department: SOM

institute: JHU

summary:
We describe and illustrate the use of a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO) assay using a commercial microarray platform.
ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model reveals time-dependent waves of transcription, with a transactome early after c-Myc induction that does not persist at a late, steady-state phase, when genes that are regulated by c-Myc and E2F predominate.

overall_design: Gene expression is compared at a global level across a 48 hour time course as measured for both nuclear run-on and total RNA using the Illumina microarray platform.

first: Jinshui

last: Fan

first: Chris

last: Cheadle


title: Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part C

first: Donald

last: Brown

address: 3520 San Martin Dr

department: Department of Embryology

institute: Carnegie Institution

summary:
Thyroid hormone (TH) controls the remodeling of the pancreas and the liver.  TH-induces dedifferentiation of the exocrine pancreas to a progenitor state (Proc. Nat. Acad Sci. 105, 8962-8967 (2008)) and it remodels the endocrine pancreas (Dev. Biol. 328, 384-391 (2009)). The redifferentiated frog pancreas resembles closely the pancreas of other typical vertebrates. Two pancreas arrays were carried out. The first one studied gene expression changes at different developmental stages of Xenopus laevis during metamorphosis. The second array studies gene expression changes at varying times after the addition of TH to premetamorphic tadpoles.

Keywords: co-expression design,development or differentiation design,reference design,time series design

overall_design:
Overall design: Thyroid hormone (TH) controls remodeling of the pancreas. The microarray was carried out to identify changes in gene expression at different stages of development during metamorphosis.. This is part 3, done on the 22K Xenopus platform version 2. This dataset was from pancreas of Xenopus tadpoles (NF52, NF62, and NF66). Each was made in triplicate.
Samples in all 3 parts of the study received the same thyroid hormone levels.


title: Mexican maize landraces under drought stress and recovery irrigation

city: Irapuato

first: June

last: Simpson-Williamson

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Plant Genetic Engineering

country: Mexico

institute: Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional

summary: Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation

overall_design: A dye balanced modified loop design was implemented. Two biological replicates (pooling five representative plants) representing each sampling point for each genotype were obtained for purified RNA from 120 randomly chosen seedlings.  This experiment involved a total of forty-eight (24 sets) of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across the three landraces. This design allowed us to determine differences in gene expression between the three different landraces under drought stress (10 and 17 days) and at recovery irrigation compared to irrigated controls.

first: Angela

last: Hayano-Kanashiro

first: Carlos

last: Calderon-Vazquez

first: Enrique

last: Ibarra-Laclette

first: Luis

last: Herrera-Estrella


title: The Sen1 Helicase Prevents Genome-Wide Spurious Transcription by Controlling Transcription Termination by RNAPII

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Expression profiling by genome tiling array

summary: It is currently believed that termination by RNAPII occurs differently depending whether a transcript contains or lacks a polyadenylation signal (PAS). By screening for factors deficient for PAS-dependent termination in an in vivo reporter assay, we identified Sen1, a putative helicase mainly known for its role in PAS-independent termination of snoRNAs. We show for the first time that Sen1 regulates transcription termination at protein-encoding genes genome-wide. As well, we show that Sen1 suppresses cryptic transcription genome-wide, besides being required for termination of most snoRNAs. We provide evidence that Sen1 controls termination through its helicase activity and by effectively recruiting to chromatin, factors implicated in PAS-dependent (Rna14 and Rat1) or PAS-independent termination (Nrd1). Importantly, we demonstrate that the effect on transcription termination of Sen1 and Nrd1, although similar, differ quantitatively and qualitatively. Our results suggest that in yeast, termination by RNAPII at protein encoding-genes makes use of redundant pathways.

overall_design:
[1] Expression profiling: Genome-wide expression profiling in Sen1 and Nrd1 mutants was performed using Affymetrix tiling microarrays. Termination defects and cryptic transcription were then assessed in pairwise comparisons with wild-type strains that were grown and assayed under the same conditions.
[2] Nucleosome profiling: The supplemental CEL files contain the raw hybridization signals from genome-wide nucleosome occupancy experiments in a SEN1tetO7 and a wild type strain. The .BAR files contain the normalized data for each mutant and wild-type compared to the total genomic DNA signal to identify nucleosome occupancy patterns.

