title: Zea mays B73 stress treatments on UA 70mer oligo slides (Maize oligo array version 1.3 array A and B)

status: Public on Jun 01 2008

city: Stanford

first: John

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Maize seedling transcriptome responses to six abiotic perturbations (heat, cold, darkness, desiccation, salt, UV-B) and 2 controls were analyzed
Keywords: comparitive transcriptome profiling

overall_design: Tissues were grown at Stanford University during the summer of 2005.  RNA was extracted and purified, cDNA generated, and amplified cRNA was labeled with Cy3 or Cy5 dyes from 4 biological replicates of each treatment.  Each replicate was composed of a pool of 10 similarly treated whole seedlings (with the endosperm and kernel removed).  Two types of biological controls were employed: 1) seedlings germinated under constant 26ºC temperature, with 16 h light and adequate water and 2) field grown juvenile leaf samples   Field seedlings emerged on day 6 or 7.

first: Virginia

last: Walbot

first: Darren

last: Morrow

first: Paula

last: Casati


title: An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity, Experiment B

status: Public on Jul 11 2008

city: Berkeley

first: Jason

middle: T

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

country: USA

institute: University of California, Berkeley

type: Genome binding/occupancy profiling by genome tiling array

summary:
Proper regulation of chromatin structure is necessary for the maintenance of cell type-specific gene expression patterns. The embryonic stem cell (ESC) expression pattern governs self-renewal and pluripotency. Here, we present an RNAi screen in mouse ESCs of 1008 loci encoding chromatin proteins. We identified 68 proteins that exhibit diverse phenotypes upon knockdown (KD), including seven subunits of the Tip60-p400 complex. Phenotypic analyses revealed that Tip60-p400 is necessary to maintain characteristic features of ESCs. We show that p400 localization to the promoters of both silent and active genes is dependent upon histone H3 lysine 4 trimethylation (H3K4me3). Furthermore, the Tip60-p400 KD gene expression profile is enriched for developmental regulators and significantly overlaps with that of the transcription factor Nanog. Depletion of Nanog reduces p400 binding to target promoters without affecting H3K4me3 levels. Together, these data indicate that Tip60-p400 integrates signals from Nanog and H3K4me3 to regulate gene expression in ESCs.
Keywords: ChIP-chip

overall_design: We identified genes encoding subunits of the Tip60-p400 complex in an RNAi screen of chromatin proteins in mouse embryonic stem cells (ESCs), which upon depletion resulted in a dramatic phenotype. To investigate the role of this complex in gene expression in ESCs, we performed ChIP-chip location analysis using genome-wide promoter tiling arrays. We immunoprecipitated chromatin with an antibody to p400 and competitively hybridized it to input material on two arrays with probes interrogating essentially all mouse promoters with 100 bp tiling of -3250 bp to +750 bp around the transcription start sites.

first: Thomas

middle: G

last: Fazzio

first: Barbara

last: Panning


title: Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster

status: Public on Jun 06 2008

city: Chicago

last: Emerson

state: IL

address: 1101 East 57th Street

institute: University of Chicago

type: Genome variation profiling by genome tiling array

summary:
The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection.

In order to characterize copy number polymorphisms  (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls.

Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletion

overall_design: In all, 17 lines were used in this study: 15 natural isolates derived from throughout sub-Saharan Africa; and 2 laboratory strains representing the reference genome for the tiling arrays and a line containing probes known to be duplicated and deleted.  Each line was represented by 3 array hybridizations, for a total of 51 hybridizations.  Normalization and subsequent analysis was conducted independently on 15 sets of 9 arrays.  Each set was composed of the 6 lab strains and the three replicates from one natural isolate.

first: J

middle: J

first: Margarida

last: Cardoso-Moreira

first: Justin

middle: O

last: Borevitz

first: Manyuan

last: Long


title: A temporal shift in regulatory networks and pathways in the bovine small intestine during Cooperia oncophora infection

status: Public on Jul 16 2008

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary: Cooperia oncophora is an important parasitic nematode of ruminants with a worldwide distribution. Twenty Holstein nematode-naive bull calves were experimentally infected with approximately 100,000 L3 stage infective larvae for 7, 14, 28, 42 days, respectively. The experiment was conducted in order to identify putative recognition and inflammatory pathways in the host-parasite relationship. Gene expression profiles in the small intestine were compared using a high-density bovine 60mer oligo microarray. A total of 310 sequences were differentially expressed during the course of infection (P<0.05). The pathways and regulatory networks significantly impacted by the infection were analyzed. A total of 22 canonical pathways (P<0.05) and 9 regulatory networks (P<10-10) were significantly affected by the infection. At the early phase of the infection (7 days post infection, 7dpi), the parasites suppressed acute phase response and complement system in the host. At 14dpi, three out of the six pathways impacted were related with RXR functions. When the infection progressed to 28dpi, the RXR functions started to fade away. The host response was shifted to lipid metabolism and signaling, especially eicosanoid production and signaling, suggesting eicosanoid-mediated inflammation possibly emerging as a major host defense mechanism. By 42dpi, the pathways impacted involved glycosphingolipid biosynthesis and TGFbeta signaling. The expression of cadherin-like 26 (CDH26) was strongly up-regulated starting at 14dpi and peaked at 28dpi with a ~150-fold increase. The extent of its expression is positively correlated with the infiltration of eosinophils (R =0.82), and in addition, coincides with the numbers of adult parasites in the tissue. CDH26 demonstrated an expression profile similar to two other cell adhesion molecules involved in recognition of carbohydrates on foreign organisms, collectin and galectin, suggesting it may serve as a pattern recognition molecule for Cooperia oncophora. Our results will undoubtedly provide a molecular roadmap for the future study in defining host immune responses and understanding protective immunity against gastrointestinal nematodes.

overall_design: A total of 20 arrays were used in a time series experiment. Four biological replicates (animals) were used for each time point including naive control (unfected)

first: Louis

middle: C

last: Gasbarre


title: Role of CSN5 in breast cancer (array CGH)

status: Public on Jan 18 2008

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

summary:
CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. Amplification of CSN5 is required for transformation of primary human breast epithelial cells by defined oncogenes. The transforming effects of CSN5 require CSN subunits for assembly of the full COP9 signalosome and the isopeptidase activity of CSN5, which potentiates the transcriptional activity of MYC. Transgenic inhibition of CSN5 isopeptidase activity blocks breast cancer progression evoked by MYC and RAS in vivo. These results highlight CSN5 isopeptidase activity in breast cancer progression, suggesting it as a therapeutic target in aggressive human breast cancers.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Keywords: strain_or_line_design

overall_design: Computed


title: The Study of Gene Expression Profiles of KG-1 Cells Treated with Antrodia Camphorata Extracts using cDNA microarray.

status: Public on Nov 18 2008

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary:
Antrodia Camphorata is well known in Taiwan as a folk medicinal fungus with anticancer and anti-inflammatory effects. In this study, we used a human acute myelogenous leukemia cell line, KG-1, as the experimental model and constructed a high-throughput gene screen integrated platform by using a combination of herbal identification, UV-VIS spectrophotometry, high performance liquid chromatography (HPLC), inductively coupled plasma mass spectrometry (ICPMS), and DNA microarray technology. Based on this science-based platform, we developed a practical quantitative method and also established an organic/inorganic chemical fingerprint for the herbal materials. In the mean while, the global gene expression patterns of the KG-1 cells treated with various A. camphorata mycelia extracts (water and methanol extracts) were compared. Furthermore, several possible biological responses and relevant marker gene would be identified by our high-throughput integrated platform.
Keywords: KG-1 treated with AC extracts for 4 days, cDNA microarray, biomarker selection.

overall_design: We used optimal loop design to calculate the gene expression profile. In this design, we used labeled RNA from each sample to labeled three slides for a total of nine arrays. Therefore, the data computations were consisted of 18 measurements (6 samples with 3 replicates) for each of 7334 genes. Besides, duplicated water-treatment samples were used as internal control

first: WaiYi

last: Peng

first: MingLong

last: Tsai

first: ChihYing

last: Hsu


title: M. sedula transcriptional response to ferrous iron and RISC supplements

status: Public on Oct 22 2008

city: Raleigh

first: Kathryne

middle: Sherlock

last: Auernik

state: NC

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Abstract: The crenarchaeal order Sulfolobales collectively contains at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. While specific respiratory complexes in certain Sulfolobales have been characterized previously as proton pumps for maintaining intracellular pH and generating proton motive force (pmf), their contribution to sulfur and iron biooxidation has not been considered. For M. sedula growing in the presence of ferrous iron and reduced inorganic sulfur compounds (RISCs), global transcriptional analysis was used to track the response of specific genes associated with these complexes, as well as other known and putative respiratory electron transport chain elements. ORFs from all five terminal oxidase or bc1-like complexes were stimulated on one or more conditions tested. Components of the fox (Msed0467-0489) and soxNL-cbsABA (Msed0500-0505) terminal/quinol oxidase clusters were triggered by ferrous iron, while the soxABCDD' terminal oxidase cluster (Msed0285-0291) were induced by tetrathionate and S°. Chemolithotrophic electron transport elements, including a putative tetrathionate hydrolase (Msed0804), a novel polysulfide/sulfur/DMSO reductase-like complex (Msed0812-0818), and a novel heterodisulfide reductase-like complex (Msed1542-1550), were also stimulated by RISCs. Furthermore, several hypothetical proteins were found to have strong responses to ferrous iron or RISCs, suggesting additional candidates in iron or sulfur oxidation-related pathways. From this analysis, a comprehensive model for electron transport in M. sedula could be proposed as the basis for examining specific details of iron and sulfur oxidation in this bioleaching archaeon.

