title: Gene expression during tumor enhancement by 3,3’-diindolylmethane in rainbow trout:  Timecourse

city: Corvallis

first: Susan

middle: C.

last: Tilton

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
Indole-3-carbinol (I3C) and 3,3’-diindolylmethane (DIM), a primary I3C derivative in vivo, are known dietary chemopreventive agents also available as dietary supplements.  However, I3C has been found to act as a tumor promoter in rat (multi-organ) and trout (liver) models.  I3C and DIM were previously found to be estrogenic in trout liver based on toxicogenomic profiles.  In this study, we compare the post-initiation effects of DIM and 17β-estradiol (E2) on aflatoxin B1 (AFB1)-induced hepatocarcinogenesis in trout.  Trout were initiated as embryos with 50 ppb AFB1, fed control diet for three months followed by diets containing 0, 120 or 400 ppm DIM or 5 ppm E2 for 18 weeks before returning all groups to control diet.  Tumor incidence was determined 13 months later and found to be significantly elevated in AFB1-initiated trout fed either 400 ppm DIM or 5 ppm E2 compared to control animals.  To evaluate the mechanism of tumor enhancement, hepatic gene expression profiles were examined in animals fed promotional diets during the course of tumorigenesis and in hepatocellular carcinomas (HCCs) of initiated animals using a rainbow trout 70-mer custom oligonucleotide array.  We demonstrate that DIM alters gene expression profiles similar to E2 in liver samples during tumorigenesis and in HCC tumors.  Further, HCCs from animals on DIM and E2 promotional diets had a transcriptional signature indicating decreased invasive or metastatic potential compared to HCCs from control animals.  Overall, these findings are the first to demonstrate tumor promotion by DIM.  They confirm the importance of estrogenic signaling in the mechanism of promotion by dietary indoles in trout liver and indicate a possible dual effect that enhances tumor incidence and decreases potential for metastasis.
Keywords: time course

overall_design: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle, 400 ppm DIM or 5 ppm E2 (n=2 replicates per treatment) in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of animals at 3-week and 15-week timepoints for microarray analysis during promotion.  At 13 months, trout were sampled for tumors for correlation with microarray data.  Hybridizations were performed using standard reference design with dye-swapping.  For each sample, equal amounts of RNA (µg) were pooled from three fish per tank for every treatment (n=2 biological replicates per treatment).  cDNA from one of the two biological replicates was dye-swapped and hybridized to two slides as technical replicates (3 arrays per treatment).

first: Jerry

last: Hendricks

first: Gayle

last: Orner

first: Cliff

middle: B

last: Pereira

first: George

last: Bailey

first: David

middle: E

last: Williams


title: Identification of downstream targets of zebrafish Hoxb1a

status: Public on Jan 01 2007

city: Chicago

first: Victoria

middle: Emma

last: Prince

state: IL

department: Organismal Biology & Anatomy

country: USA

institute: University of Chicago

summary:
Despite 30 years of Hox gene study we have a remarkably limited knowledge of the downstream target genes that Hox transcription factors regulate to confer regional identity.  Here, we have used a microarray approach to identify genes that function downstream of a single vertebrate Hox gene, zebrafish hoxb1a.  This gene plays a critical and conserved role in vertebrate hindbrain development, conferring identity to hindbrain rhombomere 4.  For example, zebrafish Hoxb1a, similar to mouse Hoxb1, is required for the migration of r4-derived facial branchiomotor neurons into the posterior hindbrain.  We have screened microarrays carrying more than 16,000 expressed sequence tags (ESTs) for genes that are differentially regulated in normal versus Hoxb1a-deficient rhombomere 4 tissue.  Using this approach, we have identified both positively and negatively regulated candidate Hoxb1a target genes.  We have used in situ hybridization to validate twelve positively regulated Hoxb1a targets.  These downstream targets are expressed in a variety of subdomains within r4, with one gene, a novel prickle homolog (pk1b), expressed specifically within the facial branchiomotor neurons.  Using morpholino knock-down we show that the Hoxb1a target Pk1b is required for facial neuron migration, a single aspect of rhombomere 4 identity.
Keywords: Comparison of normal and Hox-deficient tissue

overall_design: We used microarray analysis to compare transcripts in Hoxb1a-positive versus Hoxb1a-deficient zebrafish hindbrain tissue from 19-20 hour post fertilization embryos.  To focus our analysis specifically on the region of hoxb1a expression, we microdissected Hoxb1a-positive r4 tissue from unmanipulated embryos, and Hoxb1a-deficient r4 tissue from Hoxb1a-Morpholino injected embryos.  As a secondary source of Hoxb1a-deficient tissue, we also dissected r2 from unmanipulated embryos.  For each tissue sample we performed a total of three replicates.  Our first experiment (Replicate 1) compared normal r4 and Hoxb1a-deficient r4.  Our second experiment (Replicate 2) compared r4,  Hoxb1a-deficient r4, and r2.  Our third experiment (Replicate 3) compared r4,  Hoxb1a-deficient r4, and two separate r2 samples.

first: Monica

middle: R

last: Rohrschneider

first: Gina

last: Elsen


title: Changes in gene expression profiles under phosphate deficiency.

