title: Characterizing the expression of human olfactory receptor genes

city: Chicago

first: Omar

last: De la Cruz

state: IL

address: 5734 S University Ave

department: Department of Statistics

institute: University of Chicago

summary:
We aim, among other things, to characterize olfactory receptor (OR) genes wich are differentially expressed between olfactory epithelium (OE) and other organ tissues, in humans.
Keywords: Comparative

platform_organism:
Pan troglodytes
Homo sapiens
Canis lupus familiaris
Rattus norvegicus

overall_design: Six OE samples and ten non-OE samples, including two samples of the following tissues: liver, kidney, lung, testis, and heart.

first: Xiaohong

last: Zhang

first: Jayant

last: Pinto

first: Dan

last: Nicolae

first: Stuart

last: Firestein

first: Yoav

last: Gilad


title: The genomic landscape of histone modifications in human T cells.

status: Public on Feb 07 2007

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Rockville Pike

country: USA

institute: NHLBI, NIH

summary:
To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. Unexpectedly, we find that 3,330 gene promoters are associated with all of these histone modifications. The gene expression levels are correlated with both the absolute and relative levels of the activating H3K4me3 and the repressive H3K27me3 modifications. Our data reveal that rapidly inducible genes are associated with the H3 acetylation and H3K4me3 modifications, suggesting they assume a chromatin structure poised for activation. In addition, we identified a subpopulation of chromatin regions that are associated with high levels of H3K4me3 and H3K27me3 but low levels of H3K9acK14ac. Therefore, these regions have a distinctive chromatin modification pattern and thus may represent a distinct class of chromatin domains.
Keywords: SAGE-ChIP

overall_design: Genome-wide analysis of H3 K4 trimethylation (H3K4me3) and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells.

first: Tae-Young

last: Roh

first: S

last: Cuddapah

first: K

last: Cui


title: M. tuberculosis-M. bovis transcriptional comparison

status: Public on Jan 31 2007

city: Valdivia

first: Germán

last: Rehren

state: Valdivia

address: Campus Isla Teja

department: Biochemistry

country: Chile

institute: Universidad Austral de Chile

summary:
We used microarray hybridization to compare the total in vitro transcriptome of M. bovis and M. tuberculosis H37Rv. Our aim was to get a global view on the differences of gene expression between these pathogens as a mean to identify the genetic basis for their distinct phenotypes.Differential expression was detected in 258 genes, representing a 6% of the total genome. Of these, 13 genes were further confirmed by quantitative RT-PCR. Our findings provide new evidence concerning differences in gene expression between both pathogens, and confirm previous hypotheses inferred from genome comparisons and proteome analysis.
Keywords: Comparative genomic hibridization

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: Four independent biological replicates were analyzed for each strain, and one swap-dye experiment was included.

first: German

first: Ana

middle: M

last: Zarraga


title: Analysis of the exression and regulation of NleA-E in Escherichia coli O157:H7

status: Public on Jan 30 2007

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary:
Previous work has shown that locus of enterocyte effacement (LEE)-encoded effector proteins such as Tir and Map can be exported via the type III secretion system (T3SS) of E. coli O157:H7.  Additionally, a family of non-LEE encoded (Nle) effector proteins has been shown to be secreted from Citrobacter rodentium, homologues of which are located on the E. coli O157 chromosome. While, NleA has been shown to be secreted from pathogenic E. coli, the secretion of other Nle effector proteins has only been detected under induced conditions or using a mutated type III secretion system.   We aimed to determine if nle gene expression is regulated co-ordinately with other LEE-encoded effectors.  Using data generated from a combination of transcriptome arrays, we demonstrate that only nleA is expressed co-ordinately with the LEE effector genes.  Secretion and expression of NleA is regulated directly or indirectly by ler, a key activator of LEE expression.
Keywords: iMedia induction

overall_design: In order to assess if the nle genes were expressed co-ordinately with the LEE, whole transcript array analysis was performed.  Strain TUV93-0 was cultured in 2 minimal media: DMEM and MEM-HEPES, total RNA extracted, and hybridisations performed as described in materials and methods.  E. coli O157 strain TUV93-0 has been shown to secrete high levels of EspD and Tir effector proteins when cultured in MEM-HEPES, typically 5-10 fold higher than when the same strains are cultured in DMEM. Expression conditions were used that are highly selective for up-regulation of the LEE. The E. coli O157:H7 transcriptome was compared from bacteria cultured in MEM-HEPES with DMEM using triplicate cultures (independent biological replicates).

first: Andrew

middle: J

last: Roe

first: Luke

last: Tysall

first: Tracy

last: Dransfield

first: Dai

last: Wang

first: Douglas

last: Fraser-Pitt

first: Arvind

last: Mahajan

first: Neil

last: Inglis

first: Alison

last: Downing

first: Richard

last: Talbot

first: David

middle: G

last: Snith

middle: L

last: Gally


title: DGCR8 is required for microRNA maturation

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: RMB1018, 35 Medical Center Way

department: Urology

institute: UCSF

summary:
To determine whether DGCR8 is required for maturation of all miRNAs, we performed miRNA microarray analysis.  Using RNA from wild-type ES cells as our reference sample, we observed a global loss of miRNAs in DGCR8 knockout cells, but normal levels of expression in DGCR8 heterozygous cells. The similarity in expression levels between wild-type and heterozygous cells suggests that DGCR8 is not limiting in the maintenance of steady-state levels of miRNAs in ES cells.  Of the eighty-nine miRNA array probes that showed significant signals with wild-type RNA, eighty-two were drastically reduced in the DGCR8 knockout cells.  The remaining seven were not significantly altered in the DGCR8 knockout cells, but at least four of these seven miRNAs appear to be due to unavoidable contamination with RNA from the mouse embryonic fibroblast (MEF) feeder cells used for ES cell culture prior to the isolation of RNA.  These miRNAs were highly expressed in the MEFs and decreased when the ES cells were temporarily passaged on gelatin-coated plates without feeders.  The remaining three showed similar levels of expression in the heterozygous, knockout and MEF feeder cells.  Therefore, these signals may be small RNAs that are not processed with the help of the microprocessor complex.  Alternatively, these signals may result from unavoidable degradation products within the purified small RNA population.  In either case, our results show that DGCR8 is broadly required for miRNA processing with little evidence for redundancy or bypass mechanisms.
Keywords: cell type comparison, genetic modification

overall_design: MicroRNAs extracted from wild-type, DGCR8 heterozygous knockout and DGCR8 homozygous knockout were analyzed by microarray. In each array, wild-type samples serve as reference. Ratios were normalized based on positive control RNAs on the array. To determine if some of signals appeared in DGCR8 knockout ES cells are due to mice embryonic fibroblast (MEF) feeder cell contamination (this is unavoidable because these ES cells were grown on MEFs and passaged off MEF before RNA extraction). Two independent DGCR8 knockout ES cell lines were analyzed. For each cell line, array hybridization was done in duplicates. For DGCR8 heterozygous knockout ES cells, two independent batches of RNA samples were prepared and analyzed.


title: Cochlea Laser Timecourse

status: Public on Feb 01 2007

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

summary:
Much of human hearing loss is caused by loss of auditory hair cell (HC) function.  Mammals cannot regenerate these essential mechanoelectrical transducers of sound.  However, birds have retained the ability to regenerate HCs from surrounding supporting cells. To better understand hair cell regeneration, we have expression profiled the sensory epithelia from chicken cochleae and utricles.  Pure sensory epithelia, consisting of HCs plus supporting cells, were damaged with either neomycin or laser treatment.  Changes in gene expression at various points during regeneration were compared to undamaged control cultures on a custom microarray that interrogates the vast majority of transcription factor (TF) genes.   These experiments involved multiple biological samples and hundreds of microarray comparisons.
Keywords: timecourse

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: Hair-cell lesions in cultured cochleae sensory epithelia were created by laser microsurgery.  Sensory epithelia was allowed to recover for 30min, 1hr, 2hr, or 3hr.  There are 2 biological samples per timepoint, and experiments include technical replicates as well as dye-switches for a total of 77 microarrays.

last: Hawkins

first: Stavros

last: Bashiardes

middle: E

first: Veena

last: Bhonagiri

last: Alvarado

first: Judith

last: Speck

first: Mark

last: Warchol

first: Michael

last: Lovett


title: Temporal transcriptional response of endothelial cells to aqueous cigarette smoke extract exposure

status: Public on Jan 26 2007

city: Innsbruck

first: Blair

last: Henderson

address: Fritz-Pregl Strasse 3

department: Biocenter

country: Austria

institute: Innsbruck Medical University

summary:
Endothelial cells (HUVEC) were exposed to cigarette smoke extract for 3, 7, and 24 hours.  Total RNA was isolated and used for hybridisation to dual channel oligonucleotide genome-wide microarrays using untreated HUVEC as a control.
The objective was to find out what genes are regulated by exposure to cigarette smoke extract, and the time dependency of their regulation
Keywords: time course, stress response

overall_design:
Two biological replicates are included at each time point.
Dye swapping was used to exclude effect solely due to the Cy3 and Cy5 dyes used.

last: Bernhard

first: Michaela

last: Kind

first: Georg

last: Wick


title: Utricle Laser Timecourse

overall_design: Hair-cell lesions in cultured utricle sensory epithelia were created by laser microsurgery. Sensory epithelia was allowed to recover for 30min, 1hr, 2hr, or 3hr. There are at least 2 biological samples per timepoint, and experiments include technical replicates as well as dye-switches for a total of 33 microarrays.