first: Eduard

last: Nedea

last: van Bakel

first: Pierre-Etienne

last: Jacques

first: Daniel

last: Xia

first: Kyle

last: Tsui

first: Bernhard

last: Suter

first: Corey

last: Nislow

first: Francois

last: Robert

first: Timothy

last: Hughes

first: Jack

last: Greenblatt


title: Ocean acidification alters skeleton formation in larvae of the sea urchin Lytechinus pictus

city: San Francisco

first: Anne

last: Todgham

address: 1600 Holloway Ave

department: Biology

institute: San Francisco State University

summary: Using standard morphometric methods and gene expression profiling with a DNA microarray, we explored the impacts of high CO2 conditions on development of the sea urchin, Lytechinus pictus, a pelagic larvae that forms a calcium carbonate endoskeleton. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2 conditions based upon IPCC emissions scenarios B1 (540ppm CO2) and A1FI (970ppm CO2).

overall_design:
Larval L. pictus were cultured in seawater treated with three different concentrations of CO2. We aerated water in culture chambers with air that had been mixed to different CO2 concentrations chosen from IPCC predictions of future atmospheric CO2 levels (28). The B1 scenario, one of the most optimistic, predicts a stabilization of atmospheric CO2 levels at ~540 ppm by 2100, and the A1F1 scenario, which, reflecting a more “business as usual” scenario, predicts atmospheric CO2 levels of ~970 ppm by 2100. Compressed air (~380 ppm CO2) was used as a control condition. The culture chambers were 20 L buckets medified to allow aeration bubbles of the experimental gas to mix with and gently stir the culture water without contacting the larvae. Replacement seawater (0.35 μm filtered) was added at a constant rate of 0.5 L hr-1. Water pH of each chamber was monitored daily using a Radiometer Analytical PHM240 pH meter.
Adult L. pictus were maintained in flowing seawater at ambient temperature (~15-18 ºC) and fed kelp until use. Spawning was induced by coelomic injection of 0.5 M KCl, and eggs were collected in 0.35 μm-filtered seawater. Eggs from 5 females were combined in approximately equal concentrations. Sperm from a single male was collected in the same way, diluted with filtered seawater and added to the egg mixture; thus, all the larvae are half-siblings. Immediately following fertilization, embryos were split into 12 culture chambers providing four replicates of the three CO2 treatments.
At the 48 hour time point, a sample of 40,000 larvae was removed from each of the 8 cultures in the 380 and 970 ppm treatments and stored in1 mL Trizol at -80 ºC for later RNA analysis.
The larval cDNA samples from each treatment were competitively hybridized on each microarray following a balanced incomplete block design (BIBD) with respect to the assignment of treatments to arrays.  In this way, differential expression between all pairs of treatments is estimated with equal precision.  Although dye swaps of technical replicates were not used, treatment and dye effects are orthogonal to one another, i.e. treatment effects can be estimated independently of dye effects.

first: Gretchen

last: Hofmann

first: Katya

last: Ruggiero

first: Mary

last: Sewell

first: Michael

middle: J

last: O'Donnell

first: Latisha

middle: M

last: Hammond

first: Mackenzie

last: Zippay

first: Nann

last: Fangue


title: Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part A

first: Donald

last: Brown

summary:
Thyroid hormone (TH) controls the remodeling of the pancreas and the liver.  TH-induces dedifferentiation of the exocrine pancreas to a progenitor state (Proc. Nat. Acad Sci. 105, 8962-8967 (2008)) and it remodels the endocrine pancreas (Dev. Biol. 328, 384-391 (2009)). The redifferentiated frog pancreas resembles closely the pancreas of other typical vertebrates. Two pancreas arrays were carried out. The first one studied gene expression changes at different developmental stages of Xenopus laevis during metamorphosis. The second array studies gene expression changes at varying times after the addition of TH to premetamorphic tadpoles.