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

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: stimulus_or_stress_design

overall_design: 4 samples

first: John

last: Hammond


title: Identification of host miRNA regulated by HIV-1

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, 7, 21 and 42 and miRNA expression was analyzed by microarray.
Keywords: time course

overall_design: At each time point (0, 7, 21 and 42 days), miRNA from infected vs non-infected cells were compared in a dye-swap experiment

first: Monsef

last: Benkirane

first: Bernard

last: Mari

first: Pascal

last: Barbry

first: Robinson

last: Triboulet

last: Le Brigand


title: Differential gene expression in the bone marrow of 60 week old layer and broiler chickens

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 60 weeks of age

overall_design: Twelve hybridizations (6 dual-channel slides) are included in this dataset. Three 60 week old layer and three 60 week old broiler samples were labeled with each dye to control for dye bias.

first: Anna

middle: K

last: Bennett

first: Patricia

middle: Y

last: Hester


title: Analysis of eosinophil maturation and activation

status: Public on Dec 30 2006

city: San Francisco

last: Voehringer

state: CA

address: 521, Parnassus Ave

department: Medicine, Infectious diseases

institute: HHMI

summary:
The study compares the gene expression associated with maturation and activation of murine eosinophils. Immature (CCR3-) and mature (CCR3+) eosinophils isolated from the bone marrow were compared; and activated eosinophils isolated from the lung of Nippostrongylus brasiliensis infected mice were compared to resting eosinophils isolated from the spleen of IL-5 transgenic mice.
Keywords: cellular differentiation comparison

overall_design: We used high speed cell sorting to isolate pure populations of eosinophils at different stages during their development from age and sex matched mice on BALB/c background. RNA was amplified with the Aminoallyl mRNA amplification kit from Ambion and labelled with Cy3 and Cy5 reactive dyes and hybridized to spotted Oligonucleotide arrays.

first: Richard

middle: M

last: Locksley


title: Down-regulation of a gene encoding CCR affects... cell wall function in embryogenic cultures of Norway spruce

status: Public on Dec 27 2006

city: Uppsala

first: Johan

last: Wadenbäck

department: Plant Biology and Forest Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

summary:
An attractive objective in the breeding of forest trees is to reduce the content of lignin or alter the lignin composition. However, for long-lived forest trees, such as conifers, it is time consuming and expensive to wait until mature wood is formed for estimating how different ligninfication genes affect cell wall differentiation. The aim of this work was to examine the possibility of detecting changes in global gene expression and of genes involved in lignin biosynthesis already in embryogenic cultures carrying the native Norway spruce cinnamoyl CoA reductase (CCR) gene in antisense orientation. Several genes, including genes regulating phenylalanine ammonia-lyase and peroxidase, regulating different pathways associated with lignin biosynthesis were affected but the transcript abundances of genes regulating lignin biosynthesis were not affected. Functional assignment defined by Gene Ontology terms, which provide functional classification for genes and gene products representing their corresponding biological process, cellular component and molecular function showed that transformation with asCCR affects a broad spectrum of functional categories, especially processes taking place in the cell wall. Furthermore, many changes in genes related to chromatin, DNA and chromosome take place.
Keywords: transgenic Norway spruce, embryogenic culture

overall_design: Comparing three asCCR lines, A78:3, A78:4, A78:5; twotransformed control lines, G88:5, G88:9; and the untransformed line 95:11:22. The embryogenic lines were compared in a fully balanced loop design for each biological replicate encompassing in total 24 microarray slides.

first: Sara

last: von Arnold

first: Ulrika

last: Egertsdotter

first: Hanna

last: Göransson

first: Adam

last: Ameur

last: Clapham


title: Gene expression during tumor enhancement by 3,3’-diindolylmethane in rainbow trout:  HCC tumor samples