overall_design: 5-slide loop of Mse cells includes 5 conditions tested: yeast exact (Y), yeast extract + ferrous sulfate (YFS), yeast extract + potassium sulfate (YKS), yeast extract + potassium tetrathionate (YKT), and yeast extract + elemental sulfur (YS). Half of an RNA sample for one condition was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 replicates; spot intensities for all replicates on slide provided in associated raw data file).

middle: M

last: Kelly


title: Aberrant gene expression patterns in placentomes of cattle cloned by somatic cell nuclear transfer

status: Public on Dec 21 2007

city: Champaign

first: Robin

middle: Edward

last: Everts

address: 1201 West Gregory Drive

department: Animal Sciences

institute: UIUC

summary:
Transcription profiling of placentomes derived from somatic cell nuclear transfer (SCNT), in vitro fertilization (IVF) and artificial insemination (AI) at or near term development was performed in order to better understand why SCNT and IVF often result in placental defects, hydrops and large offspring syndrome (LOS).  Multivariate analysis of variance was used to distinguish the effects of SCNT, IVF and AI on gene expression, taking into account the effects of parturition, sex of the fetus, breed of dam, breed of fetus and disease status of the offspring.  The differential expression of 21 physiologically important genes was confirmed using quantitative PCR.  The largest effect on placentome gene expression was attributable to whether placentae were collected at term or preterm (whether the collection was due to disease or to obtain matching case-controls) followed by placentome source (AI, IVF or SCNT).  Gene expression in SCNT placentomes was dramatically different from AI (N=336 genes; 276 >2-fold) and from IVF (N=733 genes; 162 >2-fold) placentomes.  Functional analysis of differentially expressed genes (DEG) showed that IVF has significant effects on genes associated with cellular metabolism.  In contrast, DEG associated with SCNT are involved in multiple pathways, including cell cycle, cell death, gene expression, posttranslational modification, molecular transport and connective tissue development.  Many DEG were shared between the gene lists for IVF and SCNT comparisons, suggesting that common pathways are affected by the embryo culture methods used for IVF and SCNT.   However, the many unique gene functions and pathways affected by SCNT suggest that cloned fetuses may be starved and accumulating toxic wastes due to placental insufficiency caused by reprogramming errors.   Many of these genes are candidates for hydrops and LOS.
Keywords: gene expression; development; SCNT; cloning; nuclear transfer; IVF; AI

overall_design:
In total 38 placentome samples from AI, IVF,and SCNT were used for expression profiling using a 13,257-element bovine oligoarray.  All samples were hybridized to the oligoarray in duplicate using a reference design and a dye swap (total arrays hybridized and analyzed is thus 76).  Data analysis was performed using a mixed model approach in SAS software.  The obtained P-values were corrected using the Fals Discovery rate approach.

Note: in the data files, the normalized ratio is given as Cy5/Cy3 and should thus be reversed for the dye swaps.  These are all the files where the sample is labeled in Cy3 and the reference in Cy5

Note: Normalized log2 ratios only mean that instead of raw ratios the ratios are adjusted to fit the normal distribution. No other normalization has been performed.

middle: E

first: Pascale

last: Chavatte-Palmer

first: Anthony

last: Razzak

first: Isabelle

last: Hue

first: Cheryl

middle: A

last: Green

first: Rosane

last: Oliveira

first: Xavier

last: Vignon

first: Sandra

middle: L

last: Rodriguez-Zas

first: Xiuchun

last: Tian

first: Xiangzhong

last: Yang

first: Jean-Paul

last: Renard

first: Harris

last: Lewin


title: RpoS regulation of gene expression during exponential growth of E. coli K-12

status: Public on Dec 28 2007

city: Hamilton

first: Herb

last: Schellhorn

state: ON

address: 1280 Main St. W.,

department: Biology

country: Canada

institute: McMaster University

summary:
This study is to identify the RpoS regulon in MG1655 in early exponential growth. RNA samples from wild type or rpoS mutants were extracted using acidic hot phenol method and hybridized to Affymetrix E. coli Antisense Genome Array.
Keywords: Define regulon of RpoS

overall_design: A precise rpoS deletion mutant of MG1655 was constructed using the red recombinase method. Wild type and rpoS mutants were inoculated in triplicate into LB media at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at an OD600 = 0.3 after being maintained in exponential phase for at least eight generations. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol (65C) to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Antisense Genome Array according to Affymetrix's standard protocols.

first: Tao

last: Dong

first: Mark

last: Kirchhof


title: The microRNAs miR-373 and miR-520c promote tumor migration, invasion and metastasis

status: Public on Dec 04 2007

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary:
MicroRNAs (miRNAs) are single-stranded noncoding RNAs that play important roles in many biological processes. Although the oncogenic and tumor suppressive functions of several miRNAs have been characterized, the role of miRNAs in mediating tumor metastasis was only recently addressed and still remain largely unexplored. To identify potential metastasis-promoting miRNAs, we set up a genetic screen using a non-metastatic human breast tumor cell line that was transduced with a miRNA expression library and subjected to a trans-well migration assay. We found human miR-373 and 520c to stimulate cancer cell migration as well as tumor cell invasion in vitro and in vivo, and that certain cancer cell lines depend on endogenous miR-373 activity to migrate efficiently. Mechanistically, the migration phenotype of miR-373 and miR-520c can be explained by their suppression of CD44 expression. Finally, we found significant up-regulation of miR-373 expression in clinical breast cancer primary and metastasis samples that inversely correlated with CD44 expression. Taken together, our study indicates that miRNAs are involved in tumor migration and invasion and implicates miR-373 and conceivably miR-520c as metastasis-promoting miRNAs.
Keywords: human breast cancer cell MCF7 vs MCF7 expressing miR-373 vs MCF7 expressing miR-520c

overall_design: Illumina human v6 array was used for MCF7 cells, MCF7 cells stably expressing miR-373 and MCF7 cells stably expressing miR-520c. Triplicate samples were used to performe gene expression analysis on each cell lines.

first: Qihong

last: Huang

first: Kiranmai

last: Gumireddy

first: Mariette

last: Schrier

first: Carlos

last: le Sage

first: Remco

last: Nagel

first: Suresh

last: Nair

first: David

last: Egan

first: Anping

last: Li

first: Guanghua

first: Andres

last: Klein-Szanto

first: Phyllis

last: Gimotty

first: Dionyssios

last: Katsaros

first: George

last: Coukos

first: Lin

last: Zhang

first: Ellen

last: Pure

first: Reuven

last: Agami


title: RSC Regulates Nucleosome Positioning at Pol II Genes and Density at Pol III Genes

status: Public on Dec 01 2007

city: Salt Lake City

first: Timothy

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

summary:
Nucleosomes restrict the access of transcription factors to chromatin. RSC is a SWI/SNF-family chromatin-remodeling complex from yeast that repositions and ejects nucleosomes in vitro. Here, we examined these activities and their importance in vivo. We utilized array-based methods to examine nucleosome occupancy and positioning at more than 200 locations in the genome following the controlled destruction of the catalytic subunit of RSC, Sth1. Loss of RSC function caused pronounced and general reductions in transcription from Pol I, II, and III genes. At Pol III genes, Sth1 loss conferred a general gain in nucleosome density and an accompanying reduction in RNA Pol III occupancy. In contrast, we observed primarily single nucleosome changes, including movement, at Pol II promoters. Importantly, a greater number of changes were observed near the transcription start sites of RSC-occupied promoters than non-occupied promoters. These changes are distinct from those due to general loss of transcription. Thus, RSC action affects both nucleosome density and positioning in vivo, but applies these remodeling modes differently at Pol II and Pol III genes.
Keywords: ChIP-chip, nucleosome, mononucleosome, RSC, transcription

overall_design: To examine chromatin remodeling that was dependent upon RSC, we generated a customized microarray platform that focused on known RSC targets. This array (GPL5637) sampled 218 specific loci in the genome at relatively high resolution to monitor nucleosome occupancy. We first confirmed the design of the array by performing ChIP against two subunits of RSC. Since the Sth1 degron allele used in our studies is degraded under specific growth conditions, we also performed RSC ChIP under mock degradation conditions (mock-after). We next analyzed the chromatin structure of RSC target genes in the absence of RSC function. In these experiments, we compared microarray results between two strains: the Degron strain, which allows for RSC inactivation, and the Control strain, which prevents RSC inactivation. We analyzed chromatin structure using two approaches. First, general histone occupancy was examined by performing ChIP against histone H4. Second, we hybridized DNA from mononucleosomes that were released by micrococcal nuclease digestion to examine single nucleosome events, including movement, gain, and loss. We also examined the occupancy of RNA Polymerase III by ChIP. Finally, we examined single nucleosome occupancies by mononucleosome hybridization in a RNA Polymerase II mutant, rpb1-1, at both permissive and non-permissive temperatures.

first: Jason

last: Huff

first: Bradley

middle: R

last: Cairns


title: Molecular Signature of MT1-MMP: Transactivation of the Downstream Universal Gene in Cancer

status: Public on Jun 11 2008

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Genome-wide expression profiling of MT1-MMP–overexpressing versus MT1-MMP–silenced cancer cells and a further data mining analysis of the preexisting expression database of 190 human tumors of 14 cancer types led us to identify 11 genes, the expression of which correlated firmly and universally with that of MT1-MMP (P < 0.00001).