Keywords: cell cycle design,co-expression design,reference design,time series design

overall_design:
Thyroid hormone (TH) controls remodeling of the pancreas. The micro array was carried out to identify changes in gene expression between the tadpole and frog pancreas. This is part 1, done on the 44K Xenopus platform. This dataset was used only for one pancreas experiment with several data points (control, 12h, 24h, 48h and frog). Each was made in triplicate.
Samples in all 3 parts of the study received the same thyroid hormone levels.


title: A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300

status: Public on Dec 31 2009

first: Harm

last: Bakel

summary: Cwc21 (complexed with CEF1 protein 21) is a 135 amino acid yeast protein that shares homology with the N-terminal domain of human SRm300, a large serine/arginine-repeat protein shown previously to associate with the splicing coactivator SRm160. Proteomic analysis of spliceosomal complexes has suggested a role for Cwc21 and SRm300 at the core of the spliceosome. However, specific functions for these proteins have remained elusive. In this report we employ quantitative genetic interaction mapping, mass-spectrometry of tandem affinity purified complexes and microarray profiling to investigate genetic, physical and functional interactions involving Cwc21. Combined data from these assays support multiple roles for Cwc21 in the formation and function of splicing complexes. Consistent with a role for Cwc21 at the core of the spliceosome, we observe strong genetic, physical and functional interactions with Isy1, a protein previously implicated in the first catalytic step of splicing and splicing fidelity. Together, the results suggest multiple functions for Cwc21/SRm300 in the splicing process, including an important role in the activation of splicing in association with Isy1.

overall_design: S. cerevisiae mutants with single- and double-deletions for cwc21 and isy1 or cwc21 and bud13 were grown under standard conditions and genome-wide expression profiles were obtained using Affymetrix tiling microarrays. Pre-mRNA splicing defects were then assessed in pairwise comparisons with wild-type strains that were grown and assayed under the same conditions.

first: May

last: Khanna

last: van Bakel

first: Yinyi

last: Tang

first: John

middle: A

last: Calarco

first: Tomas

last: Babak

first: Grace

last: Guo

first: Andrew

last: Emili

middle: F

middle: R

first: Nevan

last: Krogan

first: Benjamin

last: Blencowe


title: Metatranscriptomic array analysis of “Candidatus Accumulibacter phosphatis”-enriched EBPR Sludge

city: Madison

first: Shaomei

last: He

address: 1550 Linden Drive

institute: University of Wisconsin-Madison

summary: Here we report a metatranscriptomic analysis of gene expression and regulation of “Candidatus Accumulibacter”-enriched lab-scale sludge during enhanced biological phosphorus removal (EBPR). Medium density oligonucleotide microarrays were generated with probes targeting most predicted genes hypothesized to be important for the EBPR phenotype. The objectives were to investigate which genes were expressed during EBPR and which genes were differentially expressed between the early stage of anaerobic and aerobic phases (defined as 15 min after acetate addition and 15 min after switching to aeration respectively).

sample_organism:
uncultured bacterium
Candidatus Accumulibacter phosphatis

overall_design:
A medium density oligonucleotide Combimatrix microarray, CustomArrayTM 12K, (Combimatrix Corporation, Mukilteo, WA) was designed by Combimatrix to target many predicted genes identified during the metabolism reconstruction of "Candidatus Accumulibacter phosphatis" and the flanking community members, bacterial community composition markers (such as 16S rRNA) and viral genes from viral metagenomic analysis of the same bioreactor. The 12,544 spots on the array consisted of 10,644 spots for user-designed probes, 326 spots for manufacture-designed quality controls, 70 spots for negative controls and 1,504 empty spots. A total of 3,548 unique probes, each with triplicate spots were randomly distributed on the array. Among them, 2,108 probes were designed to target 1,300 predicted genes from the bacterial metagenome. The remaining 1,440 probes targeted contigs from the viral metagenome. Among the 1,300 bacterial genes, 404 genes were targeted by 3 different probes and the remaining 896 genes were targeted by only one probe.
            RNA samples were collected at the early stage of anaerobic and aerobic phases (15 min after acetate addition and switching to aeration respectively). Alexa Fluor 647-labeled aRNA from the anaerobic and aerobic samples were sequentially hybridized on the microarray to perform comparison of gene expression. Briefly, after the first hybridization and imaging, the hybridized aRNA on the array was stripped off under stringent conditions. The effectiveness of stripping was verified by imaging the array. After this, a second hybridization with a different sample was hybridized to this stripped microarray. The array manufacturer indicated that an array slide could be used with good reproducibility up to four times.  The replicability of sequential uses was confirmed in our study. In this way, Alexa Fluor 647-labeled aRNA from the anaerobic and aerobic samples were sequentially hybridized on the same slide. Therefore, the comparison of gene expression profiles between anaerobic and aerobic samples was performed on two consecutive hybridizations on the same slide to minimize slide- and hybridization-dependent variation. A total of four hybridizations with alternating anaerobic and aerobic samples were applied on a single slide. Two microarray slides were used. Therefore, six pairs of such comparison on two separate slides were conducted (Hybridization 1 vs 2, 2 vs 3, 3 vs 4 on Slide 1, and Hybridization 5 vs 6, 6 vs 7 and 7 vs 8 on Slide 2).