status: Public on Dec 31 2006

first: Susan

last: Tilton

state: OR

summary:
Indole-3-carbinol (I3C) and 3,3’-diindolylmethane (DIM), a primary I3C derivative in vivo, are known dietary chemopreventive agents also available as dietary supplements.  However, I3C has been found to act as a tumor promoter in rat (multi-organ) and trout (liver) models.  I3C and DIM were previously found to be estrogenic in trout liver based on toxicogenomic profiles.  In this study, we compare the post-initiation effects of DIM and 17β-estradiol (E2) on aflatoxin B1 (AFB1)-induced hepatocarcinogenesis in trout.  Trout were initiated as embryos with 50 ppb AFB1, fed control diet for three months followed by diets containing 0, 120 or 400 ppm DIM or 5 ppm E2 for 18 weeks before returning all groups to control diet.  Tumor incidence was determined 13 months later and found to be significantly elevated in AFB1-initiated trout fed either 400 ppm DIM or 5 ppm E2 compared to control animals.  To evaluate the mechanism of tumor enhancement, hepatic gene expression profiles were examined in animals fed promotional diets during the course of tumorigenesis and in hepatocellular carcinomas (HCCs) of initiated animals using a rainbow trout 70-mer custom oligonucleotide array.  We demonstrate that DIM alters gene expression profiles similar to E2 in liver samples during tumorigenesis and in HCC tumors.  Further, HCCs from animals on DIM and E2 promotional diets had a transcriptional signature indicating decreased invasive or metastatic potential compared to HCCs from control animals.  Overall, these findings are the first to demonstrate tumor promotion by DIM.  They confirm the importance of estrogenic signaling in the mechanism of promotion by dietary indoles in trout liver and indicate a possible dual effect that enhances tumor incidence and decreases potential for metastasis.
Keywords: treatment effect

overall_design: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle, 400 ppm DIM or 5 ppm E2 (n=3 replicates per treatment) in the diet 5 days/week for 18 weeks.  At 13 months, trout were sampled for tumors.  Only HCC tumors (determined by histopathology) were used for microarray analysis.  Hybridizations were performed using standard reference design with dye-swapping.  cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates (5 arrays per treatment).

middle: C

first: Jerry

middle: D

last: Hedricks

first: Gayle

middle: A

last: Orner

first: Cliff

last: Pereira

first: George

middle: S

last: Bailey

first: David

last: Williams


title: Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent

status: Public on Dec 24 2006

city: Rotterdam

first: Wouter

last: Hendriksen

address: Dr. Molewaterplein 50

department: Pediatrics

country: Netherlands

institute: Erasmus MC

summary:
Recent murine studies have demonstrated that the role of response regulator 09 (RR09) of S. pneumoniae in virulence varies between strains. In the present study, we used a murine pneumonia model of infection to assess the virulence of a TIGR4 rr09-mutant, and found that TIGR4Δrr09 was attenuated after intranasal infection. Further, we investigated the in vitro transcriptional changes in pneumococcal rr09 mutants of two strains, D39 and TIGR4, by microarray analysis. The transcriptional profiles of the rr09 mutants in both strains displayed clear differences compared to their parental wild-type. In D39Δrr09 but not TIGR4Δrr09, genes involved in competence (e.g. comAB) were upregulated. In TIGR4, genes located on the rlrA pathogenicity islet, absent in the D39 genome, appeared to be regulated by RR09. Furthermore, several phosphotransferase systems (PTSs), believed to be involved in sugar uptake (e.g., sp0060-sp0066), were strongly downregulated in D39Δrr09, while not regulated by RR09 in TIGR4. To address the role of one of these PTS in virulence, D39Δsp0063 was constructed and tested in a murine infection model. No difference in virulence compared to the wild-type was found, indicating that downregulation of this gene alone is not the cause of the avirulent phenotype of D39Δrr09. Finally, expression of rr09 and three of our identified RR09 targets were assessed during infection in mice. This in vivo experiment confirmed differences in expression between TIGR4 wild-type and rr09-mutant, as well as between wild-type D39 and TIGR4. In conclusion, our results indicate strain-specific regulation of pneumococcal gene expression by RR09.
Keywords: genetic modification

overall_design: Each amplicon was spotted at least twice (technical replicates) on the DNA microarray. These replicates are indicated in the platforms and DNA microarray data by the addition of _rep1, _rep2, etc. The RNA for wild-type and rr09-mutant strains of D39 and TIGR4 was isolated in 3 independent biological replicates for each strain and were hybridised to at least 3 microarray slides.

middle: T

first: Nuno

last: Silva

first: Hester

middle: J

last: Bootsma

first: Clare

last: Blue

first: Gavin

last: Paterson

first: Alison

last: Kerr

first: Anne

last: de Jong

first: Oscar

middle: P

last: Kuipers

first: Peter

middle: W

last: Hermans

first: Tim

last: Mitchell


title: Gender dependent expression

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

summary:
Gender dependent gene expression in the kidney of 36 day old rats using the Affymetrix GeneChip rat expression set 230 array RAE230A.
mixed model ANOVA using log2 transformed signal intensity of PM.
Keywords: repeat

overall_design: Three rat strains Mhm, Us and MhmBN were examined. Three arrays were performed for each gender and strain combination. Total RNA from three rats was pooled for each array.