title: Homocysteine induced alterations in gene expression in neural crest cells

city: Omaha

first: Greg

last: Bennett

state: NE

address: Nebraska Medical Center 985805

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary:
The amino acid homocysteine increases in the serum when there is insufficient folic acid or vitamin B12, or with certain mutations in enzymes important in methionine metabolism. Elevated homocysteine is related to increased risk for cardiovascular and other diseases in adults and elevated maternal homocysteine increases the risk for certain congenital defects, especially those that result from abnormal development of the neural crest and neural tube.  Experiments with the avian embryo model have shown that elevated homocysteine perturbs neural crest / neural tube migration in vitro and in vivo. While there have been numerous studies of homocysteine-induced changes in gene expression in adult cells, there is no previous report of a homocysteine-responsive transcriptome in the embryonic neural crest. We treated neural crest cells in vitro with exogenous homocysteine in a protocol that induces significant changes in neural crest cell migration. We used microarray analysis and expression profiling to identify 65 transcripts of genes of known function that were altered by homocysteine. The largest set of effected genes (19) included those with a role in cell migration and adhesion. Other major groups were genes involved in metabolism (13); DNA / RNA interaction (11); cell proliferation / apoptosis (10); and transporter / receptor (6). Although the genes identified in this experiment were consistent with prior observations of the effect of homocysteine upon neural crest cell function, none had been identified previously as response to homocysteine in adult cells.
Keywords: homocysteine ● microarray ● expression profiling ● embryo ● neural crest

overall_design: Neural tube explants were obtained from stage 9+ chicken embryos to generate neural crest cell cultures. After 4 hours in culture the cells were exposed to either media or homocysteine for 6 hours. The cultures were then processed for gene expression using the affymetrics chicken chip. For these experiments 3 control (media exposed) arrays were compared to 3 homocysteine-treated (100uM final concnetration).

first: Thomas

middle: H

last: Rosenquist

first: Gregory

middle: D

first: Phil

middle: R

last: Brauer

first: Melanie

last: Stewart

first: Tammy

last: Chaudoin

last: Finnell


title: ChIP-chip analyses of SWIRM1 and SWIRM2 across the S. pombe genome.

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary:
Schizosaccharomyces pombe contains two proteins, SWIRM1 and SWIRM2, with close homology to human histone H3 lysine 4 demethylase. Both proteins contain the amino oxidase catalytic domain and a recently described DNA interaction SWIRM domain. Here we describe the biochemical isolation and the functional characterization of SWIRM1 and SWIRM2. Our results indicate that while SWIRM2 is an essential gene, cells lacking SWIRM1 are viable. We found that SWIRM1 and SWIRM2 are stably associated in a multiprotein complex, but intriguingly, unlike their human counterpart, S. pombe SWIRM complex contains neither a histone deacetylase nor any detectable demethylase activity. Genome-wide chromatin immunoprecipitation unexpectedly showed the absence of both SWIRM proteins from heterochromatic domains. Instead, consistent with biochemical analyses, SWIRM1 and SWIRM2 co-localize to a common set of target gene promoters whose functions are implicated in diverse processes including mitochondrial metabolism and transcriptional regulation. Importantly, we show that SWIRM1 is not only required for optimum transcription of its target genes but also display a global role in regulation of antisense transcription.
Keywords: ChIP-chip

overall_design: Chromatin immunoprecipitated DNA recovered with antibody against epitope-tagged protein from wild-type asynchronous growing fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto a custom Agilent 44K  in situ 60mer DNA microarray that tiles the entire Schizosaccharomyces pombe genome every 300 bp alternately on both strands. Data were processed using Agilent scanner and Feature Extraction software.

first: Estelle

last: Nicolas

first: MinGyu

last: Lee

first: Mohamed-Ali

last: Hakimi

first: Hugh

middle: P

last: Cam

middle: I

first: Ramin

last: Shiekhattar


title: Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

city: Taipei

first: Huang-Mo

last: Sung

address: 128 Sec.2 Academia Rd.

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

summary:
Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species.  To estimate their relative contributions, we examined two yeast strains, BY4741 (a laboratory strain) and RM11-1a (a wild strain), for their gene expression divergence first by microarray.  By incorporating the obtained array data with ChIP-chip data, we generated a set of single-regulator-regulated genes that showed expression divergence between BY4741 and RM11-1a.  We randomly selected 50 of these genes for further study. We found substantial variations in the DNA sequences of the promoter regions of these genes and in their regulators between the two strains, which are potential sources of expression divergence.  We then developed a step-by-step approach to assess the relative contributions of cis- and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the two alleles of BY4741 and RM11-1a in co-cultures and in hybrid diploids. Among the 50 genes studied, 4 genes showed no significant expression difference when the two strains were grown in separate cultures or in the same culture (co-culture) and 6 genes showed significant expression difference in separate cultures but not in co-culture. The remaining 40 genes showed expression divergence between the two strains in co-culture. Among these 40 genes, pyrosequencing of diploids showed that 18 cases of expression divergence (45%=18/40) can be attributed to differences in trans-acting factors alone, 7 cases (17.5%) mainly to trans-variations, 8 cases (20%) to both cis- and trans-acting factors, 3 cases (7.5%) mainly to cis-variations, and 4 cases (10%) to cis-acting factors alone.  In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed the cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.
Keywords: comparative gene expression between strains

overall_design:
Yeast strains were grown in YPAD and harvested at the mid-log phrase.  Overnight yeast cultures were used to prepare the starting cultures with OD600=0.1 and were grown in YPAD media at 30oC with 250 rpm shaking.  The yeast cells were harvested at the OD600=1.0.
Experiment was repeated eight times.  Dye-swapping was also performed in each set of experiments to eliminate dye bias (a total of 16 slides).

first: Wen-Hsiung

last: Li

first: Daryi

last: Wang

first: Tzi-Yuan

first: Chih-Jen

last: Huang

first: Peggy

last: Yang

first: Tiffany

last: Chang

first: Yang-Chao

first: Da-Lun

last: Tseng

first: Jen-Pey

last: Wu

first: Tso-Ching

first: Ming-Che

last: Shih


title: stress response

city: Heraklion

first: Elena

middle: Athina

last: Sarropoulou

department: Marine Biology and Genetics

country: Greece

institute: HCMR

summary:
Hybridization of one kidney of cortisol treated fish vs. one kidney of control fish.

Kidneys were collected from untreated juvenile sea bream (n=4) and from fish, which received for 72h a coconut-oil implant containing 10mg/Kg (fish wet weight) (n=4) cortisol. Experiments were carried out at the University of the Algarve, Portugal in accordance with National legislation for the welfare of animals. Experiments were conducted in two 125 l cylindriconical tanks supplied with a continuous through-flow of oxygenated seawater at 20+1 °C using juvenile sea bream (25 g + 3 g) adapted for 1 week to the experimental conditions. One tank contained 8 untreated fish (control) and the other tank 8 cortisol treated fish and the end of experiments fish were removed form tanks, decapitated and the kidneys rapidly removed and place in RNAlater (Qiagen) at –20 °C. No mortality occurred in the control tank but 2 fish died in the cortisol treated tank.

Keywords: other

first: Georgios

last: Kotoulas

first: Deborah

last: Power

first: Robert

last: Geisler


title: Replicative Senescence in Primary Fibroblasts

status: Public on Jan 24 2007

city: New Haven

first: Kimberly

last: Johung

state: CT

address: 333 Cedar Street

institute: Yale University School of Medicine

summary:
Senescent passage 26 fibroblasts compared to proliferating passage 8 fibroblasts
Keywords: Senescent vs. Proliferating

overall_design: A set of 28K Operon Version 2.1 and Version 2.1 upgrade -70 mer oligos. It has 48 pins with 24 columns and 25 rows in each subarrays. ID is Operon ID#.


title: Cochlea Neomycin Timecourse

first: Kara

last: Powder

overall_design: Cochleae sensory epithelia was antibiotic treated and allowed to recover for 0hr, 24hr, or 48hr.  There are 3 biological samples per timepoint, and experiments include technical replicates as well as dye-switches for a total of 51 microarrays.

first: David

last: Hawkins

first: Stavros

last: Bashiardes

first: Veena

last: Bhonagiri

last: Alvarado

first: Judith

last: Speck

first: Mark

last: Warchol

first: Michael

last: Lovett


title: HeLa/16E6-16E7d21-24 Cells (Wild-type E2-infected vs. Mutant E2-infected)

summary:
Senescent HeLa/16E6-16E7d21-24 cells compared to proliferating HeLa/16E6-16E7d21-24 cells
Keywords: Wild-type E2 Infection vs. Mutant E2 Infection


title: HeLa/16E6 Cells (Wild-type E2-infected vs. Mutant E2-infected)

summary:
Senescent HeLa/16E6 cells compared to proliferating HeLa/16E6 cells
Keywords: Wild-type E2 Infection vs. Mutant E2 Infection


title: Transcriptional profiling of Candida albicans delta-doa1 mutant

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

country: Germany

institute: Hans Knoell Institute

summary:
The Candida albicans delta-doa1 mutant was investigated.
This mutant shows lots of phenotypes.
Doa1 protein has several WD 40 repeats.
Keywords: mutant versus wildtype, comparative expression analysis

overall_design:
The expression of the Candida albicans delta-doa1 mutant was compared with that of the strain CAF2-1.
The strains were grown equally as mentioned in the description of each sample. The samples include biological repeat and dye swap.
Samples part 1 and 2 are Eurogentec arrays of the batch G300C
and part 3 of the batch H210C.