overall_design: We specifically selected HT1080 cells (HT cells)for our studies because these cells express MT1-MMP naturally. To increase the MT1-MMP expression, we transfected HT cells with MT1-MMP-WT and isolated a pool of the stably transfected HT-MT cells. As a control, we used HT-neo cells transfected with the original plasmid. To silence MT1-MMP, we transfected HT cells with the siRNA construct and isolated HT-siRNA cells. As a second control, we isolated HT-siRNAscr cells which were selected after stable transfection of HT cells with the scrambled siRNA.

first: Dmitri

middle: V

last: Rozanov

first: Alexey

middle: Y

last: Savinov

first: Kang

last: Liu

first: Vladislav

last: Golubkov

first: Stan

last: Krajewski

first: Alex

last: Strongin


title: Antidepressant actions of the exercise-regulated gene VGF

status: Public on Nov 30 2007

city: Bethesda

first: Joshua

last: Hunsberger

address: 35 Convent Drive MSC3711

institute: NIH

summary:
Gene profiling hippocampal mRNA from 1 week sedentary mice vs. 1 week voluntary exercise mice.
Keywords: Exercise study.

overall_design: Two-condition experiment, Sedentary vs. Exercise. Biological replicates: 4 sedentary, 4 exercise. One replicate per array.

first: Samuel

last: Newton

first: Alicia

last: Bennett

first: Catharine

middle: H

last: Duman

first: David

last: Russell

first: Stephen

last: Salton

first: Ronald


title: Profiling of sex-biased expression in Drosophila species

status: Public on Nov 08 2007

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

type: Expression profiling by genome tiling array

summary:
Extensive sex-biased expression has been seen in multiple surveys D. melanogaster. We were interested in broadly sampling sex-biased expression of orthologs and species- or lineage-specific genes in the Drosophila genus. To appropriately assay gene expression in multiple species, we used custom microarrays designed against each of six species that broadly sample the phylogenetic space represented by the newly completed genomes (D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis) and an array designed against D. melanogaster to determine the overall patterns of sex-biased expression in those species and their chromosome linkage.
Keywords: other

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba

overall_design: PolyA+ mRNA in duplicate were isolated from 5-7 day old adult females and males of seven drosophila species. Male and female mRNA was labeled by Cy3 or Cy5 dye separately and hybridized simultaneously to the appropriate species-specific arrays. We performed at least four two-channel hybridizations for each species including two biological replicates and dye-swaps for each of them. Only single channels which passed stringent pre-processing quality control were used. A total of 67 channels of data were used in the final analysis.

last: Sturgill

first: Yu

last: Zhang


title: Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss).

status: Public on Nov 02 2007

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

summary:
BACKGROUND: Fast, efficiently growing animals have increased protein synthesis and/or reduced protein degradation relative to slow, inefficiently growing animals. Consequently, minimizing the energetic cost of protein turnover is a strategic goal for enhancing animal growth. Characterization of gene expression profiles associated with protein turnover would allow us to identify genes that could potentially be used as molecular biomarkers to select for germplasm with improved protein accretion. RESULTS: We evaluated changes in hepatic global gene expression in response to 3-week starvation in rainbow trout (Oncorhynchus mykiss). Microarray analysis revealed a coordinated, down-regulated expression of protein biosynthesis genes in starved fish. In addition, the expression of genes involved in lipid metabolism/transport, aerobic respiration, blood functions and immune response were decreased in response to starvation. However, the microarray approach did not show a significant increase of gene expression in protein catabolic pathways. Further studies, using real-time PCR and enzyme activity assays, were performed to investigate the expression of genes involved in the major proteolytic pathways including calpains, the multi-catalytic proteasome and cathepsins. Starvation reduced mRNA expression of the calpain inhibitor, calpastatin long isoform (CAST-L), with a subsequent increase in the calpain catalytic activity. In addition, starvation caused a slight but significant increase in 20S proteasome activity without affecting mRNA levels of the proteasome genes. Neither the mRNA levels nor the activities of cathepsin D and L were affected by starvation. CONCLUSION: These results suggest a significant role of calpain and 20S proteasome pathways in protein mobilization as a source of energy during fasting and a potential association of the CAST-L gene with fish protein accretion.
Keywords: Stress response

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: We evaluated changes in hepatic global gene expression in response to 3-week starvation in rainbow trout.  Microarray analysis revealed a coordinated, down-regulated expression of protein biosynthesis genes in starved fish.  In addition, genes of lipid metabolism/transport, aerobic respiration, blood functions and immune response were decreased in response to starvation.  However, the microarray approach did not reveal a significant increase of gene expression in protein catabolic pathways.  Further studies using real-time PCR and enzyme activity assays were performed to investigate the gene expression patterns of the major proteolytic pathways, cathepsins, calpains and the multi-catalytic proteasome.  Feed restriction reduced mRNA accumulation of the calpain inhibitor, calpastatin (CAST), with a subsequent increase in the calpain catalytic activity.  In addition, starvation caused a slight but significant increase in 20S proteasome activity without affecting mRNA levels of the proteasome genes suggesting a post-transcriptional action.  Starvation did not affect activities or mRNA accumulation of cathepsin D and L.

first: Jeff

last: Silverstein

first: Caird

last: Rexroad III

first: Jianbo

last: Yao


title: Gene expression profiles of 25 normal human tissues

status: Public on Nov 14 2007

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

summary:
We performed microarray experiments to identify genes specifically expressed in human tissues and investigated association of recombination rates with the tissue-specific genes.
Keywords: Human tissue comparison

overall_design:
Microarray was used to produce a transcriptional profile of normal human tissues representing 25 distinct tissue types.
A reference sample (universal tissue mix) was prepared by mixing an equal amount of aRNA from each tissue. All samples used pooled RNA from at least 3 people.  Two independent replicates were obtained using dye-swap. Normalization was performed with LOWESS method.

first: Mamoru

last: Kato

first: Emi

last: Okutsu

first: Yonehiro

last: Kanemura

first: Tatsuhiko

last: Tsunoda


title: Genomic and Proteomic Analysis of the Alkaline-Tolerance Response (AlTR) in Listeria monocytogenes 10403S

status: Public on Jul 25 2007

city: Normal

first: Arunachalam Muthaiyan

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

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary:
Information regarding the Alkaline Tolerance Response (AlTR) in Listeria monocytogenes is very limited. In this study, L. monocytogenes was shown to exhibit a significant adaptive alkaline tolerance response (AlTR) following a 1-h exposure to mild alkaline (pH 9.5), which is capable of protecting cells from subsequent lethal alkali stress (pH 12.0).  Treatment of adapted cells with protein synthesis inhibitor chloramphenicol has revealed that AlTR is at least partially protein-dependent. In order to gain a more comprehensive perspective on the physiology and regulation of AlTR, we compared differential gene expression and protein content at pH 9.5 using microarray and two-dimensional (2D) gel electrophoresis, (combined with mass spectrometry) respectively. By interfacing the results of both approaches this study showed strong evidence that alkali tolerance response in L. monocytogenes functions as to minimize excess alkalisation and energy expenditures while mobilizing available carbon sources. Adaptive intracellular gene expression involved genes that are associated with virulence, the general stress response, cell division, and changes in cell wall structure and included many genes with unknown functions.  The variability observed between results of cDNA arrays and 2D may account for posttranslational modifications. Interestingly, several alkali induced genes/proteins can provide a cross protective overlap to other types of stresses. Alkaline pH provides therefore L. monocytogenes with nonspecific multiple-stress resistance that may be vital for survival in the human gastrointestinal tract as well as within food processing systems where similar alkaline conditions as the ones used in this study prevail.
Keywords: Transcriptomic and Proteomic Comparison Study

overall_design:
Overnight grown Listeria monocytogenes 10403S culture (100 µl) was inoculated into a 250 ml Erlenmeyer flask with 100 ml of BHI, and cultures were incubated at 30° C with shaking at 200 rpm. Cells were harvested by centrifugation when the optical density at 600 nm reached ~0.4, and then rapidly transferred to prewarmed (30 ° C) alkali adjusted BHI pH 9.5 (Adapted cultures) or not adjusted BHI (Control cultures) for 60 min. The pH of BHI medium was adjusted to 9.5 with a glycine-NaOH-NaCl buffer.  Control and alkali adapted cells were used for transcriptomic and proteomic studies.