first: Victor

last: Kunin

first: Matthew

last: Haynes

first: Hector

last: Garcia Martin

first: Natalia

last: Ivanova

first: Forest

last: Rohwer

first: Philip

last: Hugenholtz

first: Katherine

last: McMahon


title: Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli

city: Emeryville

first: Robert

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

summary: n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it.  Unfortunately, n-butanol is more toxic than ethanol to these organisms.  To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicate that n-butanol stress has components common to other stress responses and includes perturbation in respiratory functions (nuo, cyo operons), oxidative stress (sodC, katG, yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, degP, cpxPR), metabolite transport (malE, opp operon) and biosynthesis. Inducible expression of the yqhD gene was found to improve the host’s tolerance to exogenous n-butanol and confirms the role of this gene in coping with butanol stress. To survey for other potential candidates that may serve to improve host tolerance, mutant strains in several candidates which show changes at the transcript and protein levels were examined for sensitivity during butanol exposure. Chassis engineering based on these cues may be required in a high production titer, butanol-producing host.

overall_design:
This comparison is between E. coli DH1 cells treated with 0.8% n-butanol and untreated cells at 0, 30, 80, and 195 minutes after addition.  3 biological replicates were grown, total RNA was extracted, labeled, and hybridized on 3 slides for each time point.

http://www.microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1266

first: Becky

last: Rutherford

middle: H

last: Dahl II

first: Richard

last: Price

first: Peter

middle: I

last: Benke

first: Aindrila

last: Mukhopadhyay

first: Jay

last: Keasling


title: Expression analysis of wild type Fusarium verticillioides cultured in liquid media

city: Peoria

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

summary:
Investigation of whole genome gene expression level changes over time of Fusarium verticillioides wild-type in liquid fumonisin inducing media (GYAM).

Fusarium verticillioides produces a polyketide derived mycotoxin, fumonsin, over time in liquid media (Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249).

overall_design: A twelve chip study using total RNA recovered from twelve wild type cultures of Fusarium verticillioides.  Each chip measures the expression level of 13,288 genes with thirteen 60-mer probe pairs per gene.

last: Proctor

first: Daren

last: Brown


title: D. magna exposed to fluoranthene and pyrene - both as single compounds and binary mixtures

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

summary: Daphnia are an important and widely studied model species in ecological and toxicological studies throughout the world and an official (OECD) recommended test organism. Their small size, wide distribution and easy growth conditions make this an organism ideal for functional genomics based studies, including metabolic profiling and transcriptomics. In this study we used an integrated systems approach in which transcriptomic, metabolomic and energetic responses of juvenile (4 days old) daphnids were evaluated in response to exposure to two poly aromatic hydrocarbons (pyrene and fluoranthene) and binary mixtures thereof. In addition, these responses were linked to responses measured during chronic experiments (21 days) assessing survival, growth and reproductive traits. Custom Daphnia magna microarrays were used to assess transcriptomic changes. Hierarchical cluster analysis did not result in a clear distinction between the single compounds suggesting similar molecular modes of action. Cluster analysis with both the single compounds and the binary mixture treatments resulted in a separation of treatments based on differences in toxic ratios rather than component differences. Changes in the metabolic profiles of the organisms were investigated using Nuclear Magnetic Resonance spectroscopy and Gas and Liquid Chromatography Mass Spectrometry. These multivariate metabolomic datasets were analysed with Principal Components Analysis and Partial Least Squares Discriminant Analysis. The major metabolite changes responsible for the differences observed indicated a disturbance in aminosugar metabolism in all cases. The study demonstrates the potential of ’omics’ to provide screening tools for monitoring of the freshwater environment – in invertebrate species - which is reasonably rapid, cost-effective and has the potential to greatly increase the amount of information obtained from aquatic toxicology testing.