title: Genome-wide Expression Profiles of Drought and High-salinity Stresses-responsive Genes in Rice (Oryza Sativa L. Indica)

status: Public on Dec 19 2006

city: New Haven

first: Xiangfeng

last: Wang

state: CT

address: 352 OML, 165 Prospect st

department: MCDB

institute: Yale University

summary:
Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates.
Keywords: Comparison of gene expression in three tissues with stress treatment and without treatment

overall_design: To globally elucidate potential genes involved in drought and high-salinity stresses responses in rice, an oligomer microarray covering 37,132 genes including cDNA or EST supported and putative genes was applied to study the expression profiling of shoot, flag leaf, and panicle under drought or high-salinity treatment. Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates.

first: Junli

last: Zhou

first: Xingwang

last: Deng


title: Vibrio cholerae stringent response

status: Public on Dec 28 2006

city: Boston

last: Raskin

state: MA

address: 200 Longwood Avenue

department: Microbiology & Molecular Genetics

institute: Harvard Medical School

summary:
This study is an analysis of changes in gene expression during stringent response in Vibrio cholerae. V. cholerae cells in mid-log were treated with serine hydroxamate and gene expression was compared to untreated cells.
Keywords: Stress response, stringent response

overall_design: V. cholerae cells in mid-log were treated with the stringent response inducer serine hydroxamate for one doubling time, then RNA was harvested using a Trizol method.  Mock-treated cells (V. cholerae with dH2O added) also had RNA harvested.  Both serine-hydroxamate treated and wild type cell RNA was converted to cDNA, with one set incorporating Cy5, the other Cy3, with fluorophores reversed in the multiple analyses.  RNA from both conditions was applied to a whole genome PCR microarray from V. cholerae N16961, containing two sets of every ORF.  Data was analyzed by Genepix and Rosetta Resolver.


title: Steady-state analysis of genes regulated by the E. coli RNA chaperone, Hfq

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

summary:
cDNA microarray analysis to identify genes regulated by the RNA chaperone, Hfq. Four experiments were performed: 1/ Hfq+ vs Hfq- strains. 269 significantly differentially regulated genes were identified by SAM (Statistical Analysis of Microarrays), of which 120 changed more than 1.5 fold (48 increased and 72 decreased in hfq-). Amongst other genes, these experiments identified significant regulation of the sigma E and sigma 32 regulons. However, only genes induced by sigma E were similarly induced in hfq-; 8 operons repressed by sigma E were not repressed in hfq-. 2/ wt vs delta rseA. RseA is the antisigma factor for sigmaE. This comparison results in elevated steady-state levels of sigma E, and confirmed induction and repression of target regulon members. 3/ hfq+ vs hfq+ rpoE overexpression. RpoE encoding sigma E was overexpressed in an hfq+ background, confirming normal regulation of the sigma E regulon. 4/ hfq+ vs hfq- rpoE overexpression. Sigma E was overexpressed in an hfq- background. This demonstrated that 8 operons normally repressed by sigma E require hfq for this repression. The simple conclusion is that sigma E regulates small RNAs that, together with Hfq, bind target mRNAs and results in their rapid degradation. This study is detailed in Guisbert et al 2007 (J Bacteriol, 189:1963-73)
Keywords: Genetic modification

overall_design: This series consists of 4 separate experiments: 1/ Hfq+ vs Hfq- strains, 8 independent replicates; 2/ wild type vs delta rseA, 7 independent replicates; 3/ hfq+ vs hfq+ rpoE induced overexpression, 3 independent replicates; 4/ hfq+ vs hfq- rpoE induced overexpression, 3 independent replicates. All strains were grown to in M9 complete until mid log. For experiments 1/ and 2/, samples were then harvested from separate cultures for comparative microarray analysis. For experiments 3/ and 4/, cultures were induced with 1 mM IPTG to induce overexpression of rpoE, and samples collected from all strains 20 min after induction.

first: Eric

last: Guisbert

first: Nidhi

last: Ahuja

first: Emily

last: Witkin

first: Carol

last: Gross


title: Sir2-family of histone deacetylase regulated gene expression in Candida glabrata

status: Public on Jan 04 2007

city: Baltimore

first: Brendan

last: Cormack

state: MD

address: Hunterian Building 617, 725 N. Wolfe St.

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

summary:
Sir2-family of NAD-dependent histone deacetylases are involved in gene transcription repression in yeast. The C. glabrata genes encoding members of this family are SIR2 (CAGL0K01463g), HST1 (CAGL0C05357g), HST2 (CAGL0L08668g), HST3 (CAGL0H08239g) and HST4 (CAGL0F05621g). SIR4 (CAGL0K11396g) encodes a factor that forms a functional complex with Sir2. In this experiment, the transcription profile of C. glabrata HST1 null, HST2 null, SIR2 null or SIR4 null strain individually comparing with that of wild type strain was determined. All strains were grown in YPD liquid medium in Log phase at 30 C.
Keywords: transcriptional profiling by microarray

overall_design:
For HST1, GSM152133, GSM153296 are dye-swap experiment #1; GSM153702, GSM153703 are dye-swap experiment #2; and GSM153704, GSM153705 are dye-swap experiment #3.