In array analysis several controls were employed to minimise technical and biological variations, and ensure the quality of the data, i.e. i) each ORF was present in duplicate in each array, ii) each RNA preparation was used to make probes for at least two-separate arrays with reversal of incorporated dye and iii) three independent RNA batches from each condition were analysed. Only differences of ≥ 2 fold change in the levels of gene expression, which also had SAM 'q' values of 0.05, were recorded as significant.

first: Efstathios

last: Giotis

first: Arunachalam

last: Muthaiyan

last: McDowell

first: Ian

last: Blair

last: Wilkinsons


title: Role of σ54 in the regulation of genes involved in biogenesis of type I and type IV pili in Xylella fastidiosa

status: Public on Oct 22 2007

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary:
The phytopathogen Xylella fastidiosa produces two classes of pili, long type IV pili and short type I pili, which are involved in motility and adhesion. In this work, we have investigated the role of σ54 factor and its involvement in the regulation of fimbrial biogenesis in X. fastidiosa. An rpoN null mutant was constructed from citrus strain J1a12, and analyses of global gene expression profile by microarrays comparing the wild type and rpoN mutant strains showed that few genes exhibited differential expression. At least one gene, pilA1 (XF2542), which encodes the structural pilin protein of type IV fimbriae, showed decreased expression in the rpoN mutant whereas an operon encoding proteins of type I fimbriae were twofold more expressed in the mutant. Quantitative real time RT-PCR (qRT-PCR) analysis confirmed that pilA1 transcript was significantly reduced in the rpoN mutant. The transcriptional start site of pilA1 was determined by primer extension, and a canonical σ54-dependent promoter was found upstream of the start site. Genome sequence analysis of X. fastidiosa revealed five paralogues of pilA, but microarray and qRT-PCR data demonstrated that only the pilA1 transcript was significantly affected in the rpoN mutant. The rpoN mutant made more biofilm than the wild type strain and presented a cell-cell aggregative phenotype. These results indicate that σ54 regulates biofilm formation, probably via differential regulation of genes involved in type IV and type I fimbrial biogenesis.
Keywords: rpoN mutant strain, pili

overall_design: Direct comparison between wild type strain J1a12 and mutant strain rpoN-.

first: Jose

middle: F

last: da Silva Neto

first: Suely

last: Gomes

first: Marilis

last: Marques


title: Comparative Genomic Analyses among Citrus-Associated strains of Xylella fastidiosa

status: Public on Jul 18 2007

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

summary:
With the aid of a biochip, carrying  representative sequences from approximately 2200 sequences from the genome of isolate 9a5c from X. fastidiosa (Xf), microarray-based comparisons have been performed with 6 different Xf isolates obtained from citrus plants (Table 1). Four of these isolates (56a, 9.12c, 187b, and 36f) were obtained from CVC-affected trees and are representatives of the most prevalent Xf haplotypes found in sweet orange orchards across the state of São Paulo, while isolate CV21 was obtained from a non-symptomatic tree from the same region. Isolate Fb7, on the other hand, was obtained from a sweet orange tree that displayed symptoms of “Pecosita”, a disease similar to CVC that occurs in some citrus-growing regions of Argentina.
Keywords: Comparative Genomic Hybridization

overall_design: DNA from the 9a5c isolate was used as a reference in competitive hybridization experiments against DNA from 6 different Xf isolates obtained from citrus plants. Equimolecular amounts of each DNA have been labelled with either Cy3- or Cy5-dCTP and hybridized with a 9a5c Xf biochip. Statistical validation of fold change variations was performed with the aid of the Significance Analysis of Microarrays (SAM) method  Tusher and coworkers, using the software developed by B. Narasimham and available at http://www-stat.stanford.edu/~tibs/SAM/index.html. Spots that showed a Reference/Test ratio <1:2 were considered to be present in greater copy number in the test over the reference strain, as proposed by Smoot and coworkers, while spots that showed an average Reference/Test ratio >5:1 were considered to be missing in the test strain. The application of these criteria in a direct sequence comparison between strains 9a5c and Temecula-1, which have been completely sequenced, provided an estimated error rate below 0.3%

first: Vivian

last: da Silva

first: Cláudio

last: Shida

first: Fabiana

middle: B

last: Rodrigues

first: Diógenes

last: Ribeiro

first: Alessandra

last: de Souza

first: Helvécio

middle: D

last: Coletta-Filho

first: Marcos

last: Machado

first: Regina

last: de Oliveira


title: UCP exposure of ovalbumin sensitized and challenged mice

status: Public on Jul 01 2007

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
To gain insight into the promoting effect of ultrafine particle inhalation on development and progression of allergic asthma, we selected an experimental approach involving exposure to ultrafine carbon particles (UCP) and gene expression profiling of lungs from mice with experimental, ovalbumin induced allergy. Comparative gene expression analysis was performed by hybridizing pooled cDNA samples from lavaged lungs of different groups.
The results suggest that allergic sensitization may represent an susceptibility factor for effects of UCP on gene expression in the lung. In sensitized individuals UCP exposure, such as found in polluted air, thus may contribute to the development and/or aggrevation of allergic asthma.
Keywords: Particle Inhalation, lung, ovalbumin sensitized and challanged, expression profling

sample_organism:
Homo sapiens
Mus musculus

overall_design: Lungs of groups of six sensitized  or sensitized and challanged BALB/cJ mice, either subjected to particle-free or UCP containing air; two replicates including one dye swap experiment have been performed for lungs: a) sensitized particle free air versus sensitized UCP exposure; b) sensitized and challanged particle free air versus sensitized and challanged UCP exposure

first: Johannes

last: Beckers

first: Holger

last: Schulz

first: Tobias

last: Stöger

first: Sandra

last: Rieger


title: Molecular Profiling of Breast Cancer Cells after Gemcitabine exposure

status: Public on May 29 2007

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Human breast cancer cell lines were exposed to IC50 gemcitabine (Gemzar) for 24 and 48 hours. RNA was extracted, amplified and hibridized onto Oncochip microarray slides.
Keywords: Time and Dose Response

overall_design: Human breast carcinoma cell lines MCF7 and MDA-MB-231 were cultured in DMEM with Glutamax-1, supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Cells were grown and passaged by trypsinization.

first: Jose

last: Palacios

first: Gema

last: Moreno-Bueno


title: Comparative whole genome profiling of post-transplant lymphoproliferative disorders and diffuse large B-cell lymphomas.

status: Public on Jun 15 2007

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ transplantation and represent a cause of severe morbidity and mortality among transplanted patients. Apart from EBV infection, knowledge of the pathogenesis of monoclonal PTLD is limited. Powerful analysis techniques, such as whole genomic DNA profiling (arrayCGH), can improve our understanding of PTLD pathogenesis. Toward this aim, we obtained the whole genome profiling using the Affymetrix GeneChip Human Mapping 10k 2.0 from 20 cases of PTLD and we compared them with those assessed in 25 cases of DLBCL from immunocompetent patients, as a control group. Recurrent lesions were detected among all the samples. Chromosome 18q, 7q, 3q and 12 were the most common gains in DLBCL of immunocompetent hosts. Chromosomes 5p and 11p were commonly gained in PTLD-DLBCL. The latter had frequent losses of 6q, 17p, 1p, and 9p. Chromosome 12p was the most frequent target of deletions among PTLD-DLBCL. The LOH pattern was characterized by involvement of chromosomes 13q and 17p in DLBCL and 10, 1q, 9p and 11q among PTLD-DLBCL. Interestingly, LOH did not always match the DNA loss. In particular, chromosome 10 seemes to be targeted by uniparental disomy in PTLD. Small deletions and gains, involving both known (BCL2 and PAX5) and unknown genes (ZDHHC14), have been identified. Our data suggest that PTLD share, at a lower frequency, common genetic aberrations with DLBCL from immunocompetent patients. The demonstration of 9p13 amplification indicates the importance of PAX5 in PTLD. The combination of DNA copy number and LOH assessment lead to the hypothesis that uniparental disomy may be a potential mechanism in B-cell lymphomagenesis. Twenty specimens of monoclonal B-cell PTLD, collected from 20 solid organ transplant recipients.
Keywords: Genomic DNA on Affymetrix 10K SNP array

overall_design:
20 PTLD samples. No technical replications.
25 DLBCL samples (20 patient + 5 cell lines). No technical replications.

first: Andrea

last: Rinaldi

first: Ivo

last: Kwee


title: T47D_MTVL treatment with JAK/STAT inhibitor AG490 with/without R5020

status: Public on Oct 12 2007

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary:
Gene expression of the breast cancer cell line T47D-MTVL induced by progestin R5020, in the absense or presence of the JAK/STAT signaling pathway inhibitor AG490.
Keywords: Gene expression - T47D-MTVL- hormonal treatment+inhibitors comparison

overall_design: Two biological replicates of breast cancer cell line T47D-MTVL cell line samples were treated with eiter progestin R5020 or with the drug vehicle Ethanol. One hour before this treatment, samples were treated with the JAK/STAT inhibitor AG490. Cell line sample was labeled with Cy5 and hybridized against Universal Human Reference RNA (Stratagene) labeled with Cy3.

first: Alicia

last: Subtil

first: Albert

last: Jordan

first: Belen

last: Minana

first: Ballare

last: Cecilia

first: Beato

last: Miguel

first: Sumoy

last: Lauro


title: Ovalbumin sensitized and challenged induces differential gene expression in mouse lungs

first: Martin

last: Irmler

summary:
To gain insight into the promoting effect of ultrafine particle inhalation on development and progression of allergic asthma, we selected an experimental approach involving exposure to ultrafine carbon particles (UCP) and gene expression profiling of lungs from mice with experimental, ovalbumin induced allergy. Comparative gene expression analysis was performed by hybridizing pooled cDNA samples from lavaged lungs of different groups.