overall_design:
Two independent experiments were performed, each with two biological replicates. As a result, every treatment was measured four times with the exception of the two highest mixtures doses where we only had two available replicates. In general, a universal reference design was used in which the reference sample was a pool composed of aliquots from all samples. Dye-bias effects were accounted for by labeling two samples of every treatment with Cy3 and two with Cy5.

Exp1Rep1 (reference Cy3, sample Cy5); Exp1Rep2 (reference Cy5, sample Cy3); Exp2Rep1 (reference Cy5, sample Cy3) and Exp2Rep2 (reference Cy3, sample Cy5)

first: Nathalie

last: Dom

first: Wim

last: De Coen


title: MicroRNA expression signatures in Barrett's esophagus and esophageal adenocarcinoma

city: Houston

first: Hushan

last: Yang

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

summary: Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that frequently develops from Barrett’s esophagus (BE), a premalignant pathological change occurring in the lower end of esophagus. To identify BE patients at high risk of malignant transformation is essential to the prevention of EAC. Although microRNA (miRNA) expression signatures have been associated with the etiology and prognosis of several types of cancers, their roles in the development of EAC have not been extensively evaluated.

overall_design: We analyzed the expression patterns of 470 human miRNAs using Agilent miRNA microarray in 32 disease/normal-paired tissues from 16 patients diagnosed with BE of either low or high grade dysplasia, or EAC

first: Jian

last: Gu

first: Kenneth

last: Wang

first: Wei

last: Zhang

first: Jinliang

last: Xing

first: Zhinan

last: Chen

first: Jaffer

last: Ajani

first: Xifeng

last: Wu


title: The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue

city: St Lucia

first: Daniel

last: Aguirre de Carcer

state: QLD

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

summary: Recent advances in (meta)genomic methods have provided new opportunities to examine host-microbe-environment interactions in the human gut.  While opportunities exist to extract DNA from freshly sourced colonic tissue there are potentially valuable sources of DNA from historical studies that might also be examined.  We examined how four different tissue DNA extraction methods employed in past clinical trials might impact the recovery of microbial DNA from a colonic tissue sample as assessed using a custom designed phylogenetic microarray for human gut bacteria and archaebacteria.  While all methods of DNA extraction produced similar phylogenetic profiles some extraction specific biases were also observed.  Real time PCR analysis targeting several bacterial groups substantiated this observation.  These data suggest that while the efficacy of different DNA extraction methods differs somewhat all the methods tested produce an accurate representation of microbial diversity.  This suggests that DNA samples archived in biobanks should be suitable for retrospective analyses.

platform_organism: Bacteria Archaea

overall_design: Three technical replicates per sample (extraction method) were analysed

first: Páraic

last: Ó Cuív

first: Michelle

last: Jones

first: Eline

last: Klaassens

middle: L

last: Worthley

first: Vicki

last: Whitehall

first: Seungha

last: Kang

first: Christopher

last: McSweeney

first: Barbara

last: Leggett

first: Mark

last: Morrison


title: Staphylococcus aureus REX mutant

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

country: Germany

institute: University of Muenster

summary: The transcription level of a rex-deficient S. aureus mutant in comparison to its parental strain S. aureus SH1000 was analyzed using DNA microarrays.