first: Donika

last: Kunze


title: HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila

status: Public on Feb 02 2007

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by array

summary:
Heterochromatin is important for the maintenance of genome stability and regulation of gene expression, yet our knowledge of heterochromatin structure and function is incomplete. We identified four novel Drosophila heterochromatin proteins. Three of these proteins (HP3, HP4, and HP5) interact directly with HP1, while HP6 in turn binds to each of these three proteins. Immunofluorescence microscopy and genome-wide mapping of in vivo binding sites shows that all four proteins are components of heterochromatin.  Depletion of HP1 causes redistribution of all four proteins, indicating that HP1 is essential for their heterochromatic targeting. Finally, mutants of HP4 and HP5 are dominant suppressors of position effect variegation, demonstrating their importance in heterochromatic gene silencing. These results indicate that HP1 acts as a docking platform for several mediator proteins that contribute to heterochromatin function.
Keywords: DamID knock-down

overall_design: DamID is based on the in vivo expression of a chimaeric protein consisting of a chromatin protein of interest fused to E. coli DNA adenine methyltransferase (Dam). Expression of low amounts of this fusion protein leads to preferential adenine methylation of DNA in the vicinity of native binding sites of the chromatin protein. Subsequently, adenine-methylated DNA fragments are isolated, labeled with a fluorescent dye, and hybridized to a microarray. Genomic binding sites of the protein can then be identified based on the methylation pattern. To correct for nonspecific binding of Dam, methylated DNA fragments from cells transfected with Dam alone served as a reference, and binding data are expressed as Dam-fusion:Dam methylation ratios. We performed DamID on heterochromatin proteins HP1 and Su(var)3-9. In addition we performed DamID on four interaction partners identified by Giot et al. (2003) that were previously unknown to be heterochromatin proteins (we named these HP3, HP4, HP5 and HP6). As a control non-heterochromatin protein we mapped the transcription factor Jra. The novel heterochromatin proteins HP3 and HP6 were also mapped after knock-down of HP1 and after knock-down of the white gene (as a control).

first: Frauke

middle: A

last: Greil

first: Elzo

last: de Wit

first: Harmen

last: Bussemaker


title: HeLa/16E6 Cells (Wild-type E2-infected vs. Mock-infected)

summary:
Senescent HeLa/16E6 cells compared to proliferating HeLa/16E6 cells
Keywords: Wild-type E2 Infection vs. Mock Infection


title: Functional genomics of cactus host shifts in Drosophila mojavensis

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

summary:
   Understanding the genetic basis of adaptation to novel environments remains one of the major challenges confronting evolutionary biologists.  While newly developed genomic approaches hold considerable promise for addressing this overall question, the relevant tools have not often been available in the most ecologically interesting organisms.  Our study organism, Drosophila mojavensis, is a cactophilic Sonoran Desert endemic utilizing four different cactus hosts across its geographic range.  Its well-known ecology makes it an attractive system in which to study the evolution of gene expression during adaptation.  As a cactophile, D. mojavensis oviposits in the necrotic tissues of cacti, therefore exposing larvae and even adults to the varied and toxic compounds of rotting cacti.

   We have developed a cDNA microarray of D. mojavensis to examine gene expression associated with cactus host use. Using a population from the Baja California population we examined gene expression differences of third instar larvae when reared in two chemically distinct cactus hosts, agria (Stenocereus gummosus, native host) vs. organpipe (S. thurberi, alternative host).  We have observed differential gene expression associated with cactus host use in genes involved in metabolism and detoxification.
Keywords: host adaptation, stress response, detoxification

overall_design: The experiment was composed of 5 sets of dye-flips (rep1-5).  Larvae were reared in either necrotic agria or organpipe cactus tissues.  They were then collected at the third instar stage and its total RNA extracted.

first: Thomas

last: Watts

first: Benjamin

last: Bitler

first: Carlos

last: Machado

first: Therese

last: Markow


title: RAD methods paper - Threespine Stickleback Lateral Plate Mapping

city: Eugene

first: Eric

last: Johnson

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular biology

institute: University of Oregon

summary:
Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags.  Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome.  Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping.  First, we show that these markers can be identified and typed on pre-existing microarray formats.  Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers.  We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback.  The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype.  Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems.
Keywords: microarray genotyping

overall_design: These data are normalized ratio data from the RAD tag hybridization experiments used to demonstrate the RAD marker genotyping method.  20 hybridization are present here that represent 18 unique experiments and 2 experimental replicates.

last: Miller

first: Joseph

last: Dunham

first: Angel

last: Amores

first: William

last: Cresko


title: Temporal Cortex Alzheimer's Disease

status: Public on Jan 23 2007

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

summary:
Ion channel splice array data from temporal cortex brain tissue samples collected from Alzheimer's disease patients.
Keywords: disease associated splicing changes

overall_design: Temporal cortex (Alzheimer's disease affected brain tissue structure) and cerebellum (Alzheimer's disease unaffected brain tissue structure) samples from control subjects were compared to temporal cortex and cerebellum of patients with Alzheimer's disease.

first: David

middle: B

last: Goldstein


title: Cerebellum Control (Alzheimer's disease control)

summary:
Ion channel splice array data from cerebellum brain tissue samples collected from control (non Alzheimer's disease) subjects.
Keywords: disease associated splicing changes


title: Temporal Cortex Control (Alzheimer's disease control)

summary:
Ion channel splice array data from temporal cortex brain tissue samples collected from control subjects (no Alzheimer's disease).
Keywords: disease associated splicing changes


title: Cerebellum Alzheimer's Disease

summary:
Ion channel splice array data from cerebellum brain tissue samples collected from Alzheimer's disease patients.
Keywords: disease associated splicing changes


title: Profile expression of genes involved in plant reaction to lead: uptake tolerance and defense.

status: Public on Jan 22 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary:
The aim of the experiment is to study the pattern of genes expression involved in defense to heavy metals and their transport and distribution within plant organs. Most of the plant species inhibits heavy metals entrance to the roots and their transport and accumulation to/in above ground organs after toxic ions penetrate roots. Some species of Brassicacea differ in the pattern of defense gene expression in the roots in a way that allow for greater transport of toxic ions to the above ground part. If so, by harvesting such plants toxic elements will be extracted from the soil.  Identification of these differences in the gene expression is crucial in development of the newly emerging environmental biotechnology phytoremediation in which plants as well as being green lungs play also a role of a green liver. Results of our studies with mustard plants showed among others that exposure for 12 hr to 12.5mg of Pb/1L of hydroponics solution is efficient to increase of constitutive genes expression and in de novo induction of genes expression coding for Pb tolerance and that this response is organ specific. Sequencing of the whole genome of A. thaliana opens the opportunity to study this phenomenon at molecular level more widely including the signaling (two-component system) and plasmolemma and tonoplast transporters genes. Therefore in our further steps we are going to use Arabidopsis as a model plant and the transcriptomics aproach is the only way for such studies. At first based on results with mustard physiological study we will conduct for elucidating Arabidopsis plant responses to lead in order to choose the most appropriate dose and time of treatment. In the trascriptome experiment we would like to study the profile gene expression in above ground parts and in the roots of arabidopsis plants in response to toxic ions of lead. Results of this study, besides promising applicable aspects, will also lead to a better understanding of plant acclimation and adaptation to antropogenic stresses. We expect to obtain mutant(s) tolerant to Pb and if so, they will be provided to NASC.
Keywords: organism_part_comparison_design

overall_design: 6 samples

first: Stanislaw

last: Gawronski


title: Temporal Cortex Control (mesial temporal lobe epilepsy control)

summary:
Ion channel splice array data from temporal cortex brain tissue samples collected from control subjects (no mesial temporal lobe epilepsy).
Keywords: disease associated splicing changes

overall_design: Temporal cortex samples from control subjects were compared to temporal neocortex of patients with mesial temporal lobe epilepsy


title: A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly post-transcriptional

city: Waltham

first: Dan

last: Tardiff

state: MA

address: 415 South Street

department: Biology

institute: Brandeis University

summary:
Recent ChIP experiments indicate that spliceosome assembly and splicing can occur cotranscriptionally in S. cerevisiae. However, only a few genes have been examined, and all have long second exons. To extend these studies, we analyzed intron-containing genes with different second exon lengths, by ChIP as well as by whole-genome tiling arrays (ChIP-CHIP). The data indicate that U1 snRNP recruitment is independent of exon length. Recursive splicing constructs, which uncouple U1 recruitment from transcription, suggest that cotranscriptional U1 recruitment contributes to optimal splicing efficiency. In contrast, U2 snRNP recruitment as well as cotranscriptional splicing is deficient on short second exon-genes. We estimate that approximately 90% of endogenous yeast splicing is post-transcriptional, consistent with an analysis of post-transcriptional snRNP-associated pre-mRNA.
Keywords: ChIP-CHIP

overall_design: ChIP-CHIP was performed on tagged U1, U2, and U5 snRNPs to address spliceosome assembly on intron-containing genes in S. cerevisiae. Data expressed as log2 (immunoprecipitation/input) ratios.

middle: F

first: S

last: Lacadie

first: M

last: Rosbash


title: Temporal neocortex mesial temporal lobe epilepsy

summary:
Ion channel splice array data collected from temporal neocortex brain tissue collected from patients with mesial temporal lobe epilepsy.
Keywords: disease associated splicing changes


title: Expression profiling of whole liver in 31 BxD mouse strains

status: Public on Jan 20 2007

city: Sydney

first: Rohan

middle: Benjamin Hugh

last: Williams

state: NSW

address: High St, Randwick

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

summary:
A genetical-genomics study underaken in 31 BxD strains using whole liver: as used in Williams, Cotsapas et al, Nature Genetics, 2006.
Keywords: genetical-genomics

overall_design: Each sample is a single hybridisation from a given BxD strain to a C57 reference sample. Two-colour glass arrays were used. No dye swaps were employed. Full details are avaiable in the supplementary material of PMID:16874319.