These results suggest that allergic sensitization may represent a susceptibility factor for effects of UCP on gene expression in the lung. In sensitized individuals UCP exposure, such as found in polluted air, thus may contribute to the development and /or aggravation of allergic asthma.
Keywords: Particle Inhalation, lung, ovalbumin sensitzed and challanged, experssion profiling

overall_design: Lungs of groups of six non-sensitized, ovalbumin sensitized, or sensitized and ovalbumin challenged BALB/cJ mice, either subjected to particle-free or UCP containing air; two replicates including one dye swap experiment have been performed for lungs: a) non-sensitized particle free air versus sensitized and ovalbumin challenged sensitized particle free air; b) non-sensitized UCP containing air versus sensitized and ovalbumin challenged sensitized UCP containing air

first: Johannes

last: Beckers

last: Stoeger


title: Develomental Time Course of the Retinal Pigment Epithelial Transcriptome

status: Public on Jul 02 2007

city: New Haven

first: Lawrence

middle: J

last: Rizzolo

state: CT

address: 333 Cedar St

department: Dept of Surgery

institute: Yale University

summary:
Purpose: The morphology of the RPE shows minimal change as the neural retina and choriocapillaris differentiate. Nonetheless, initial studies of barrier-related proteins suggest extensive remodeling of the RPE in response to this changing environment. A genomic approach was used to investigate the extent of this remodeling.
Methods: RPE was isolated from E7, E10, E14 and E18 chick embryos and total RNA extracted for probing the entire genome on Affymetrix microarray chips.  Statistical parameters using ANOVA were adjusted to yield a theoretical false discovery rate of 5%. STEM software was used to cluster genes into statistically related patterns of expression.  Gene ontology clustering, using Affymetrix software was used for functional clustering.  The proteinlounge.com database was used as a source of known biological pathways.
Results: Of the 37,694 probe sets on the microarray, 17,199 were not absent.  Of the 20,495 expressed probes, the expression of 8,889 was developmentally regulated.  4814 of these could be clustered into 12 patterns of expression that were statistically significant.  The developmental patterns of expression for 22 tight and adherens junction proteins have been reported.  Only two showed small variations from the patterns revealed by the microarray.  Further, as would be predicted, expression of genes that promote progression through the cell cycle decreased and genes that inhibit progression increased with age.  The data indicate extensive remodeling of the extracellular matrix, cell surface receptors, cell-cell junctions, transcellular ion transport and signal transduction pathways throughout development.  Notably, the appearance of claudin 20, ZO-3 and cadherins 13 and 20 very late in development suggest barrier properties continue to change after functional junctions are formed.
Conclusions: The data reveal a far more dynamic view of the RPE and its interactions with its environment than would be expected from morphological examination. The remodeling of junctional complexes, extracellular matrix interactions and transcellular transport capabilities indicates a continuous remodeling of the blood-retinal barrier. These data provide a standard whereby culture models of RPE function and regulation may be judged.
Keywords: time course

overall_design: Sheets of RPE were isolated from chicken embryos on Embryonic day 7 (E7), E10, E14 and E18 and stored in RNAlatter (Qiagen, Valencia, CA), as described <Rahner C, Fukuhara M, Peng S, Kojima S, Rizzolo LJ. The apical and basal environments of the retinal pigment epithelium regulate the maturation of tight junctions during development. J Cell Sci. 2004;117:3307-18>. To isolate total RNA, the RNeasy Protect kit (Qiagen) was used according to the manufacturer's protocols. For each age, 3-4 independent preparations were used for analysis on Affymetrix microarrays of the chicken genome (Santa Clara, CA). For each preparation, sheets of RPE were pooled from 20-30 eyes. The quality of the total RNA was assessed by the Keck Center, Yale University using formamide gels and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

first: Xiang

last: Chen

first: Matthew

last: Weitzman

first: Ru

last: Sun

first: Heping

last: Zhang


title: Role of CSN5 in breast cancer (siRNA transfections)

status: Public on Jan 18 2008

city: South San Francisco

first: Adam

last: Adler

address: 1 DNA Way

institute: Genentech

summary:
CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. Amplification of CSN5 is required for transformation of primary human breast epithelial cells by defined oncogenes. The transforming effects of CSN5 require CSN subunits for assembly of the full COP9 signalosome and the isopeptidase activity of CSN5, which potentiates the transcriptional activity of MYC. Transgenic inhibition of CSN5 isopeptidase activity blocks breast cancer progression evoked by MYC and RAS in vivo. These results highlight CSN5 isopeptidase activity in breast cancer progression, suggesting it as a therapeutic target in aggressive human breast cancers.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

overall_design: Computed


title: Identification of NO Response Network in E. coli

status: Public on Apr 26 2007

city: Logan

first: Daniel

last: Hyduke

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

summary:
The goals of this project were: to use transcriptomics as a starting point for reverse engineering the NO response network of E. coli, and to identify the targets responsible for NO-induced bacteriostasis.  The data is associated with Hyduke DR*, Jarboe LR*, Tran LM, Chou KJY, Liao JC 2007 "Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. "Proc. Natl. Acad. Sci. USA 104(20):8484-8489.
Keywords: Comparative genomic response.

overall_design: The associated samples were analyzed with Network Component Analysis and the transcription factor perturbations were verfied with knockouts and phenotypic assays.

first: Laura

last: Jarboe

first: Linh

last: Tran

first: Katherine

last: Chou

first: James

middle: C

last: Liao


title: Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing

status: Public on Apr 24 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary:
Expression profiling, ChiP-CHIP and phenotypic analysis were used to investigate the functional relationships of class III NAD+-dependent HDACs (Sirtuins) in fission yeast. We detected significant histone acetylation increases in Sirtuin mutants at their specific genomic binding targets and were thus able to identify an in vivo substrate preference for each Sirtuin. At heterochromatic loci, we demonstrate that although Hst2 is mainly cytoplasmic, a nuclear pool of Hst2 co-localises with the other Sirtuins at silent regions (cen, mat, tel, rDNA) and that like the other Sirtuins, Hst2 is required for rDNA and centromeric silencing. Interestingly we found specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation. Hst2 directly represses genes involved in transport and membrane function whereas Hst4 represses amino acid biosynthesis genes and Tf2 retrotransposons. A specific role for Hst4 in Tf2 5’ mRNA processing was revealed. Thus, Sirtuins share functions at many genomic targets, but Hst2 and Hst4 have also evolved unique functions in gene regulation.
Keywords: chromatin; fission yeast; gene silencing; retrotransposon; Sirtuin; HDAC

overall_design:
The combined microarray strategy in this study was performed essentially as outlined in (Wiren et al., 2005). cDNA expression profiling was carried out according to (Xue et al., 2004). We used the S. pombe ORF and combined IGR+ORF spotted microarrays (Eurogentec, Belgium custom DNA microarray services). For histone acetylation maps, ChIP-CHIP method was used using according to (Robyr and Grunstein, 2003). Specific acetylation antibodies were used against H3K9ac, H3K14ac, H4K5ac, H4K16ac and H4K12ac (Suka et al., 2002). The histone ‘H3cter’ antibody was purchased from Upstate and used for ChIP according to manufacturers recommendations. For HDAC bindings maps we used we used the ChIP- CHIP procedure described by (Kurdistani et al., 2002). Corrections for nucleosome loss were performed as described in (Wiren et al., 2005). GeneSpring software was used for all data analysis. Expression profiling and histone acetylation mutant vs wt data sets were normalized using Lowess (per spot per chip) intensity-dependent normalization, which corrects nonlinear rates for dye incorporation.  Cut off values of 1,5 and 2,0 were used to generate ‘high’ and ‘low’ gene lists for ORF and IGR regions. The HDAC-binding data were normalized using per chip (the 50th percentile). For HDAC binding, Sir2-Myc data were extracted from (Wiren et al., 2005), ProtA-Hst4 binding were carried out …( Fredrik fill in here).
Media and spotting assays
Standard fission yeast genetic techniques and media were used according to (Moreno et al., 1991). For microarray analysis, cells were grown in YES media. Silencing assays plating and serial dilution experiments were performed as described (Allshire et al., 1994). Fivefold dilutions were plated onto EMM plates as a growth control (+ura), onto EMM plates lacking uracil (-ura) and onto 5-FOA plates (+FOA). Thiabendazole (TBZ; Sigma) was dissolved in DMSO to give stock solution at 20 mg/ml.
Construction of strains
Haploidization of diploid heterozygote strain h+/h+ ade6-M210/ade6-M216 leu1-32/leu1-32 ura4-D18/ura4-D1 hst2/hst2∆::kanMx4 (Bioneer Corporation) was performed in YES liquid media containing 10µg/ml of TBZ during 2-3 days. Then the cells were plated on YES (–ade) plates containing 150µg/ml G418 (Sigma). G418 resistant haploid colonies with red or pink colony color were then selected, checked by PCR and backcrossed with the wt strain Hu303.
13xMyc epitope tagging of Hst2 was performed according (Bahler et al., 1998). The heterozygous diploid h+/h+ ade6-M210/ade6-M216 hst2::kanMx4/hst2+ leu1-32/leu1-32 ura4-D18/uraD-18 knockout strain was obtained from Bioneer company (South Korea).  Diploid cells were haploidized as described above. All strains used in this study are listed in supplementary data Table S1.
Northerns and RT PCR…
IF microscopy…

first: Mickaël

last: Durand-Dubief

first: Indranil

last: Sinha

first: Fredrik

last: Fagerström-Billai

first: Carolina

last: Bonilla

first: Anthony

last: Wright

first: Michael

last: Grunstein


title: Decoding global gene expression programs in liver cancer by noninvasive imaging

status: Public on Apr 07 2007

middle: S

summary:
ABSTRACT: Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. Here we show that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer. Combinations of twenty-eight imaging traits can reconstruct 78% of the global gene expression profiles, revealing cell proliferation, liver synthetic function, and patient prognosis. Thus, genomic activity of human liver cancers can be decoded by noninvasive imaging, thereby enabling noninvasive, serial and frequent molecular profiling for personalized medicine.
Keywords: disease_state_design