overall_design:
S. aureus N315 microarrays were purchased from Scienion (Scienion AG, Berlin, Germany) and were produced by spotting 2,338 PCR products of the 2,593 ORFs comprising annotated genome of S. aureus N315 [reference identification: NC_002745] on a glass slide. Each ORF is present in duplicate on the microarray (further details can be found at http://www.scienion.com), cDNA was synthesized from total RNA with the LabelStar Array Kit from QIAGEN using the QIAGEN protocol with slight modifications: Random hexamer primer were used (Invitrogen, Karlsruhe, Germany) and Cy3- and Cy5-dCTP were purchased from Perkin-Elmer (Rodgau - Juegesheim, Germany). As recommended by Scienion, 10 µg RNA from either SH1000 or AK1 were used for cDNA synthesis. After hybridisation for 72 h, the microarrays were washed as recommended by the manufacturer.
Data analysis. The hybridized microarrays were scanned with a GenePix 4000B microarray scanner (MDS Analytical Technologies GmbH, Ismaning, Germany). A geometric raster was laid over the resulting microarray picture to distinguish the signals from the background. After localization of single spots, intensities and global background were calculated automatically. The hybridization patterns and intensities were quantitatively analyzed using the Imagene 6 software (BioDiscovery, El Segundo, CA). The replicates were averaged, and the spots identified by Imagene 6 (BioDiscovery) as flawed were omitted. The data set was normalized by application of the LOWESS algorithm. In a next step, the intensity values of all arrays for each time point as well as for all time points combined were used for t tests. Genes with a change of <0.5- or ≥2.0-fold were characterized as having significantly differing amounts of transcripts based on t tests with a P value cut-off of at least 0.05. Gene functions were assigned to the respective accession numbers and annotations as compiled on DOGAN, a web page for S. aureus N315 (http://www.bio.nite.go.jp/dogan/MicroTop?GENOME_ID=n315G1).
The parental strain SH1000 and the Rex deficient mutant AK1 were applied on full-genome microarrays to get a detailed view on the differences in the transcriptional profiles which are caused – directly or indirectly – by the introduced mutation. More specifically, expression levels were compared at five time points, covering different growth phases. To highlight the general changes in the expression profile between SH1000 and the rex mutant, the microarray data of all five time points were also analyzed in a combined way using standard statistical methods. In further experiments, we focused on those genes, which seemed to flag the general difference between the investigated strains.

first: Gunnar

last: Sander

first: Andreas

last: Uekötter

last: Seggewiß

first: Peter

last: McNamara

first: Audrey

last: Klingele

first: Simon

last: Strompen

first: Nahed

last: Al Laham

first: Susanne

last: Engelmann

first: Richard

last: Proctor

first: Karsten

last: Becker

first: Georg

last: Peters

first: Christof

last: von Eiff


title: Comparison of gene expression in the salmon parr precocious and non-precocious testis

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

summary: The objective was to compare gene expression in salmon precocious and non-precocious parr testis tissue.

overall_design: Nine microarray hybridisations were carried out in total as part of this loop design. Total RNA from 3 pools(PG1-PG3) each of 4 precocious fish testes were compared with 3 pools (NP1-NP3) each of 10 non-precocious fish testes. There were no direct dye swaps but there was overall dye balance in the loop

first: Sophie

last: Hubert

first: Allan

last: O'Keeffe

first: Aoife

last: Guiry

first: Deirdre

last: Cotter


title: Aerobic cultivation vs Respiratory conditions

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: The effect of respiration (aerobic cultivation in the presence of heme and vitamin K2) was compared with unsupplemented aerobic cultivation with Lactobacillus plantarum.

overall_design:
Two-condition experiment, aerobic vs respiring cells. Biological replicates: 3 aerobic cultures, 3 respiring cultures, independently grown and harvested. One replicate per array.  Respiring cultures are called reactor 1-3; Aerobic cultures are called reactor 4-6
In the subsequent analysis data from reactor 4 were not used. There was likely a mistake made during quenching. This was concluded as new labeling/hybridisation gave same (bad) results (128a); slide 128b was dye-swap.

first: Rob

last: Brooijmans


title: Comparison of precocious and non-precocious salmon brain

summary: The objective was to compare gene expression in salmon precocious and non-precocious parr brain tissue.

overall_design: Eight microarray hybridisations were carried out in total as part of this design. To compare brain samples total RNA from 10 individual brains (dissected of hypothalamus and pituitary) of precocious fish and 10 brains of non-precocious fish were pooled to give two pools each of five precocious (PA and PB) and non-precocious (NPA and NPB) brains. Each pool of precocious brains was compared in a dye swap experiment with each pool of non-precocious brains.