first: Chris

last: Cotsapas

first: Mark

last: Cowley

first: Eva

last: Chan

last: Nott

first: Peter

last: Little


title: Changes in gene expression specific to the depletion of major nutrients

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Background: Since chemical assays of soil nutrients are unreliable the UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yields and quality. Excessive fertiliser applications are both costly and can lead to unnecessary pollution. A possible solution to this problem is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression profiles under incipient nutrient deficiency. The aim of this project is to identify genes upregulated in the early stages of nutrient depletion. Methods: Arabidopsis ecotype Col-5 (N1644) will be grown hydroponically using established techniques. In parallel experiments NP and K will be withdrawn individually after 21 d growth. RNA will be extracted from shoots of nutrient replete (control) and nutrient depleted plants 24 h after the removal of nutrients. Shoot nutrient content will be assayed by ICP-EMS as a reference. By comparing expression profiles we will be able to differentiate between genes that are upregulated by lack of specific nutrients and those upregulated by a universal stress-response system. Promoters and transcripts of these genes will underpin the development of novel sensor technologies and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition.
Keywords: growth_condition_design

overall_design: 4 samples

first: Philip

last: White


title: Transcription profiling of Arabidopsis acclimation to light intensity

summary:
The acclimation of plants to environmental factors (light/temperature/nutrient availability) plays a crucial role in determining their tolerance to stress their ability to compete with other plants and the efficiency with which external inputs are used for growth and productivity.  Some of the clearest responses involve the major modifications in the composition of the photosynthetic apparatus in response to light intensity.  Photosynthetic acclimation. The acclimation response involves changes in the abundance of a large number of proteins in different cell compartments occurring at different intensity thresholds. The signal transduction chain is complex and involves crosstalk between redox control and other pathways that control photosynthetic gene expression but is poorly understood. Over the past 7 years we have laid the foundations for a molecular genetic approach by characterising the responses of Arabidopsis thaliana to growth in and transfer between high and low light conditions(1-6). Arabidopsis exhibits all the key features of photosynthetic acclimation: changes in maximum photosynthetic rate in leaf structure and in the levels of light-harvesting complexes photosystems and enzymes of carbon metabolism.  Method: Samples A-1, A-2 and A-3 were grown at a light intensity of 400 umol.m-2.s-1 until rosette growth was complete. Plants for samples A-2 and A-3 were then transferred to 100 umol.m-2.s-1. Samples A-4, A-5 and A-6 were grown at 100umol.m-2.s-1 until rosette growth was complete, when plants for samples A-5 and A-6 were transferred to 400 umol.m-2.s-1. Samples were taken 24 hours after transfer to the different light intensity and samples A-3 and A-6 were taken 72 hours after transfer.
Keywords: Photosynthesis

overall_design: Number of plants pooled:

first: Caroline

last: Howard


title: Identification of genes involved in the induction of storage reserve mobilisation

summary:
Aim  To identify genes specifically involved in the storage reserve mobilisation programme in Arabidopsis.  Background  During germination and early post-germinative growth in Arabidopsis seed storage reserves are broken down to provide energy and nutrients for the developing seedling. Genes encoding enzymes involved in the mobilisation of both storage lipid and protein are expressed strongly 1-2 days following imbibition and then fall to very low levels. The regulatory mechanisms controlling expression of these genes are poorly understood. Although germination and reserve mobilisation occur at the same time we have obtained evidence using Abscisic Acid (ABA) treated seeds that the events are regulated by two separate programmes. Arabidopsis seeds treated with 10mM ABA still express genes involved in the mobilisation of storage reserves and break down storage lipid even though germination is blocked. ABA treated seeds therefore provide a powerful system for the identification of genes involved specifically in the reserve mobilisation programme.  Microarray analysis will allow us to gain a global undertanding of the processes involved in storage reserve mobilisation and should also result in the identification of regulatory genes involved in this process.  Experimental Set-up  All seeds are Col-4 imbibed on plates containing 1/2 MS media for 4 days in the dark. All plant material will be grown in controlled environment growth rooms under defined light and temperature regimes. There are two parts to the experimental design.  1. Time course to identify genes involved in both seed storage reserve and germination programmes  Comparison of mRNAs from seeds immediately after imbibition (storage reserve and germination programme genes being induced) with 2 day (storage reserve genes maximally expressed) and 7 day old seedlings (storage reserve and germination programme genes off, photoautotrophic genes on) will allow the identification of genes exclusively presentor present at enhanced levels at the peak of reserve mobilisation (day 2).  2. ABA treatment experiment to identify genes involved in the storage reserve programme  ABA treatment blocks germination but does not block reserve mobilisation. Microarray analysis will be performed on RNA isolated from 2 day old seed imbibed in the presence of 10mM ABA. Comparison of the results of this experiment with those of the time course experiment should allow us to distinguish between genes involved in the two major programmes that we have uncovered.
Keywords: development_or_differentiation_design

first: Sarah

last: Pritchard


title: Cytological and molecular responses of Medicago truncatula to Erysiphe pisi

status: Public on Jan 25 2007

city: St Paul

first: Kathryn

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary:
For transcript analysis of early hypersensitive and susceptible responses of Medicago truncatula to the powdery mildew pathogen, Erysiphe pisi, we compared transcripts from pathogen-inoculated and control (non-inoculated) plants 12 h after infection in resistant (A14), partially resistant (A20), and susceptible (DZA315.16) genotypes.

Published in:
Medicago truncatula to the powdery mildew 1 and anthracnose pathogens, Erysiphe pisi and Colletotrichum trifolii.
Molecular Plant Pathology 8(3):307-319

Keywords: 1 time points and 3 genotypes

overall_design:
Single time point (12 h ) and 3 lines; consists of 18 microarrays.
Each genotype experiment consists of three direct (reps1, 2, 3) and three dye-swapped (reps 4, 5, 6) technical replicates.

first: Dawn

last: Foster-Hartnett

first: Dariush

last: Danesh

first: Silvia

last: Peñuela

first: Natasha

last: Sharopova

first: Gabriella

last: Endre

first: Nevin

last: Young

first: Deborah

last: Samac


title: HeLa/16E6-16E7 Cells (Wild-type E2-infected vs. Mutant E2-infected)

first: Kimberly

last: Johung

summary:
HeLa/16E6-16E7 cells after expression of wild-type E2 compared to an E2 DNA-binding mutant
Keywords: Wild-type E2 Infection vs. Mutant E2 Infection


title: fiber transformation with activation of CaN pathway

status: Public on Jan 18 2007

city: Baltimore

first: Xiaodong

last: Mu

address: 108 N. Greene street

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

summary:
Comparing the gene expression profile of day 3 of in vitro cultured FDB fibers with or without activation of calcineurin signaling pathways, with amplified RNA (cRNA probes).
constitutively active calcineurin was overexpression in one group of FDB fibers.
Keywords: cell treatment

overall_design: 3 independent experiments (bilological replicates) of reference design.

first: Martin

last: Schneider


title: fiber transformation in un-stimulated culture

summary:
Comparing the gene expression profile of day 3 of in vitro cultured FDB fibers to day 0 FDB fibers, with amplified RNA (cRNA probes).
Keywords: cell treatment

overall_design:
3 independent experiments (bilological replicates) of reference design.
comparing FDB fibers with or without 3 days of un-stimulated culturing.


title: fiber transformation with inhibition of CaMK pathway(KN93 vs KN92)

summary:
Comparing the gene expression profile of day 3 of in vitro cultured FDB fibers with or without inhibition of CaMK signaling pathways(KN93 vs KN92), with amplified RNA (cRNA probes).
Two indepenedent comparisons in conditions of culturing FDB fibers with or without slow-fiber-type pattern of electrical stimulation were both conducted.
----Un-stimulated culture: GSM153971, GSM153972, GSM153975,
and GSM153976.
----Electric-stimulated culture: GSM153978, GSM153980, GSM153984,
GSM153985, GSM153986, and GSM153987.
Keywords: cell treatment

overall_design: 3 independent experiments (bilological replicates) of reference design, for either conditions, with or without slow type electrical stimulation.


title: slow/fast muscle with or without amplification

summary:
Comparing the gene expression profiles of slow and fast skeletal muscle (soleus VS FDB) with either amplified RNA (cRNA probes) or original mRNA (cDNA probes). The fidelity of mRNA amplification method in identifying the gene expression profiles of our samples were validated.
Keywords: cell type comparison

overall_design:
there are two independent experiments.
one dye-swap design: GSM153745, GSM153746, GSM153747, and GSM153748.
one loop design:GSM154112, GSM154115, GSM154119, and GSM154120


title: Gene expression-based, individualized outcome prediction for surgically treated lung cancer patients

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

summary:
Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 8,644 genes in 50 non-small cell lung cancer (NSCLC) cases, which had been consecutively operated on within a defined short period of time and followed up more than five years.  The resultant classifier of NSCLCs yielded 82% accuracy for forecasting survival or death five years after surgery of a given patient.  In addition, since two major histologic classes may differ in terms of outcome-related expression signatures, histologic type-specific outcome classifiers were also constructed.  The resultant highly predictive classifiers, designed specifically for non-squamous cell carcinomas, showed a prediction accuracy of more than 90% independent of disease stage.  In addition to the presence of heterogeneities in adenocarcinomas, our unsupervised hierarchical clustering analysis revealed for the first time the existence of clinicopathologically relevant subclasses of squamous cell carcinomas with marked differences in their invasive growth and prognosis.  This finding clearly suggests that NSCLCs comprise distinct subclasses with considerable heterogeneities even within one histologic type.  Overall, these findings should advance not only our understanding of the biology of lung cancer but also our ability to individualize post-operative therapies based on the predicted outcome.
Keywords: cell type comparison and prognosis prediction

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised learning method-based individualized outcome prediction classifiers with high accuracy.  In addition, the identification by means of unsupervised hierarchical clustering analysis of two distinct subclasses of squamous cell carcinomas with interesting histologic distinctions and a significant difference in their prognosis is also reported.

first: Shuta

last: Tomida

first: Katsumi

last: Koshikawa

first: Yasushi

last: Yatabe

first: Tomoko

last: Harano

first: Nobuhiko

last: Ogura

first: Tetsuya

last: Mitsudomi

first: Masato

last: Some

first: Kiyoshi

last: Yanagisawa

first: Toshitada

first: Hirotaka

last: Osada


title: Identification of host miRNA regulated by HIV-1 - complementary datas

status: Public on Jan 17 2007

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
Time-dependent profile of differentially expressed miRNA following HIV-1 infection. Small RNAs were extracted from HIV-1 infected and non-infected pNL4-3 Jurkat cells at days 0 and 21 and miRNA expression was analyzed by microarray.
Keywords: time course

overall_design: At each time point (0 and 21), miRNA from infected vs non-infected cells were compared in a dye-swap experiment

first: Robinson

last: Triboulet

first: Thomas

last: Maurin

first: Bruno

last: Cardinaud

first: Bernard

last: Mari

first: Pascal

last: Barbry

first: Monsef

last: Benkirane

last: Le Brigand


title: Brain transcriptomics in response to beta-naphthoflavone treatment in rainbow trout: The role of AhR signaling.