title: Ventilator-induced lung injury in wild-type and jnk1 knockout mice

status: Public on May 08 2007

city: Philadelphia

first: Tamas

last: Dolinay

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

summary:
Background: Mechanical ventilation causes ventilator-induced lung injury in animals and humans. Mitogen-activated protein kinases have been implicated in ventilator-induced lung injury though their functional significance remains incomplete. We characterize the role of p38 mitogen-activated protein kinase/ mitogen activated protein kinase kinase-3 and c-Jun-NH2-terminal kinase-1 in ventilator-induced lung injury and investigate novel independent mechanisms contributing to lung injury during mechanical ventilation. Methodology and Principle Findings: C57/BL6 wild-type mice and mice genetically deleted for mitogen-activated protein kinase kinase-3 (mkk-3-/-) or c-Jun-NH2-terminal kinase-1 (jnk1-/-) were ventilated, and lung injury parameters were assessed. We demonstrate that mkk3-/- or jnk1-/- mice displayed significantly reduced inflammatory lung injury and apoptosis relative to wild-type mice.  Since jnk1-/- mice were highly resistant to ventilator-induced lung injury, we performed comprehensive gene expression profiling of ventilated wild-type or jnk1-/- mice to identify novel candidate genes which may play critical roles in the pathogenesis of ventilator-induced lung injury.  Microarray analysis revealed many novel genes differentially expressed by ventilation including matrix metalloproteinase-8 (MMP8) and GADD45a. Functional characterization of MMP8 revealed that mmp8-/- mice were sensitized to ventilator-induced lung injury with increased lung vascular permeability.
Conclusions: We demonstrate that mitogen-activated protein kinase pathways mediate inflammatory lung injury during ventilator-induced lung injury. C-Jun-NH2-terminal kinase was also involved in alveolo-capillary leakage and edema formation, whereas MMP8 inhibited alveolo-capillary protein leakage.
Keywords: response to injury, genetically modified mouse

overall_design: We analyzed the gene expression patterns of 3 control a 4 ventilated mice`s lungs in both wild type and jnk1 knockout animals.

first: Naftali

last: Kaminski

first: Wei

last: Wu

first: Augustine

last: Choi


title: Overexpression of wild-type and dominant-negative form of tao-1

status: Public on Apr 20 2007

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

summary:
Tao-1 is a member of evolutionarily conserved family of ste20-related serine/threonine kinases that regulate fundamental cellular processes including apoptosis. Drosophila tao-1 is expressed in pole cells during embryogenesis. To identify genes that act downstream of tao-1 in the pathway within pole cells, we compared the gene expression profiles of pole cells expressing dominant-negative form Tao-1 (D168A) and wild-type Tao-1 (D168D) by microarray analysis.
Keywords: wild type v.s. dominant-genative form

overall_design:
The following embryos were used as source material: E1 and R1, Stage 8-14 embryos derived from nosGal4:VP16/nosGal4:VP16 females (E1) and yw
females (R1) mated with UAS-tao-1(D168A); EGFP-Vas males;E2 and R2, Stage 8-14 embryos derived from nosGal4:VP16/nosGal4:VP16 females (E2) and yw females (R2) mated with UAS-tao-1(D168D); EGFP-Vas males. Pole cells were isolated from these embryos by using FACS. We compared gene expression profiles between E1 and R1 pole cells, and between E2 and R2 pole cells.

first: Kimihiro

last: Sato

first: Yoshiki

last: Hayashi

first: Yuichi

last: Ninomiya

first: Kayo

last: Arita

first: Masanori

last: Mukai

first: Satoru

last: Kobayashi


title: Prediction and Testing of Novel Transcriptional Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment

status: Public on Apr 18 2007

city: Toronto

first: Emily

last: Walker

address: 164 College Street Room 407

department: Institute for Biomaterials and Biomedical Engineering

institute: University of Toronto

summary:
We have used mouse embryonic stem cells (ESCs) as a model to study the signaling mechanisms that regulate self-renewal and commitment to differentiation. We hypothesized that genes critical to stem cell fate would be dynamically regulated at the initiation of commitment. Time course microarray analysis following initiation of commitment led us to propose a model of ESC maintenance in which highly regulated transcription factors and chromatin remodeling genes (down-regulated in our time course) maintain repression of genes responsible for cell differentiation, morphogenesis and development (up-regulated in our time course). Microarrays of Oct4, Nanog and Sox2 shRNA knockdown cell lines confirmed predicted regulation of target genes.  shRNA knockdowns of candidate genes were tested in a novel high throughput screen of self-renewal, confirming their role in ESC pluripotency. We have identified genes that are critical for self-renewal and those that initiate commitment and developed draft transcriptional networks that control self-renewal and early development.
Keywords: genetic modification

overall_design: Gene expression in Oct4 knockdown, Sox2 knockdown and their empty vector contol ES cells was analyzed.

first: Wen

last: Zhang

first: Timothy

last: Hughes

first: William

last: Stanford


title: Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization

city: King of Prussia

first: Joel

last: Greshock

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

summary:
Tumor-derived cell lines are used as in vitro cancer models, but their ability to accurately reflect the phenotype and genotype of the parental histology remains questionable, given the prevalence of documented cell line–specific cytogenetic changes. We have addressed the issue of whether copy number alterations seen in tumor-derived cell lines reflect those observed in studies of fresh tissue by carrying out a meta-analysis of array-based comparative genomic hybridization data that considers both copy number alteration frequencies and the occurrence of cancer gene amplifications and homozygous deletions.
Keywords: comparative genomic hybridization

overall_design: The objective of this study was to determine if frequency patterns of observed DNA copy number alterations in panels of cell lines mirrored that in their parent histology.  To accomplish this, panels of both tumors and cell lines of several common cancers were profiled by array CGH.  These included breast cancers (n = 69), ovarian cancers (n = 103), sarcomas (n = 81) and melanomas (n = 62).  These data were merged with publicly available data for lung, panreatic and colon cancers.

first: Barbara

last: Weber

first: Tal

middle: Z

last: Zaks


title: Identification of rust-induced genes in poplar using Populus 4.6K cDNA macroarray

status: Public on Mar 15 2007

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

institute: INRA

summary:
cDNA macroarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response.
For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse either with spores of avirulent strain 93ID6 (incompatible interaction, I) or spores of virulent strain 98AG31 (compatible interaction, C) of the pathogenic rust fungus Melampsora larici-populina. Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled at 12, 24 and 48 hours post-inoculation (hpi) in a time-course experiment before (12 hpi) and after (24 and 48 hpi) that the fungus attempt to penetrate plant cells in mesophyll.
Keywords: Plant tissue infection, Plant defense response, cDNA macroarray

overall_design: Three biological replicates named Rep1, Rep2 and Rep3 were obtained for each treatment (i.e., T, C and I) at each timepoint (i.e., 12, 24, 48 hpi). At each timepoint, two comparisons were performed: control treatment T versus compatible interaction C on one side and control treatment T versus incompatible interaction I on the other side. For each comparison, biological triplicates were used to identify transcripts significantly differentially accumulated between treatments at the considered timepoint using the CyberT statistical framework.


title: Histone turnover marks the boundaries of cis-regulatory domains

status: Public on Mar 01 2007

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
Cellular memory is maintained at the Drosophila homeotic gene clusters by cis-regulatory elements who mechanism of action is unknown. We have examined chromatin dynamics in the Drosophila genome by measuring histone turnover levels at high resolution. Surprisingly, homeotic gene clusters display characteristic histone turnover profiles with conspicuous peaks at boundaries of cis-regulatory domains superimposed over regions of very low turnover. Peaks of histone turnover precisely correspond to nuclease hypersensitive sites for epigenetic silencing proteins. Our results suggest that epigenetic regulation is facilitated by histone turnover, which maintains continuous accessibility ov cis-regulatory DNA.
Keywords: Chromatin affinity-purification on microarray

overall_design: Chromatin affinity profiling of histones H3 and H3.3 on Drosophila tiling arrays

first: Yoshiko

last: Mito

middle: G

first: Steven


title: Fungal peptide destruxin a plays a specific role in suppressing the innate immune response in Drosophila melanogaster

status: Public on Feb 10 2007

city: College Park

first: Subhamoy

last: Pal

address: 5126 Plant Sciences Building

department: Center for Biosystems Research

institute: University of Maryland

summary:
Destruxins are a class of insecticidal, anti-viral and phytotoxic cyclic depsipeptides that are also studied for their toxicity to cancer cells. They are produced by various fungi and a direct relationship has been established between Destruxin production and the virulence of the entomopathogen Metarhizium anisopliae. Aside from opening calcium channels, their in vivo mode of action during pathogenesis remains largely uncharacterized. To better understand the effects of a destruxin, we looked at changes in gene expression following injection of Destruxin A into the fruit fly Drosophila melanogaster. Microarray results revealed reduced expression of various antimicrobial peptides (AMPs) that play a major role in the fly’s humoral immune response. Flies co-injected with a non-lethal dose of Destruxin A and the normally innocuous Gram-negative bacteria Escherichia coli, showed increased mortality and an accompanying increase in bacterial titers. Mortality due to sepsis was rescued through ectopic activation of components in the IMD pathway, one of two signal transduction pathways that are responsible for AMP induction. These results demonstrate a novel role for Destruxin A in specific suppression of the humoral immune response in insects.
Keywords: Gene Expression

overall_design: Gene expression 4 hours after injection of sub-lethal doses of Destruxin A compared to PBS controls, was examined in this experiment for adult Drosophila melanogaster.


title: RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

status: Public on May 25 2007

city: Santa Clara

first: Thomas

last: Gingeras

state: CA

address: 3380 Central Expressway

institute: Affymetrix, Inc.

summary:
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.