first: Denis

last: Flynn


title: SEA BREAM_CONFINEMENT

middle: Taylor

department: MRI

summary:
Juvenile gilthead sea bream of 10-15 g initial body weight were randomly distributed in eight 500-L tanks in a seawater re-circulatory system equipped with physical and biological filters, and a heat-unit system that maintained water temperature above 18-19 ºC. Fish grew from July to December at a density of 8-10 kg/m3 with an overall daily growth index of 1.9 ± 0.01. Extruded pellets (47 % protein, 21% lipid; Proaqua, Palencia, Spain) were offered to visual satiety. Feeding was stopped one day before confinement exposure, and batches of 10 fish were then transferred from two 500-L tanks to cylinder net baskets of 10-L volume  (117-123 Kg/m3), suspended each one in 90-L tanks with a high flow of seawater (10 L/min) to avoid water deterioration (Oxygen > 5 ppm; unionised ammonia < 0.02 mg/L). Fish from seven additional 500-L tanks were established as control groups, and remained undisturbed prior to sampling at zero and each sampling time. At each sampling time (1.5, 3, 6, 24, 72 and 120 h), eight fish from one control and one confinement tank were netted into a bucket to be anaesthetized with 0.1 g/L 3-aminobenzoic acid ethyl ester (MS-222). Fish were killed by cervical section and liver was taken, frozen immediately in liquid nitrogen and stored at -80 ºC until RNA isolation.  Only 6h, 72h and 120h  were analysed on the microarray. The experimental design was a reference design with the reference being prepared from a pool of all (confined and control) RNAs used in the microarray analysis. All samples were hybridised twice (except L72C5R, L120C2F, L120S4F, L24C4F) with one being the dye swap of the other.

Keywords: Time Course

overall_design: 72 samples

first: MichaelT

first: Grace

last: Davey

first: Jaume

last: Pérez-Sánchez

first: Josep

last: Calduch-Giner

first: Benoit

last: Houeix


title: Differential accumulation of small RNAs and microRNAs during ovule and fiber development in allotetraploid cotton

city: Bethesda

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

summary: To examine expression of miRNAs in cotton fiber development, we employed miRNA microarrays and compared miRNA accumulation level in cotton fibers, cotton leaves and mutant fibers.

overall_design: A total of 9 hybridization intensities in three biological replicates per miRNA were obtained.

first: Zengjian

last: Chen

first: Mingxiong

last: Pang

first: Andrew

last: Woodward

first: Vikram

last: Agarwal

first: Xueying

last: Guan

first: Vanitharani

last: Ramachandran

first: Xuemei

first: Barbara

last: Triplett

first: David

last: Stelly


title: Nonsense Mediated mRNA decay mutes the splicing defects of spliceosome component mutations

city: Los Angeles

first: matteo

last: Pellegrini

state: CA

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

summary: The role of many splicing factors in pre-mRNA splicing and the involvement of these factors in the processing of specific transcripts have often been defined through the analysis of loss of function mutants in vivo. Here we show that inactivating the nonsense mediated mRNA decay (NMD) results in an enhancement of splicing phenotypes associated with several splicing factors mutations. Tiling microarrays showed that inactivation of the NMD factor Upf1p in the prp17Δ and prp18Δ mutant strains reveals a larger spectrum of splicing defects than what is observed in the single mutants, including new transcripts previously shown unaffected by Prp17p or Prp18p inactivation. In addition, inactivation of Upf1 in the prp22-1 mutant enhances the unspliced precursor accumulation phenotype of several specific transcripts and partially suppresses growth defects associated with the prp17Δ or prp22-1 mutations. These results support the idea that RNA surveillance by NMD mutes some of the effects of splicing factors mutations and show that the roles of splicing factors and their transcripts specificity cannot be fully understood in vivo unless RNA degradation systems that degrade unspliced precursors are also inactivated.

overall_design: Three samples from the Prp17delta, Prp18delta, Prp17deltaUpf1delta and Prp18Upf1delta mutants were grown indepedently and analyzed by tiling arrays to understand the role of the NMD component Upf1 in minimizing the accumulation of unspliced RNAs generated by the Prp17delta and Prp18delta splicing mutations.

first: Tadashi

last: Kawashima

first: Matteo

first: Guillaume

last: Chanfreau