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

institute: Woods Hole Oceanographic Institution

summary:
Polychlorinated biphenyls (PCBs) exposure disrupts steroid production in teleostean fishes. While this suppression of plasma steroid levels is thought to involve aryl hydrocarbon receptor (AhR) signaling, the target tissues impacted and the molecular mechanisms involved have rarely been addressed. We tested the hypothesis that AhR activation downregulates genes involved in neuroendocrine function, including the control of brain-pituitary-interrenal (BPI) and -gonadal (BPG) axes in rainbow trout. To elucidate receptor-specific signaling, we utilized a pharmacological approach using beta-naphthoflavone (BNF) and resveratrol (RVT) as AhR agonist and antagonist, respectively. The gene expression pattern in the brain was analysed using a low-density targeted trout cDNA array enriched with genes encoding proteins involved in endocrine signaling, stress response and metabolic adjustments. Upregulation of AhR and CYP1A1 gene expression with BNF and the inhibition of this response by RVT confirmed AhR-dependent signaling. RVT by itself impacted only a few genes, while BNF treatment significantly modulated the transcript level of 49 genes, many of which are involved in the neuroendocrine control of stress and reproduction. Of these, only 27% of the BNF-mediated transcriptional response was blocked by RVT, suggesting molecular regulation of neuroendocrine pathways that are also AhR-independent. Gene expression pattern for select genes seen with the microarray analysis was also confirmed using quantitative real-time PCR. Overall, our results reveal for the first time that BNF disrupts several key genes involved in the neuroendocrine control of stress and sex steroid biosynthesis, while the mode of action involves both AhR-dependent and -independent pathways in trout.
Keywords: Aryl hydrocarbon receptor, rainbow trout, brain transcriptomics, resveratrol, beta-naphthoflavone

overall_design:
The details of the experimental protocol was published recently (Aluru and Vijayan, 2006) and we only used the unstressed groups from this study for the brain transcriptomics analysis.  Briefly, groups of 8 fish each were randomly distributed in 12 tanks (100 liter) and acclimated for two weeks prior to the experiment. Treatments were assigned to the tanks (3 tanks per treatment x 4 treatments) randomly and the fish were fed with feed laced with either vehicle (ethanol laced feed) or vehicle containing resveratrol (RVT; 20 mg/kg body mass/day), β -naphthoflavone (BNF; 10 mg/kg body mass/day) or a combination of BNF and RVT (RBNF; 20 mg RVT and 10 mg BNF/kg body mass/day) for 5 days.  The feed was laced by evenly submerging in 95% ethanol alone (control) or ethanol containing RVT, BNF or RBNF to ensure adequate coating of the pellets. The ethanol was allowed to evaporate by air-drying and the feed was stored in a cool and dry place. The method and duration of feeding was based on our previous study (Aluru et al., 2005).

Microarray experiments were designed to comply with minimum information about microarray experiment (MIAME) guidelines. The development and application of the targeted trout cDNA microarray has been described in detail elsewhere (Wiseman et al., in review).  For hybridization, each sample was co-hybridized with a reference RNA pool (RP), made by pooling equal amounts of RNA from all the samples (4 fish per treatment X 4 treatments).  Hence, there were a total of 16 array slides for this experiment, each consisting of a sample and a reference RNA pool. Dye swapping was carried out for each treatment such that two slides had samples labeled with Cy3 and reference RNA with Cy5, while the other two was the opposite.

first: Vijayan

middle: M

last: Mathilakath


title: SKS mutant (snakeskin) vs wildtype

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
SKS mutant (snakeskin) vs wildtype
Keywords: strain_or_line_design

overall_design: 2 samples

first: Cathlene

last: Eland


title: High-throughput Mapping of the Chromatin Structure of Human Promoters

status: Public on Jan 15 2007

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

summary:
Understanding how chromatin structure affects cellular functions such as transcription and replication in human cells has been limited by a lack of sufficient nucleosome positioning data. We describe a high-resolution microarray approach combined with a novel analysis algorithm to examine the translational nucleosome positions in 3,692 promoters within seven human cell lines. Unlike unexpressed genes without transcription pre-initiation complexes at their promoters, expressed genes or genes containing pre-initiation complexes exhibit characteristic nucleosome-free regions at their transcription start sites. Coupling these data to ChIP-chip analyses reveals that the melanocyte master transcriptional regulator MITF binds predominantly to nucleosome-free regions, supporting the model that nucleosomes limit sequence accessibility. This study thus presents the first global view of human nucleosome positioning and provides a high-throughput tool for analyzing chromatin structure in development and disease.
Keywords: Nucleosome positions, MNase digestion, cell type comparison

overall_design: 12 samples in 7 cell types (A375 duplicates, IMR90 triplicates, MALME triplicates, MCF7, T47D, Primary Melanocyte, Mammary Epithelial Cells)

first: Fatih

last: Ozsolak

first: Xiaole

last: Liu

first: David

last: Fisher


first: Takashi

last: Takahashi

summary:
Widespread metastasis is the major cause of human lung cancer-related deaths, but there is much to be elucidated about underlying mechanism. Based on the genome-wide expression analysis of the highly metastatic lung cancer cell line NCI-H460-LNM35 (LNM35), we identified a cancer metastasis signature composed of 45 genes with previously uncharacterized features but well-known associations with human cancers including CXCL1, IER3, PTTG1, DAD1, METAP2, E-cadherin and galectin 3. In addition, the 45-gene metastasis signature gene set was significantly associated with a subset of primary tumors with poor prognosis not only in the lung but also the breast.
Keywords: cell-line morphologic comparison

overall_design: Two sets of membrane cDNA microarrays (GeneFilter Human Microarrays Release I and Release II; Invitrogen, Carlsbad, CA), containing a total of 11,168 spots corresponding to 8,644 independent genes, were used to analyze genome-wide expression analysis in duplicate between highly metastatic lung cancer cell line NCI-H460-LNM35 and low metastatic NCI-H460-N15.

first: Shuta

last: Tomida

first: Kiyoshi

last: Yanagisawa

first: Katsumi

last: Koshikawa

first: Yasushi

last: Yatabe

first: Tetsuya

last: Mitsudomi

last: Osada

first: Takahashi

last: Takashi


title: early developmental stages of sea bream

first: Elena

last: Sarropoulou

summary:
Five different developmental stages, neurula (1), hatching (48 h post-fertilization) (2), pectoral fin budding (96 h post-fertilization) (4), mouth opening (144 h post-fertilization) (6), and eye pigmentation (168 h post-fertilization) (7) were compared directly to each other in all possible combinations (Loop design).All experiments were perfomed by dye swap hybridizations.
Keywords: time-course

first: Georgios

last: Kotoulas

first: Robert

last: Geisler


title: Alternate splicing in Tlr4 pathway in LPS Stimulated BMMs

city: St Lucia

first: Sean

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute of Molecular Bioscience, Uni of QLD

summary:
Pairwise comparison of expression of alternate splicing in the Tlr4 pathway using custom designed Combimatix oligonucleotide arrays. Bone marrow derived macrophages (BMMs) from C57Bl6/J mice (6 wks male) exposed to LPS (10ng/ml) for 7hrs.
Keywords: Response to LPS

overall_design:
Pairwise design
4 technical replicates

first: Christine

last: Wells

first: Alistair

last: chalk

last: Forrest

first: Darrin

last: Taylor

last: Hume

first: Mark

last: Crowe

first: Piero

last: Carninci

first: Yoshihide

last: Hayashizaki


title: Establishing the action(s) of nitric oxide in plants.

status: Public on Jan 08 2007

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Nitric oxide (NO.) is a well-established signal in mammalian cells regulating e.g. smooth muscle tone, neurotransmission and apoptosis. NO interacts with superoxide (O2-) to derive the highly reactive peroxynitrite (ONOO-) radical leading to the generation of lipid hydroxy-peroxides (ROO.) and cell death. Thus the recent reports implicating of .NO in the Hypersensitive Response (HR) a form of programmed cell death elicited by pathogens in plantsis suggestive of parallel roles in animals and plants.  As part of BBSRC funded programmes which are investigating oxidative signaling and cell death in Arabidopsis we have collaborated with the Trace Gas Detection facility at the University of Nijmegen to be the first to measure NO in planta from a developing HR (Mur et al.paper in prep). The challenge remains to understand the spatio-temporal role(s) of .NO during the HR and disease development. In line with other groups e.g. Klessig et al.(2000) PNAS 978849-55 we have observed that .NO mediated event are both SA- dependent and independent.  We propose a two-stage programme to investigate NO events which will lead to subsequent BBSRC grant bids.  Firstly to exploit the GARNET Affymetrix transcriptomic service to identify genes which are upregulated by .NO (see programme below). These will be compared with similar data generated by other members of the consortium; Dr. Steve Neill for oxidative stress (Desikan et al. (2001). Plant Physiol 127(1): 159-72; Clarke et al.2000 Plant J.; 24:667-77); Dr. Paul Kenton who is mainly interested in signaling by the oxylipid Jasmonic acid (Kentonet al. (1999). MPMI 12(1): 74-78) as well as from other sources. Though these data in themselves will suggest modes of NO action. However as a second approach we will clone the promoter of a strongly NO-responsive gene which will be fused to positive and negative selectable markers as well as reporter genes e.g. LUC. to identify Arabidopsis EMS mutants which are perturbed in NO-mediated events.  Programme.   Our in planta measurement show that from a baseline production of 1nl.g fwt-1h-1 NO levels rise to 6nl. g fwt-h-1  (_plus/- 1.1 SE) prior to cell death and to 25nl g fwt-h-1  (_plus/- 4.2 SE) at cell death following which the concentration falls. At this juncture we will intend to gas Arabidopsis to ~75ppb (the head-space concentration when NO production was at 6nl. g fwt-h-1). Prior to using the DNA RNA will establish that this does not elicit cell death over the proposed treatment period and that both PR1 (SA-dependent) and PAL1 (SA-independent) genes are induced. We will compare this plant with sealed but non-treated Arabidopsis.  Future targets for DNA RNAs analysis induce plant treated with both NO (Sodium Nitro Prusside) and O2- (Xanthine oxidase) generators and depending on their effectiveness (to be assessed by NO measurement) HR lesions treated with Nitric Oxide Synthase inhibitors.
Keywords: compound_treatment_design

overall_design: Number of plants pooled:8

first: Luis

last: Mur


title: fiber transformation without CaMK pathway in electric-stimulation

first: Xiaodong

last: Mu

summary:
Comparing the gene expression profiles of day 3 of in vitro cultured FDB fibers with or without slow-fiber-type pattern of electrical stimulation, with inhibition of CaMK signaling pathways(KN93 or KN62), with amplified RNA (cRNA probes).