For HST2, GSM153706, GSM153708 are dye-swap experiment #1 and GSM153713, GSM153715 are dye-swap experiment #2.

For SIR2, GSM153742, GSM153743 are dye-swap experiment #1 and GSM153744, GSM153749 are dye-swap experiment #2.

For SIR4, GSM153750, GSM153752 are dye-swap experiment #1 and GSM153753, GSM153754 are dye-swap experiment #2.

first: Biao

last: Ma


title: Changes in gene expression due to CgtA-depletion in Vibrio cholerae.

first: David

summary:
A cgtA-depletion strain in V. cholerae was constructed and used to identify changes in gene expression that occur due to loss of the gene product.  This information was then used to characterize the role of the gene, which was found to be involved in stress response.
Keywords: Depletion strain, stress response

overall_design: V. cholerae cells from a cgtA-depletion strain were used.  This strain requires arabinose for growth.  Cells were grown to mid-log, washed, and split into two cultures, one with arabinose, one without.  These cells were grown for one doubling time, then RNA was harvested using a Trizol method. Both depleted and non-depleted cell RNA was converted to cDNA, with one set incorporating Cy5, the other Cy3, with fluorophores reversed in the multiple analyses.  RNA from both conditions was applied to a whole genome PCR microarray from V. cholerae N16961, containing two sets of every ORF.  Data was analyzed by Genepix and Rosetta Resolver.


title: NSH79 Tn Library Mouse Pools

status: Public on Dec 15 2006

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary:
Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. 2007. Screen in NSH79 H. pylori strain background. Original 2000 clone transposon library was plated and patched to make 25 pools of 48 clones. Clones were infected into 4-8 C57Bl/6 mice and stomach bacteria from at least two mice were harvested at 1 week or one month. Semi-random PCR was used to amplify and label the DNA next to the transposon insertion from the input (Cy3) and output pool (Cy5) genomic DNA for each array. Two arrays were done per mouse. One array labeled from the left side of transposon (primers S, 2C) and one array labeled from the right side of the transposon (primers N3, 2C). Transposon insertions were defined by spots with signal four standard deviations above background in both arrays. We also counted insertions where two adjacent gene spots (after arranging the data in genome order) gave signal from the two different sides of the transposon (but not both).
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Keywords: pathogenicity_design

overall_design: Computed

last: Baldwin


title: M-CGH data from Bacillus subtilis strains from both subspecies and Bacillus vallismortis

status: Public on Dec 13 2006

first: Ashlee

last: Earl

address: 200 Longwood Avenue D-1, Rm 219

summary:
This series represents the work described in the publication Bacillus subtilis Genome Diversity by Earl et al. (Journal of Bacteriology, accepted)
Keywords: comparative genomic hybridization

sample_organism:
Bacillus vallismortis
Bacillus spizizenii
Bacillus subtilis subsp. subtilis

overall_design: The aim of this study was to examine genome diversity among Bacillus subtilis species members.  Strains were chosen from within both recognized subspecies and one close relative, Bacillus vallismortis.


title: Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase

status: Public on Dec 11 2006

city: Madison

first: Christopher

middle: Lawrence

last: Warren

state: WI

address: 1400 University Ave

institute: University of Wisconsin - Madison

type: Genome binding/occupancy profiling by genome tiling array

summary:
Functional engagement of RNA polymerase II (Pol II) with eukaryotic chromosomes is a
fundamental and highly regulated biological process. Here we present the first high-resolution map of Pol II occupancy across the entire yeast genome. We compared a wild-type strain with a strain bearing a substitution in the Sen1 helicase, which is a Pol II termination factor for non-coding RNA genes. The wildtype pattern of Pol II distribution provides unexpected insights into the mechanisms by which genes are repressed or silenced. Remarkably, a single amino acid substitution that compromises Sen1 function causes profound changes in Pol II distribution over both non-coding and protein-coding genes, establishing an important function of Sen1 in the regulation of transcription. Given the strong similarity of the yeast and human Sen1 proteins, our results suggest that progressive neurological disorders caused by substitutions in the human Sen1 homolog, Senataxin, may be due to misregulation of transcription.
Keywords: transcription termination, attenuation, silencing, non-coding RNA, Pol II, ChIP-chip

overall_design: 4 identical arrays tiling the S. cerevisiae genome.  Two arrays for wild-type, two arrays for Sen1 mutant.  Dye swap.  In first of each pair, IP is cy3 and input is cy5.  In second of each pair, IP is cy5 and input is cy3.  Input is defined as genomic DNA sonicated, amplified, and labeled as in IP (skip crosslinking and antibody steps).