Processed data files:
Graph files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/graphs/
Transfrag files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/transfrags/

CEL files available on each Sample record
tpmap files available on each Platform record

Keywords: tiling, RNA population complexity profiling

overall_design: See publication for details

first: Philipp

last: Kapranov

first: Jill

last: Cheng

first: Sujit

last: Dike

first: David

last: Nix

first: Radharani

last: Duttagupta

first: Aarron

middle: T

last: Willingham

first: Peter

last: Stadler

first: Jana

last: Hertel

first: Joerg

last: Hackermueller

first: Ivo

last: Hofacker

first: Ian

last: Bell

first: Evelyn

last: Cheung

first: Jorg

last: Drenkow

first: Erica

last: Dumais

first: Sandee

last: Patel

first: Gregg

last: Helt

first: Ganesh

last: Madhavan

first: Srinka

last: Ghosh

first: Antonio

last: Piccolboni

first: Victor

last: Sementchenko


title: Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays (Expression Data)

status: Public on Jan 25 2007

city: Columbus

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

summary:
It has been proposed that ZNF217, which is amplified at 20q13 in various tumors, plays a key role during neoplastic transformation. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. However, the function of ZNF217 has not been well characterized due to a lack of known target genes. Using a global ChIP-chip approach, we have identified thousands of ZNF217 binding sites in three tumor cell lines (MCF7, SW480, and Ntera2). Further analysis of ZNF217 in Ntera2 cells has shown that many promoters are bound by ZNF217 and CtBP2, and that a subset of these promoters are activated upon removal of ZNF217. Thus, our in vivo studies corroborate the in vitro biochemical analyses of ZNF217-containing complexes and support the hypothesis that ZNF217 functions as transcriptional repressor. Gene ontology analysis shows that ZNF217 targets in Ntera2 cells are involved in organ development, suggesting that one function of ZNF217 may be to repress differentiation. Accordingly, we show that differentiation of Ntera2 cells with retinoic acid leads to downregulation of ZNF217. Our identification of thousands of ZNF217 target genes will enable further studies of the consequences of aberrant expression of ZNF217 during neoplastic transformation.
Keywords: mRNA Expression

overall_design: Expression measurement in Ntera2 by treating siZNF217

first: Sheryl

last: Krig

first: Mark

last: Beida

first: Henny

last: O'Geen

first: Roland

last: Green

first: Peggy

last: Farnham


title: Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays (Promoter Arrays)

summary:
It has been proposed that ZNF217, which is amplified at 20q13 in various tumors, plays a key role during neoplastic transformation. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. However, the function of ZNF217 has not been well characterized due to a lack of known target genes. Using a global ChIP-chip approach, we have identified thousands of ZNF217 binding sites in three tumor cell lines (MCF7, SW480, and Ntera2). Further analysis of ZNF217 in Ntera2 cells has shown that many promoters are bound by ZNF217 and CtBP2, and that a subset of these promoters are activated upon removal of ZNF217. Thus, our in vivo studies corroborate the in vitro biochemical analyses of ZNF217-containing complexes and support the hypothesis that ZNF217 functions as transcriptional repressor. Gene ontology analysis shows that ZNF217 targets in Ntera2 cells are involved in organ development, suggesting that one function of ZNF217 may be to repress differentiation. Accordingly, we show that differentiation of Ntera2 cells with retinoic acid leads to downregulation of ZNF217. Our identification of thousands of ZNF217 target genes will enable further studies of the consequences of aberrant expression of ZNF217 during neoplastic transformation.
Keywords: ChIP-chip

overall_design: ChIP-chip assays on Promoter arrays using anti-ZNF217

last: Bieda


title: cDNA microarray data of bovine placenta

status: Public on Apr 27 2007

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

institute: National Institute of Agrobiological Sciences

summary:
Gene expression patterns of bovine placenta from initial to late stage of pregnancy were investigated by using the our custom designed utero-placental cDNA microarray.
Keywords: Time course

overall_design: We analyzed 20 arrays performed using 10 polyA RNA samples. Total RNA were collected from bovine carancular and cotyledonary tissues (Day25, 60, 150, 250 of gestation) and endometrial tissues of non-pregnant cows. All hybridizations were performed in duplicate (Cy3 and Cy5 dyes), where reverse labeling was done.

first: Toru

last: Takahashi

first: Misa

last: Hosoe

first: Hiroko

last: Ishiwata

first: Kanako

last: Kaneyama

first: Keiichiro

last: Kizaki

first: Kazuyoshi

last: Hashizume


title: Frequent Partial Uniparental Disomy Due to Somatic Recombination in Acute Myeloid Leukemias

status: Public on Apr 11 2007

city: London

first: Manoj

last: Raghavan

address: Charterhouse Square

department: Centre for Medical Oncology, Institute of Cancer

country: United Kingdom

institute: Barts and the London, Queen Mary's School of Medicine and Dentistry

summary:
Genome-wide analysis of single nucleotide polymorphisms in 64 acute myeloid leukemias has revealed that 20% exhibited large regions of homozygosity that could not be accounted for by visible chromosomal abnormalities in the karyotype. Further analysis confirmed that these patterns were due to partial uniparental disomy (UPD). Remission bone marrow was available from five patients showing UPD in their leukemias, and in all cases the homozygosity was found to be restricted to the leukemic clone. Two examples of UPD11p were shown to be of different parental origin as indicated by the methylation pattern of the H19 gene. Furthermore, a previously identified homozygous mutation in the CEBPA gene coincided with a large-scale UPD on chromosome 19. These cryptic chromosomal abnormalities, which seem to be nonrandom, have the characteristics of somatic recombination events and may define an important new subclass of leukemia.
Patient No. from Table 1 of Raghavan et al 2005 and Sample name
Patient No: 1 = Sample name: AML sample 35 diagnosis
Patient No: 1 = Sample name: AML sample 107 remission
Patient No: 2 = Sample name: AML sample 37 diagnosis
Patient No: 3 = Sample name: AML sample 10 diagnosis
Patient No: 3 = Sample name: AML sample 44 remission
Patient No: 4 = Sample name: AML sample 20 diagnosis
Patient No: 5 = Sample name: AML sample 65 diagnosis
Patient No: 6 = Sample name: AML sample 69 diagnosis
Patient No: 6 = Sample name: AML sample 94 remission
Patient No: 7 = Sample name: AML sample 40 diagnosis
Patient No: 7 = Sample name: AML sample 41 remission
Patient No: 8 = Sample name: AML sample 64 diagnosis
Patient No: 9 = Sample name: AML sample 7 diagnosis
Patient No: 10 = Sample name: AML sample 49 diagnosis
Patient No: 10 = Sample name: AML sample 106 remission
Patient No: 11 = Sample name: AML sample 76 diagnosis
Patient No: 12 = Sample name: AML sample 79 diagnosis
Keywords: DNA copy number, loss of heterozygosity

overall_design: DNA from 64 diagnostic AML samples were analysed using Affymetrix 10K SNP arrays. Large regions of homozygosity were identified and compared with remission bone marrow where available.

first: Debra

middle: M

last: Lillington

first: Spyros

last: Skoulakis

first: Silvana

last: Debernardi

first: Tracy

last: Chaplin

first: Nicola

last: Foot

first: T

middle: A

last: Lister

first: Bryan

last: Young


title: Identification of rust-induced genes in poplar using Populus 2.0 NimbleGen oligoarray

first: Sebastien

last: Duplessis

summary:
Oligoarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response.
For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse either with spores of avirulent strain 93ID6 (incompatible interaction I48) or spores of virulent strain 98AG31 (compatible interaction C48) of the pathogenic rust fungus Melampsora larici-populina. Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll.
Keywords: Plant tissue infection, Plant defense response, Oligonucleotide array

sample_organism:
Populus trichocarpa
Populus deltoides

overall_design: Three biological replicates named Rep1, Rep2 and Rep3 were obtained for each treatment (i.e., T48, C48 and I48). Two comparisons were performed: control treatment T48 versus compatible interaction C48 on one side and control treatment T48 versus incompatible interaction I48 on the other side. For each comparison, biological triplicates were used to identify transcripts significantly differentially accumulated between treatments using the bayesreg script of the CyberT statistical framework.

first: Sébastien

first: Cécile

last: Rinaldi

first: Annegret

last: Kohler

first: Francis

last: Martin

first: Pascal

last: Frey


title: Genome-wide mapping of meiotic DSB induced by Gal4BD-Spo11

status: Public on Jan 01 2007

city: Paris

first: Valerie

last: Borde

address: 26, rue d'Ulm

institute: Institut Curie

summary:
We mapped the binding and DSB sites in a strain expressing the fusion protein Gal4BD-Spo11, as well as the DSB sites in strains expressing endogenous Spo11, pADH1Spo11 and pADH1Gal4BD.
Keywords: ChIP-chip

overall_design: To distinguish between binding and DSB sites, we mapped the binding sites with crosslinking at t=0h after meiosis induction, and the DSB sites without crosslinking at t=6h after meiosis induction. Each experiment was done in triplicates, from independant cultures (except DSB measurement in the Spo11-Myc pADH1-Gal4BD strain, done from two independent experiments).

first: Nicolas

last: Robine

first: Alain

last: Nicolas

first: Norio

last: Uematsu

first: Emmanuel

last: Barillot


title: Transcriptome associates with rice organogenesis

status: Public on Dec 25 2006

first: Kun

last: He

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

summary:
Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.
Keywords: transcriptome

overall_design: Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays.