----CaMK inhibition (KN93): GSM154001, GSM154002, GSM154003,
      GSM154004, GSM154025, and GSM154026.
----CaMK inhibition (KN62)GSM154027, GSM154028, GSM154029,
      GSM154030, GSM154031, and GSM154032.
----Negative control (KN92): GSM154033, GSM154034, GSM154035,
      GSM154036, GSM154037, and GSM154038.

Keywords: cell treatment

overall_design: 3 independent experiments (bilological replicates) of reference design for each kind of treatment.

first: Martin

last: Schneider


title: Enhanced Bone Regeneration Associated with Decreased Apoptosis in Mice with Partial HIF-1Alpha Deficiency

status: Public on Jan 12 2007

city: Stony Brook

first: Michael

last: Hadjiargyrou

address: Psy A, Room 338

department: Biomedical Engineering

institute: Stony Brook University

summary:
HIF-1a activates genes under hypoxia and was hypothesized to regulate bone regeneration.  Surprisingly, HET HIF-1a fracture calluses are larger, stronger and stiffer than WT HIF-1a calluses due to decreased apoptosis.  These data identify apoptosis inhibition as a means to enhance bone regeneration.

Introduction: Bone regeneration subsequent to fracture involves the synergistic activation of multiple signaling pathways.  Localized hypoxia following fracture activates hypoxia-inducible factor 1 alpha (HIF-1a) leading to increased expression of HIF-1 target genes.  We therefore hypothesized that HIF-1a is a key regulator of bone regeneration

Materials and Methods: Fixed femoral fractures were generated in mice with partial HIF-1a deficiency (HET HIF-1a) and wild type littermates (WT HIF-1a).  Fracture calluses and intact contralateral femurs from post fracture day (PFD) 21 and 28 (N=5-10) were subjected to MicroCT evaluation and 4-point bending in order to assess morphometric and mechanical properties.  Molecular analyses were carried out on PFD 7, 10 and 14 samples (N=3) to determine differential gene expression at both mRNA and protein levels.  Finally, TUNEL staining was performed on PFD 14 samples (N=2) to elucidate differential apoptosis.

Results: Surprisingly, fracture calluses from HET HIF-1a mice exhibit greater mineralization and are larger, stronger and stiffer.  Microarray analyses focused on hypoxia-induced genes revealed differential expression (between genotypes) of several genes associated with the apoptotic pathway.  Real-time PCR confirmed these results, demonstrating higher expression of pro-apoptotic PP2A and lower expression of anti-apoptotic BCL2 in WT HIF-1a calluses.  Subsequent TUNEL staining demonstrates that WT HIF-1a calluses contain larger numbers of TUNEL positive chondrocytes and osteoblasts than HET HIF-1a calluses.

Conclusions: We conclude that partial HIF-1a deficiency results in decreased chondrocytic and osteoblastic apoptosis; thereby allowing the development of larger, stiffer calluses and enhancing bone regeneration.  Furthermore, apoptosis inhibition may be a promising target for developing new treatments to accelerate bone regeneration.
Keywords: Bone, Fracture, Apoptosis, Hypoxia, Microarray

overall_design: Unilateral femoral fractures were induced in WT HIF-1a and HET HIF-1a mice.  Total RNA from fracture calluses corresponding to post fracture day (PFD) 7, 10 and 14 was analyzed.  Comparisons were made between genotypes at each time point.  Focused microarrays for hypoxia-induced and angiogenesis related genes were utilized.

first: David

last: Komatsu

first: Marta

last: Bosch-Marce

first: Gregg

last: Semenza


title: Comparison of gene expression in spo0J mutant and wild-type B. subtilis

status: Public on Jan 10 2007

city: Cambridge

first: Adam

last: Breier

address: 77 Massachusetts Ave Bldg. 68-540D

institute: Massachsetts Institute of Technology

summary:
We investigated the genome-wide DNA binding of the chromosome partitioning and sporulation protein and ParB family member Spo0J in Bacillus subtilis using chromatin immunoprecipitation and DNA microarrays.  We identified ten parS loci to which Spo0J binds, two of which were unexpectedly distant (>1 Mb) from the origin of replication.  We used all ten sites to refine the consensus sequence for parS.  We found that Spo0J spreads along the DNA around each site.  Binding was near maximal levels up to 1.6 kb away from parS, and significantly above background as far away as 18 kb.  Deletion of soj (parA) had no detectable effect on spreading.  In contrast, the spo0J93 allele appeared to cause a significant decrease in spreading in vivo, without significantly affecting the DNA binding affinity in vitro.  spo0J93 causes a phenotype similar to that of a spo0J null mutant and alters the region thought to be involved in interaction between Spo0J dimers.  Our findings indicate that spreading is important for in vivo function of Spo0J.  Gene expression in areas near parS sites was similar in wild-type and a spo0J null mutant, indicating that binding and spreading of Spo0J on DNA does not silence transcription of nearby genes.
Keywords: genetic modification

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Gene expression was compared in spo0J mutant and wild-type B. subtilis by isolating total RNA from three independent cultures of each strain and comparing them on microarrays.  One of the arrays (GSM152506) used the reverse dye assignments relative to the other two.

first: Alan

last: Grossman


title: fiber transformation in electric-stimulated culture

summary:
The gene expression profile of day 3 of in vitro cultured FDB fibers subjected to slow-fiber-type pattern of electrial stimulation was compared to that of day 3 control FDB fibers without stimulation, with amplified RNA (cRNA probes).
Keywords: cell treatment

overall_design:
3 independent experiments (bilological replicates) of dye-swap design.
comparing day 3 of cultured FDB fibers with or without 3 days of slow-type electrical stimulation.


title: Mapping autism risk loci using genetic linkage and chromosomal rearrangements

status: Public on Feb 20 2007

city: Toronto

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

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

summary:
Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with = 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD.
Keywords: Autism spectrum disorder, Affymetrix SNP genotyping, linkage analysis, copy number analysis, chromosomal rearrangements.

overall_design: This is a large linkage study undertaken by The Autism Genome Project (AGP) Consortium to search for candidate genes underlying the etiology of autism.  1168 Muliplex families (= 2 affected individuals) consisting of 7600 individuals were genotyped using Affymetrix 10K whole genome mapping arrays. Copy number analysis was performed using DNA Chip (dChip) Analyzer.

first: Stephen

middle: W

last: Scherer

first: Bernie

last: Devlin


title: Gene Expression Time Courses of CH999 with High or Low Copy Number Plasmids

city: Stanford

first: Ryan

middle: C

last: Fong

address: 318 Campus Dr. W-300 Clark Center

department: Chemical Engineering

institute: Stanford University

summary:
Time courses of Streptomyces CH999/pKOS011-26 and CH999/pKOS011-26* the low and high copy number strains, respectively, to examine gene expression differences between these two strains. Of particular interest were the transcript levels of the activator gene actII-ORF4 and the polyketide synthase gene cluster eryA. Mycelia were grown in 50 mL R5 liquid medium with thiostrepton drug selection at 50 micrograms per mL in a 30 degrees Celsius shaker incubator. mRNA were harvested at the time points indicated. These data show that actII-ORF4 and eryA transcripts were more highly expressed in the high copy number strain than in the low copy number strain.
Groups of assays that are related as part of a time series.
Strain Name
Elapsed Time: Hours after inoculation
Keywords: time_series_design

overall_design: User Defined


title: TGFb/Smad4 targets promter in IOSE cells

status: Public on Jan 13 2007

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

summary:
Unlike ovarian cancer, normal ovarian epithelium response to TGFb1 induced growth inhibition. This study tried to idenify promoters that showed Smad4 binding after additionof TGFb1 in immortalized ovarian surface epithelial cells (IOSE) which is derived from normal ovarian epithelial cells
Keywords: ChIP-chip

overall_design: IOSE cells were treated with TGFb1 for 0 or 3 hrs. Cells were cross-linked and harvested for chromatin. ChIP assays were performed using antibodies against Smad4). The immunoprecipitated DNA was used to probe the Agilent human promoter microarray. Two experiments were performed.