last: Steinmetz

middle: L

first: Jason

middle: N

last: Kuehner

first: Bahman

last: Panbehi

first: Aseem

middle: Z

last: Ansari

last: Brow


title: Investigation of pneumococcal two-component signal transduction system RR/HK06 in D39

status: Public on Dec 23 2006

city: Adelaide

first: Alistair

last: Standish

address: North Terrace

department: School of Molecular and Biomedical Sciences

country: Australia

institute: University of Adelaide

summary:
We wanted to identify genes regulated by the two-component signal transduction system RR/HK06 in Streptococcus pneumoniae. We used microarray in order to discover regulated genes, investigating the effects of the over-expression of RR06 in D39 (serotype 2).
Keywords: Gene Regulation

overall_design: The RNA used for microarray analysis was extracted from S. pneumoniae D39 over-expressing RR06 and D39 containing over-expression vector without insert. RNA used was from two biological replicates with dye-swap performed for each.

first: Uwe

middle: H

last: Stroeher

first: James

last: Paton


title: NB4 cell line untreated and induced to differentiate by a 48h exposure to 1µM ATRA

status: Public on Dec 22 2006

city: Montpellier

first: Commes

last: Therese

address: 141 rue de la cardionille

department: Groupe d'Etude des Transcriptomes

institute: Institut de Génétique Humaine

summary:
NB4 is a cell line model of acute promyelocytic leukemia (APL).The t(15;17) translocation and consequent expression of the PML (Promyelocytic Leukemia Protein)/RARalpha (Retinoic Acid Receptor Alpha) fusion protein blocks differentiation at the promyelocytic stage.The PML portion of the PML/RARalpha fusion protein has a high affinity for the corepression complex, preventing RARalpha transcriptional activity. To induce complete remission in a high proportion of patients, a pharmacological dose of ATRA is required to destabilize this interaction and re-establish the differentiation program.
Keywords: SAGE Sau3A

overall_design: NB4 cell line untreated and treated by ATRA


title: 1/10 LC50 metal exposures to Daphnia magna

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary:
Background: Toxicogenomics provides new opportunities for innovative and proactive approaches to chemical screening, risk assessment, and predictive toxicology.  If applied to ecotoxicology, genomics tools could greatly enhance the ability to detect toxicants and understand the modes of toxicity in an environmental setting.  However, few studies have yet to illustrate the potential of genomic techniques in ecotoxicology.

Objective: Therefore, our objective was to demonstrate the potential utility of gene expression   profiling in ecotoxicology using Daphnia magna, a standard aquatic ecotoxicity test organism.

Methods: D. magna were exposed to copper, cadmium, and zinc at the 1/10 LC50 for 24 hours.  Following each exposure, RNA was isolated, reverse transcribed, and the cDNA was hybridized to a 5000 clone cDNA microarray for D. magna.  Differentially expressed cDNAs were sequenced and homology searches revealed each gene product's potential function.  Real time PCR was used to verify the differential expression of several genes, and enzyme assays were used to assess the significance of these changes.

Results: We identified distinct expression profiles in response to acute copper, cadmium, and zinc exposures and discovered specific biomarkers of exposure including two probable metallothioneins, and a ferritin mRNA with a functional IRE.  The gene expression patterns support known mechanisms of metal toxicity and reveal novel modes of action including zinc inhibition of chitinase activity.

Conclusions: Using a cDNA microarray for traditional ecotoxicology organism, D. magna, we have identified novel biomarkers of exposure and revealed possible modes of toxicity, providing experimental support for the utility of ecotoxicogenomics.

Keywords: comparative toxicant exposure

overall_design:
Three different metals used in this study: Cu, Cd, and Zn.
Daphnia magna were treated to these metals via. water exposure at the 1/10 LC50 as determined in 24-h acute toxicity assays.
The exposure was 24-h.
Three seperate biological replicates for each metal (1,2,3)
Two technical replicates for each exposure (A or B) for a total of six replicates for each exposure concentration.
Dye swap done for each technical replicate (A = control labeled with cy3, B= exposured treated with cy3).

first: Julia

middle: R

last: Varshavsky

first: Bonnie

last: Chang

first: Patricia

last: Holman

first: Alexandre

middle: V

last: Loguinov

first: Darren

last: Bauer

first: John

middle: K

last: Colbourne

first: Kelly

last: Komachi

first: Edward

last: Perkins

first: Owen

last: Hughes

first: Chris

last: Vukpe


title: Array CGH in retinoblastoma

status: Public on Dec 20 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

type: Genome variation profiling by genome tiling array

summary:
This series represents the data set described in the publication “Allelic loss in a minimal region on chromosome 16q24 is associated with vitreous seeding of retinoblastoma
Keywords: array CGH

overall_design:
Two patients with retinoblastoma were hybridised on a submegabase resolution whole genome tiling path BAC array. Detailed step-by step protocols for labelling and hybridisation can be downloaded from our website.
Each case was hybridised once. No background subtraction was done and signal intensities were normalized by subgrid LOWESS. Circular binary segmentation was employed to define segments of the same DNA copy number change. Aberrations were defined as segments, which exceeded a fixed log2 threshold of +/- 0.2.