first: Ning

last: Su

first: Yuling

last: Jiao

first: Xing-Wang

last: Deng


title: Genome wide mapping of transcription factor downstream targets using STAGE

status: Public on Nov 23 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets of transcription factors in vivo. STAGE is based on high-throughput sequencing of concatemerized tags derived from target DNA enriched by chromatin immunoprecipitation. We optimized the STAGE protocol and developed analysis methods to allow the identification of transcription factor targets in human cells. We used STAGE to identify targets of human transcription factors c-myc and STAT1. STAGE provides a means of identifying the chromosomal targets of DNA-associated proteins in any sequenced genome.
Keywords: ChIP Sequencing

overall_design: STAGE is based on high-throughput sequencing of tags of defined length that are derived from DNA enriched by ChIP. Proteins were cross-linked to their binding sites in vivo with formaldehyde and chromatin was extracted and sheared. The cross-linked protein-DNA complexes were immunoprecipitated, cross-links were reversed and ChIP DNA was amplified by PCR using biotinylated primers. Amplified DNA fragments were digested with NlaIII, which cuts at 5'-CATG sites. Fragments with ends containing the NlaIII site were isolated by binding to streptavidin beads. They were separately ligated to one of two linkers containing a MmeI site, then incubated with MmeI, which cleaves 21 bp away from its recognition site. The 21-bp tags attached to linkers were isolated and ligated to create ditags. Ditags were amplified by PCR using nested primers and trimmed by digesting with NlaIII. Trimmed ditags were gel purified, concatemerized by ligation, cloned and sequenced. With the advent of pyrosequencing, ditags were directly sequenced without the need for any cloning.

first: Jonghwan

last: Kim

first: Akshay

last: Bhinge

first: Ghia

last: Euskirchen

first: Michael

last: Snyder

first: Vishwanath

middle: R


title: Gene Transcription Profile of Local Innate and Adaptive Immunity during Early Phase of IBV Infection

status: Public on Nov 03 2006

city: Brookings

first: Xiuqing

last: Wang

state: SD

address: NPB 252, SDSU

department: Department of Biology and Microbiology

institute: South Dakota State University

summary:
To understand the mechanistic basis of local innate and adaptive immunity against infectious bronchitis virus (IBV) at the molecular level, we examined the gene transcription profile of tracheal epithelial layers at 3 days after infection of chickens with an attenuated IBV-Massachusetts strain.
Keywords: Disease State Analysis, Early mucosal immune response, FHCRC 13k chicken array

overall_design: For the DNA microarray experiment, total RNA was reverse transcribed and labeled with Cy3 and Cy5 fluorescent dyes and hybridized to the chicken 13K cDNA microarray (FHCRC, Seattle, WA) which contains 13,000 genes derived from both embryonic and adult chicken tissues including immune genes. The experiment was repeated four times using swapped Cy3 or Cy5 dye labeling.

first: Artur

last: Rosa

first: Henrique

last: Oliverira

first: Guilherme

first: Xueshui

last: Guo

first: Mark

last: Travnicek

first: Theodore

last: Girshick


title: Transcriptome analysis reveals season-specific RbcS gene expression profiles in diploid Lolium  perenne L.

status: Public on Nov 09 2006

city: Auckland

first: Sathish

last: puthigae

address: PO box 109185, Newmarket,

country: New Zealand

institute: Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd

summary:
Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24–31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE™) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE™ tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE™ tags, which were present more than once in our SAGE™ library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE™ tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.
Keywords: paddock samples, pasture, perennial ryegrass, Serial Analysis of Gene Expression (SAGE™), season specific expression, monocot

overall_design:
Ryegrass tissue
Perennial ryegrass (Lolium perenne L.) cv. Bronsyn was used throughout this study. Field-grown samples, comprising mainly viable leaves and pseudostems, were collected at midday from livestock-active monocultural paddocks at Dexcel, Hamilton, New Zealand during the peak of each season, and frozen immediately in liquid nitrogen. Samples were transported in dry-ice and stored at −80 oC until use. During spring and summer, care was taken not to include any floral stems in the tissue sample. Grass samples were collected from pregrazed (15–60 days post-grazing) and post-grazed (1 day post-grazing) ryegrass swards, which were visibly healthy and free of any pests.

Construction of SAGE™ libraries
RNA was extracted using TRIZOL®  reagent (Invitrogen, Carlsbad,CA, USA). For each SAGE™ library, 100 ug of pre- and post-grazed sample-derived total RNA was employed, and the libraries were created using an I-SAGE™ or I-SAGE™Long Kit (Invitrogen) according to the manufacturer’s protocol. Pre- and post-grazed SAGE™ libraries were sequenced at the Australian Genome Research Facility (Brisbane, Australia), and the tags were extracted using SAGE2000 software and combined to produce the transcript profile for the season.

first: Puthigae

last: Sathish

first: Nimali

last: Withana

first: Margaret

last: Biswas

first: Catherine

last: Bryant

first: Kerry

last: Templeton

first: Muhannad

last: Al-Wahb

first: Claudia

last: Smith-Espinoza

first: John

last: Roche

first: Kieran

last: Elborough

first: Jonathan

last: Phillips


title: Whole Genome Drosophila Embryogenesis Time Course

status: Public on Nov 02 2006

city: New Haven

first: Christopher

middle: E

last: Mason

address: 1 Gilbert Street

department: Genetics

institute: Yale University

summary:
We analyzed the expression of every gene in the Drosophila genome during the first 24 hours of development to examine patterns of gene activatio and repression responsbile for early development.
Keywords: Expression Arrays time course

overall_design: We isolated mRNA from each time point and hybridized against a reference set of RNA that was pooled from time points across all of development.

first: Sean

last: Hooper

first: Stephanie

last: Boue

first: Roland

last: Krause

first: Lars

last: Jensen

first: Murad

last: Ghanim

first: Eileen

last: Furlong

first: Kevin

middle: P

last: White

first: Peer

last: Bork


title: FAIRE performed in human foreskin fibroblast cells

status: Public on Sep 01 2006

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

summary:
To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray.  FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters.
Keywords: Genome wide map of active chromatin

overall_design: Human foreskin fibroblast (ATCC CRL 2091) cells were cultured in 245 x 245 cm plates (90% confluent). Formaldehyde was added directly to the plates at room temperature to a final concentration of 1%; and incubated for 1, 2, 4, or 7 minutes.  Cells were glass bead disrupted and sheared using sonication, yielding fragments of DNA 0.5 to 1 kb.  Proteins and DNA fragments crosslinked to proteins were removed using a phenol/chloroform extraction.

first: Paul

last: Giresi

first: Jonghwan

last: Kim

first: Vishwanath

last: Iyer


title: SAGE in Cultured Murine COC During Early Maturation

city: Raleigh

first: Charlotte

middle: E.

last: Farin

address: 231B Polk Hall

department: Department of Animal Science

institute: North Carolina State University

summary:
In cultured cumulus oocyte complexes (COC) FSH induces gene transcription required for germinal vesicle breakdown (GVBD). Experiments were performed to determine the critical period when gene transcription is required for GVBD and identify candidate mRNAs involved. Experiment I: murine COC were cultured 4h in the presence of FSH with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) added at different intervals after the start of culture. COC cultured with FSH underwent GVBD (82+/-7%). When DRB was added at 0, 5 or 10 min after culture initiation, oocyte maturation was blocked (17+/-7%, 14+/-6% and 21+/-6% GVBD, respectively). When DRB was added after 15, 20 or 30 min, progressively more COC underwent GVBD (37+/-6%, 39+/-6% and 66+/-6%, respectively). The critical period of transcription required for GVBD occurred between 15 and 30 min after culture initiation. Experiment II: COC were cultured for 25 min in the presence (plusDRB) or absence (minusDRB) of DRB. SAGE libraries were generated from COC RNA of each treatment group. A total of 48,431 and 45,367 tags were sequenced for the plusDRB and minusDRB libraries, respectively. Criteria used to identify transcripts of interest included a total tag count of at least 10 across both libraries and a 3-fold or greater difference in expression between libraries. Using these criteria, 39 and 27 transcripts were identified as differentially expressed at the P</=0.01 and P</=0.001 levels, respectively. Differentially expressed transcripts were classed into major categories that included cell growth, development and regulation of gene expression. Differentially expressed transcripts represent candidates potentially involved in regulating maturation of murine COC.
Keywords: Analysis of treatment effect using SAGE library comparisons

overall_design: Mouse cumulus oocyte complexes (COC) cultured 25 min in presence (plusDRB) or absence (minusDRB) of 120 uM DRB, a transcriptional inhibitor.  SAGE libraries were constructed from 9 to 10 ug RNA from each treatment group.  Approx. 48,000 tags seqenced from each library.  Comparison of these 2 libraries used to identify potential candidate mRNAs associated with regulation of germinal vesicle breakdown in murine COC.

first: K

last: Rodriguez

first: L

last: Blomberg

last: Zuelke

first: J

last: Miles

last: Alexander

first: C


title: cDNA microarray analysis of human keratinocytes irradiated by ELF-EMF

status: Public on Oct 12 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

institute: nthu

summary:
The ami of this study was to investigate the possible biological effects of ELF-EMF by cDNA microarray.
Keywords: ELF-EMF, cDNA microarray, keratinocyte, cytoskeleton

overall_design: We used a loop design for the microarray study. In this design, there are five sample sets introduced: a sample set without treatment (Ctrl), two identical sample sets with ELF-EMF exposure (EMF), a sample set with UVB irradiation (UV), and a sample set with UVB irradiation followed by ELF-EMF exposure (UE). We hybridized each slide with labeled RNA from two sample sets, the RNA of one sample was labeled with Cy3 and the RNA of the other sample was labeled with Cy5.