first: Huaxia

last: Qin

last: Chan

first: Kenneth

last: Nephew

first: Ramana

last: Davuluri

first: Tim

middle: H

last: Huang


title: Identification of novel functional TBP-binding sites and general factor repertoires

city: Nijmegen

first: S

last: Denissov

address: Geert Grooteplein 26

institute: NCMLS

summary:
We performed a comprehensive ChIP-on-chip analysis for 28 transcription factors on a large set of known and novel TBP binding sites experimentally identified via ChIP-cloning. A large fraction of identified TBP binding sites is located in introns or lacks a gene/mRNA annotation and found to direct transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG- and non-CpG islands suggesting distinct transcription initiation pathways.
Keywords: TBP, Promoter, ChIP-on-chip, transcription factor profiling

overall_design:
DNA fragments from ChIP with TBP antibodies and human U2OS cells were cloned, amplified and printed on glass slides to obtain TBP-binding sites microarray. ChIP has been performed with 28 antibodies against transcripton factors and histone marks, DNA from ChIP and input was amplified and hybridyzed on the TBP-binding sites microarray.
The median ChIP/input ratios were normalized to median value of negative controls (myoglobin exons and promoter), averaged between 2 hybridizations and calculated as log2. For correlation analysis those targets with TBP ratio >2 were selected. Additionally, these targets were split to 2 datasets which contain targets overlapped and non-ovelapped with CpG islands (alignment and definition of UCSC genome browser).


title: Transcriptomic analysis of the plastid protein import 1 (ppi1) and ppi3 mutants

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Aim: To identify regulatory factors that control: (1) chloroplast protein importand (2) chloroplast-to-nucleus signalling. This project is a joint proposal from the Jarvis lab which is interested in chloroplast protein import [1] and the Moller lab which is interested in plastid-to-nucleus signalling [2].  Background: The majority of chloroplast proteins are encoded in the nucleus and imported post-translationally into chloroplasts. The abundance of chloroplast proteins may therefore be regulated at multiple levels. It is well documented that the nuclear gene expression is responsive to (largely unknown) signals from the chloroplast [23] and evidence is now emerging that protein import is also a regulated process [1]. Protein import into chloroplasts is mediated by protein complexes in the outer and inner envelope membranes called Toc and Tic respectively. Biochemical studies of pea chloroplasts identified several Toc/Tic components. These proteins are mechanistic or structural components of the import apparatus. Arabidopsis homologues of the pea Toc/Tic proteins were identified by the AGI. Pea Toc34 is represented in Arabidopsis by two genes "Toc33 and Toc34" and pea Toc75 is represented by three genes. These different Tocs have different expression patterns and are proposed to have different precursor protein recognition specificities. The factors that regulate Toc expression in concert with the needs of plastids in developmentally different cells are unknown.  Proposal: Two Arabidopsis mutants will be analysed. The ppi1 mutant is null for the putative precursor protein receptor Toc33 [1]and the ppi3 mutant is null for a putative component of the protein import channel Toc75-IV (on chromosome IV). ppi1 plants are yellow-green in appearance but remarkably healthy and grow only slightly more slowly than wild type. By contrast ppi3 plants are indistinguishable from wild type by eye although analysis of the mutant's chloroplast proteome is beginning to reveal some differences (K. Lilley personal communication). Gene expression changes in ppi1 are likely to be quite extensive. Retardation of chloroplast development in ppi1 will activate retrograde signalling pathways so that many nuclear photosynthetic genes are down-regulated. Changes in the expression of photosynthetic genes and of the genes responsible for mediating these responses may therefore be observed. Any regulatory and signalling genes identified will be of interest to the Moller lab. The expression of factors that regulate Toc/Tic gene expression may also be altered in ppi1. It should be possible to distinguish these factors from those involved in the general control of chloroplast gene expression by comparing the results from the two mutants. Genes affected in both mutants are more likely to be involved in regulating chloroplast import since it is unlikely that widespread changes in gene expression will be observed in ppi3. Changes in the expression of factors that regulate import post-translationallyand of the Toc/Tic genes themselves (many are on the RNA) may also be observed.  References: 1. Jarvis P. et al. (1998) Science 282: 100-103. 2. Moller S.G. et al. (2001) Genes Dev. 15:90-103. 3. Jarvis P. (2001) Curr. Biol. 11: R307-R310.
Keywords: strain_or_line_design

overall_design: Number of plants pooled:

first: Paul

last: Jarvis


title: Hypoxia response in C. neoformans in H99, CM092 and CM098

status: Public on Jan 09 2007

first: Cheryl

last: Chun

institute: UC San Francisco

summary:
(1) The identification of genes that are transcriptionally regulated in response to exposure to hypoxia (~0.2% oxygen) in H99 (WT) and strains CM092 and CM098.
(2) The identification of genes that are differentially-regulated in the strain CM093 compared to H99 (WT)
Keywords: hypoxia response, comparative transcriptional hybridization

overall_design: 8 cultures for each strain (4 grown in normoxia and 4 grown in hypoxia) are analyzed on 4 microarrays for each strain (normoxia hybridized against hypoxia).  Two out of four microarrays contain dye-swaps.

first: Oliver

last: Liu

first: Hiten

last: Madhani


title: Array CGH in TAR syndrome

status: Public on Jan 07 2007

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

type: Genome variation profiling by genome tiling array

summary:
The series represents the analysis data of four TAR syndrome patients by submegabase resolution BAC array.
Keywords: array CGH

overall_design: This study aimed to detect submicroscopic rearrangements in patients with TAR syndrome by using a submegabase resolution BAC array.

first: Eva

last: Klopocki

first: Harald

last: Schulze

first: Gabriele

last: Strauss

first: Claus-Eric

last: Ott

first: Judith

last: Hall

first: Fabienne

last: Trotier

first: Luitgard

last: Neumann

first: Rolf

last: Habenicht

first: Rainer

last: König

last: Seemanova

first: André

last: Megarbane

first: Hans-Hilger

last: Ropers

first: Denise

last: Horn

first: Stefan

last: Mundlos


title: FNR- vs WT in anoxic conditions

status: Public on Jan 05 2007

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

address: 720 4th Ave S

institute: St. Cloud State University

summary:
Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. However, the role of FNR in S. Typhimurium is largely unknown. To assess its role in S. Typhimurium, we constructed an FNR-   mutant (NC983) in the pathogenic wild-type (WT) strain, ATCC14028s.
Keywords: FNR, Salmonella, anaerobic, virulence

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The WT and the fnr- mutant strains were grown under anaerobic conditions in a Coy Anaerobic Chamber. Total RNAs were isolated when the cultures reached an OD600 of 0.3 (mid-log). Microarray slides were used to compare the global expression patterns of the two strains (i.e., 14028s vs. NC983). On each slides there were three replicas of the Salmonella genome and we swapped dyes, thus having a total of six replicates for each gene.

first: Matthew

last: Evans

first: Steffen

last: Porwollik

first: Michael

last: McClelland

first: Hosni

last: Hassan


title: Transcriptional analysis of a Vibrio choleare rpoH mutant vs wild-type after a heat-shock

status: Public on Jan 03 2007

city: Boston

first: Leyla

last: Slamti

address: 136 Harrison Ave

department: Molecular biology and microbiology

institute: Tufts University/HHMI

summary:
Vibrio cholerae, the cause of cholera, can grow in a variety of environments outside of human hosts. During infection, the pathogen must adapt to significant environmental alterations, including the elevated temperature of the human gastrointestinal tract. σ32, an alternative sigma factor encoded by rpoH, activates transcription of genes involved in the heat-shock response in several bacterial species. We defined the V. cholerae RpoH regulon by comparing the whole genome transcription profiles of the wild-type and rpoH mutant strains after a temperature up-shift. Most of the V. cholerae genes expressed in an RpoH-dependent manner after heat-shock encode proteins that influence protein fate, such as proteases and chaperones, or are of unknown function.
Keywords: heat-shock response, rpoH

platform_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: 3 independent experiments were performed, each in duplicate with dye swaps.

middle: K

last: Waldor


title: A retroviral strategy that efficiently creates chromosomal deletions in mammalian cells

city: Montreal

first: Guy

last: Sauvageau

state: Quebec

address: Marcelle-Coutu Building 2900 Boul. Edouard Montpetit Quai 20

department: Université de Montréal

institute: IRIC

summary:
Background
We have developed and validated a set of complementary retroviruses that creates a wide range of nested chromosomal deletions. When applied to mouse ES cells, this retrovirus-based method generated deletions ranging from 6 kb to 23 Mb (average 2.9 Mb), with an efficiency of 64% for drugs-selected clones. Importantly, several of engineered ES cell clones, mostly those with large deletions, showed major alteration in cell fate.

The set of complementary replication-defective retroviruses exploited the Cre-loxP recombination system and reconstitution of a functional neomycin cassette for selection of recombination events. The first loxP sequenced was delivered using the anchor virus A1.  The integration was selected on puromycin.  ES cell clones containing one copy of the virus A1 were isolated and expanded (primary clones).  A second loxP was introduced by retroviral gene transfer using the saturation virus S1, selected on hygromycin (secondary clones).  The transient expression of the recombinase Cre in secondary clones allowed the recombination between the loxP sites and the functional reconstitution of a split neomycin expression cassette.  Neomycin resistant clones (tertiary clones) were isolated and expanded.  Chromosomal deletions are expected to have occurred in neomycin resistant clones that have lost both puromycin and hygromycin resistance genes.  In addition, other chromosomal rearrangements (e.g., inversions, translocations, etc.) are achievable using this system.

Aim
Inverse-PCR, array-based comparative genomic hybridization (aCGH) and spectral karyotyping were employed to confirm deletions (or other Cre-induced rearrangements) in several tertiary clones and to assess the genomic integrity of the ES cells altered.

Conclusions
aCGH conclusions are summarized together with complementary results from inverse-PCR and  spectral karyotyping in 3 tables:
Table 1: Summary of the virus A1 integration
Table 2: Characteristics of independent deletions confirmed by IPCR-aCGH
Table 3: Confirmed or suspected recombination events in trans

Notes for Table 2:
Mapping and deletion analyses were done using the UCSC Genome Browser (NCBI mouse Build 33). {a} Tertiary clones are labeled according to their family number (same integration of virus A1), followed by a specific id number.  If more than one clone presented a redundant rearrangement within the same group infected with virus S1, only one is reported for clarity. {b} Anomaly that was not present in the primary clone from which the tertiary clone was derived, as determined by aCGH or SKY.    ( -), no anomaly; (+), additional anomaly. {c} The deletion is not observed, in agreement with the resolution of aCGH. {d} Normal except for the loss of chromosome Y.  {e} Amplification of chromosome 1. {f} Amplification of chromosome 8. {g} Many chromosomes were lost according to SKY. {h} Amplification on chromosome 14.  Id, identification; kb, kilobase pairs; no., number; aCGH, array-based comparative genomic hybridization; SKY, spectral karyotyping; I-PCR, inverse-PCR; n.d., not determined.