first: Sandrina

last: Gratias

first: Harald

last: Rieder

first: Ludger

last: Klein-Hitpass

first: Stephanie

last: Schneider

first: Reka

last: Bölöni

first: Martin

last: Kappler

first: Dietmar

last: Lohmann


first: Justin

last: Borevitz

department: Ecology and Evolution

institute: University of Chicago

type: Expression profiling by genome tiling array

summary:
four biological replicates of arabidopsis accession columbia 78h old whole seedling expression data
Keywords: exon/intergenic comparison

overall_design: expression values of the four repliates of columbia were used for intensity distribution of exonic regions or intergenic regions


title: Expression data from healthy (control) and Staph aureus mastitis cows' milk somatic cells (MSCs)

status: Public on Dec 06 2006

city: Guelph

first: Wenjing

last: Tao

state: ON

address: Gordon street

department: Department of Pathobiology

country: Canada

institute: University of Guelph

summary:
Analysis of gene expression changes in milk somatic cells (MSCs) that occur with Staph Aureus mastitis. We used in house microarrays to indicate the changes that occur in gene expression in the BMCs as a result of mastitis
Keywords: single time point, comparison mastitis animal vs control animal

overall_design: Milk was taken from 7 pairs of Holstein cows identified as chronic S. aureus carriers (mastitis susceptible) and the ages, herds, stage of lactation and parity-matched control cows with no evidence or previous history of S. aureus mastitis.  Total RNA was extracted from milk somatic cells (MSCs) and reverse transcripted to cDNA.  Labelled cDNA probes (Cy3 and Cy5) derived from BMCs and MSCs) of infected quarters and healthy quarters of controls were hybridised to a bovine immune-endocrine cDNA array containing immune and endocrine related genes and the resulting changes in gene expression were analysed.

first: Bonnie

last: Mallard


title: velvetleaf/corn competition study

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
This study was designed to look for differential gene expression in the annual dicot weed velvetleaf when it is grown in competition with corn relative to when it is grown in monoculture.
Keywords: weed/crop competition

overall_design: There were three biological replicates for each treatment [growth with corn (W1, W2, and W3) and growth in monoculture (C1, C2, and C3)]. These were compared directly in a rolling circle dye swap design and included two additional cross circle hybridizations.

first: Sharon

last: Clay


title: Mouse adapted strain CGH

first: Nina

last: Salama

summary:
Microarray based comparative genomic hybridization of mouse adapted strains: 10700 pre-mouse SS1, SS1(A.L.)Sydney strain obtained directly from Adrian Lee, NSH79 Salama lab strain labeled as SS1-now know distinct, G27 obtained from Antonello Covacci. Genomic DNA from est strain (Cy5), genomic DNA from reference strains used for array fabrication (equimolar mix of 26695 and J99 genomic DNA)
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs


title: The activation of inflammatory response genes by LPS is blocked by HDAC inhibitor Trichostatin A (TSA)

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary:
TSA treatment blocks LPS-induction of several inflammatory target genes in primary macrophages. The microarray experiment was performed to identify LPS-inducible, LXR-sensitive target genes that retained LPS-induction in the presence of TSA.
Thioglycollate-elicited macrophages were isolated from  mice by peritoneal lavage 3 days following peritoneal
injection of 2.5 ml 3% thioglycollate (DIFCO). Cells were plated in
RPMI medium 1640 and 10% fetal bovine serum, washed after 5 h the
medium was removed and cells were fed with fresh medium containing
0.5% fetal bovine serum. Cells were treated with TSA (Wako) at 100nM and/or with LPS (Sigma) at
concentration of 100 ng/ml in the absence or
presence of receptor-specific agonist for LXR (GW3965) at 1 µM.

Keywords: TSA, LPS, LXR agonist

overall_design: six samples were analyzed

first: sumito

last: ogawa

first: chris

last: benner

last: glass


title: Differential Recruitment of the Splicing Machinery during Transcription Predicts Genome-wide Patterns of mRNA Splicing