Keywords: comparative genomic hybridization

overall_design: aCGH (n=30) were conducted between our mouse ES cell samples and a control normal mouse genomic DNA.  Selected tertiary clones (n= 20) were compared to their corresponding primary clones (n=9), in order to find anomalies that was not present in the primary clones from which they were derived.  Primary clones were compared together and to the unmodified R1 ES cells (n=1) to assess the genomic integrity.

first: Mélanie

last: Bilodeau

first: Simon

last: Girard

first: Josée

last: Hébert


title: Differential gene expression in the bone marrow of 15 week old layer and broiler chickens

status: Public on Jan 01 2007

city: Ames

first: Diane

last: Spurlock

state: IA

address: 243 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
Osteoporosis is a major problem for the laying hen industry due to welfare issues and economic losses related to bone fractures.  The objective of this research was to better understand genetic influences on bone integrity by comparing gene expression profiles from bone marrow of chickens expressing phenotypic differences for a number of bone characteristics.  Global expression profiles of genes included on the Fred Hutchinson Cancer Research Center (FHCRC) Chicken 13K array were assessed in broiler and layer chickens.
Keywords: Gene expression comparison between two chicken lines at 15 weeks of age

overall_design: Twelve hybridizations (6 dual-channel slides) are included in this dataset. Three 15 week old layer and three 15 week old broiler samples were labeled with each dye to control for dye bias.

first: Anna

last: Bennett

first: Patricia

middle: Y

last: Hester


title: Identification of Adr1 regulated genes

city: Marburg

first: Britta

last: Winterberg

address: Karl-von-Frisch-Str.

department: Orgnaismische Interaktionen

institute: Max-Planck-Institut für terrestrische Mikrobiologie

summary:
Adr1 of Ustilago maydis is a protein kinase that is activated after separation from the regulatory subunit mediated by high cAMP levels. A copy of the gene under the control of the arabinose-inducible crg1 promotor was introduced into the Cbx locus of the wild type strain FB1 creating strain HE140. To monitor the transcriptional changes upon adr1 induction by arabinose, we conducted a time course experiment comparing the wild type transcriptional response before and 75 or 180 min after medium shift to complete medium containing arabinose, as well as the response of the mutant HE140 before and 75 or 180 min after induction of the additional copy of adr1 by arabinose.
Keywords: gene induction

overall_design: Strains FB1 (control) and HE140 (a1b1 ipr[pcrg1:adr1]ips) were grown in CM medium containing glucose and were shifted to CM medium containing arabinose and grown for 75 or 180 min. Samples were taken before and after arabinose induction from two (glucose) or three (arabinose) biological replicates each.

first: Heiko

last: Eichhorn

first: Franziska

last: Lessing

first: Jan

last: Schirawski

first: Joerg

last: Kaemper

first: Philip

last: Mueller

first: Regine

last: Kahmann


title: The Transposon Insertion site Profiling Chip (TIP-chip)

city: Baltimore

first: Sarah

last: Wheelan

state: MD

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

summary:
We have developed a microarray intended for use in finding all transposons in a region of interest. By selectively amplifying and hybridizing transposon flanking DNA to our array, we can localize all transposons in the region present on our TIP-chip, a dense tiling array. We have tested our technology in yeast and have been successful.
Keywords: transposon insertion profiling, genomic DNA, yeast

overall_design: The two FY2 hybridizations are technical replicates and serve as a benchmark -- we compared these results to the published S288C sequence. The two GRF167 samples are also technical replicates and these are the base strain for the L27-10 hybridizations, and therefore serve as controls for those hybridizations. The three L27-10 hybridizations are all technical replicates.

middle: J

first: Lisa

middle: Z

last: Scheifele

first: Francisco

last: Martinez-Murillo

first: Rafael

last: Irizarry

first: Jef

middle: D

last: Boeke


title: Identification of iron regulated genes.

summary:
Identification of transcriptional changes of Ustilago maydis wild type strain FB1 grown in axenic culture in complete medium containing glucose without or with the addition of 10 µM FeSO4.
Keywords: gene induction

overall_design: Strain FB1 (wt) was grown in CM glucose medium in the presence or absence of 10 µM FeSO4.


title: Identification of genes regulated by the iron dependent transcription factor Urbs1.

summary:
Urbs1 of Ustilago maydis is a transcription factor that has been shown to repress its target genes (e.g. sid1, sid2) in the presence of iron. To identify additional genes regulated by Urbs1, we compared transcriptional profiles of the Ustilago maydis wild type strain FB1 grown in complete medium containing glucose with the addition of 10 µM FeSO4 to the Ustilago maydis urbs1 deletion mutant BW12 grown under the same conditions.
Keywords: gene induction

overall_design: Strains FB1 (control) and BW12 (urbs1 deletion mutant) were grown in CM glucose in the presence of iron.


title: Examination of gene expression levels in mutants of phytochrome-related protain

city: Meguro

first: Mitsunori

last: Katayama

state: Tokyo

address: 3-8-1 Komaba

institute: University of Tokyo

summary:
To identify novel phototransduction pathways in cyanobacteria, mutants defective for phytochrome-related proteins in Synechocystis sp. PCC 6803 that exhibit increased or decreased gene expression levels. were screened.
Keywords: array-based

overall_design: Gene expression level was compared between phytochrome mutants and the wild type strain grown in continulosly illumiantde consitions (strain name_WT_1 or 2), and between dark and light (strain name_Light_Dark1 or 2). Each experiment was carried out twice. In all twenty five microarray data were included.

first: Mtsunori

first: Xiao-Xing

last: Geng

first: Mari

last: Kobayashi

first: Fumiko

last: Yano

first: Minoru

last: Kanehisa

first: Masahiko

last: Ikeuchi


title: Expression Profiling of Oct4/GCTM2 Imunosorted Human ES cells

status: Public on Jan 11 2007

first: Sean

last: Grimmond

summary:
Boxed comparsion of Oct4/GCTM2 Imunosorted Human ES cells
Keywords: Oligonucleotide array

overall_design:
Boxed comparsion of Oct4/GCTM2 Imunosorted Human ES cells, comparing 4 populations:
P4: V.Low/ V.Low expression of Oct4 & GCTM2
P5: Low/ Low expression of Oct4 & GCTM2
P6: Mid / Mid expression of Oct4 & GCTM2
P7: High / high expression of Oct4/ GCTM2

first: Andrew

last: Laslett

first: Brooke

last: Gardiner

first: Haylock

last: David

first: Martin

last: Pera


title: Androgen responsive intronic non-coding RNAs

city: São Paulo

first: Eduardo

last: Reis

address: Av. professor Lineu Prestes, 748

department: Departamento de Bioquímica

country: Brazil

institute: Instituto de Química da Universidade de São Paulo

summary:
BACKGROUND: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. RESULTS: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5-5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. CONCLUSIONS: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.
Keywords: Time course study – effect of androgen on gene expression

overall_design:
Prostate carcinoma cell line LNCaP were treated with synthetic androgen or ethanol vehicle (control) and harvested for RNA isolation at several time points: 0, 6, 9, 12, 18, 24, and 48 hours. Each time point was hybridized twice, giving a total of 26 Samples, with at least 4 expression data of each spotted cDNA (2 internal replicates in each slide). In addition, hybridizations included a reference pool of RNA from 3 prostate carcinoma cell lines: LNCaP, DU145 and PC3 (cultured following ATCC suggested media), labeled using Cy3-dCTP. We decided to use the single-color approach  to calculate the treatment to control sample ratios using only Cy5-labelled sample measurements. The mean intensity signal (40% trimmed) of each dataset was used for normalization between experiments (best normalization procedure tested). The Cy3-labeled reference RNA pool was used only as a general quality control of experiments.
Spots with statistically significant expression changes in at least 3 consecutive time points in response to androgen stimulation were identified using the Significance Analysis of Microarray data (SAM) approach, using as parameters: two-class response (paired data), 1000 permutations, K-Nearest Neighbors Imputer, fold-change ≥ 1.5 and false discovery rate (FDR) < 5%.

first: Rodrigo

last: Louro

first: Helder

middle: I

last: Nakaya

first: Paulo

middle: P

last: Amaral

first: Fernanda

last: Festa

last: Sogayar

first: Aline

last: da Silva

first: Sergio

last: Verjovski-Almeida


title: Hyperhomocysteinemia alters the cardiac substrate metabolism by impairing NO bioavailability through oxidative stress

status: Public on Dec 31 2006

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

summary:
Hyperhomocysteinemia (HHCy) has been established as a risk factor for development of cardiovascular disease. Previous studies have focused on the alterations in vascular biology such as vasodilation and white cell infiltration. We have shown that in rats and mice with HHCy, superoxide reduces the ability of NO to regulate mitochondrial function. Molecular mechanisms responsible for HHCy changes in cardiac function and myocardial metabolism are not yet understood. This study was undertaken to determine the global changes in cardiac gene expression in dogs with chronic HHCy using Affymetrix Canine Array.
Keywords: Disease state analysis

overall_design: This study was undertaken to determine the global changes in cardiac gene expression in dogs with chronic HHCy using Affymetrix Canine Array. Methionine was added to the drinking water for two weeks. Cardiac RNA was extracted at two weeks from the control and methionine fed groups (n=4).

first: Nobuhiro

last: Suematsu

first: Shintaro

last: Kinugawa

first: Xiaobin

last: Xu

first: Fabio

middle: A

last: Recchia

first: Thomas

last: Hintze