first: Michael

last: Moore

address: 200 Longwood Ave

department: Systems Biology

type: Genome binding/occupancy profiling by array

summary:
The splicing machinery associates with genes to facilitate efficient co-transcriptional mRNA processing.  We have mapped these associations by genome localization analysis to ascertain how splicing is achieved and regulated on a system-wide scale.  Our data show that factors important for intron recognition sample nascent mRNAs and are retained specifically at intron-containing genes via RNA-dependent interactions.  Spliceosome assembly proceeds co-transcriptionally, but completes post-transcriptionally in most cases.  Some intron-containing genes were not bound by the spliceosome, including several developmentally regulated genes.  On this basis we predicted and verified regulated splicing, and observed a role for nuclear mRNA surveillance in monitoring those events.  Finally, we present evidence that co-transcriptional processing events determine the recruitment of specific mRNA export factors.  Broadly, our results provide mechanistic insights into the coordinated regulation of transcription, mRNA processing, and nuclear export in executing complex gene expression programs.
Keywords: ChIP-chip

overall_design:
We analyzed the genomic localization of spliceosome components by chromatin IP followed by microarray analysis (ChIP-chip).  All factors examined were C-terminally tagged at their genomic loci with either -myc or -HA epitopes.  Between 3 and 6 biological replicates were performed for each factor.

DNA from ChIPs and WCE input was amplified by linker-mediated PCR and labeled by Klenow incorporation of Cy3- or Cy-5 UTP using a random primer mix.  In at least one replicate for each factor, fluorophores were swapped to control for bias during dye-labeling.  ChIP and WCE fractions for each sample were competitively hybridized to the University Health Network (UNS) yeast ORF array (v6.4k), washed, and scanned using the GenePix 4000B scanner.  Raw data was then uploaded onto Rosetta Resolver, and individual replicates were combined to give the raw data files submitted here.

middle: C

last: Yu

first: Pamela

last: Silver


title: NSH57 Tn Library Mouse Pools

summary:
Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. Screen in NSH57 H. pylori strain background. Original 50,000 clone transposon library was plated and patched to make 25 pools of 48 clones. Clones were infected into 4-8 C57Bl/6 mice and stomach bacteria from at least two mice were harvested at 1 week or one month. Semi-random PCR was used to amplify and label the DNA next to the transposon insertion from the input (Cy3) and output pool (Cy5) genomic DNA for each array. Two arrays were done per mouse. One array labeled from the left side of transposon (primers S, 2C) and one array labeled from the right side of the transposon (primers N3, 2C). Transposon insertions were defined by spots with signal four standard deviations above background in both arrays. We also counted insertions where two adjacent gene spots (after arranging the data in genome order) gave signal from the two different sides of the transposon (but not both).
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Keywords: pathogenicity_design

last: Baldwin


title: Targeting the NF-κB signaling pathway in Notch1-induced T cell leukemia

status: Public on Dec 02 2006

city: Collegeville

first: Tomas

last: Vilimas

state: PA

address: 1250 S. Collegeville Rd.

department: Oncology Discovery Technology Group

institute: GlaxoSmithKline

summary:
T cell acute lymphoblastic leukemia (T-ALL), unlike other ALL types, is only infrequently associated with chromosomal aberrations, but it was recently shown that the majority of TALL patients carry activating mutations in the NOTCH1 gene. However, the signaling pathways and target genes responsible for Notch1-induced neoplastic transformation remain undefined. We report here that constitutively-active Notch1 activates the NF-κB pathway transcriptionally and via the IκB kinase (IKK) complex, thereby causing increased expression of multiple well-characterized NF-κB target genes in bone marrow hematopoietic stem cells and progenitors. Our observations demonstrate that the NF-κB pathway is highly active in established human T-ALL and that inhibition of the pathway can efficiently restrict tumor growth both in vitro and in vivo. These studies identify NF-κB as one of the major mediators of NOTCH1-induced transformation and suggest that the NF-κB pathway is a potential target of future targeted therapies of T-ALL.
Keywords: gene expression analysis, signaling pathway alteration

overall_design:
Number of samples: 2.
Replicates: no.
Dye swaps: yes (Cy3, Cy5).
Reference sample: 1.

first: Iannis

last: Aifantis


title: Candida glabrata transcription profile when grown under Niacin starvation or in human urine

first: Brendan

last: Cormack

summary:
The transcription profile of Candida glabrata grown under two different Niacin limitation conditions were determined. Condition 1 is comparing log phase C. glabrata cells (O.D. 0.5-0.6) grown in synthetic medium containing 0.016 uM versus 3.25 uM nicotinic acid (NA), a common form of Niacin. The NA concentration of 3.25 uM is the standard concentration in synthetic complete (SC) medium. Condition 2 is comparing log phase C. glabrata cells (O.D. 0.4-0.6) grown in 3 individual human urine samples (supplemented with 2% glucose) versus in SC medium.
Keywords: transcriptional profiling by microarray

overall_design:
GSM151863, GSM151869 are dye-swap experiment #1 and GSM151880, GSM151881 are dye-swap experiment #2 for Niacin limitation condition 1.
GSM151934, GSM152116 are dye-swap experiment #1, GSM152118, GSM152119 are dye-swap experiment #2 and GSM152130, GSM152131 are dye-swap experiment #3 for Niacin limitation condition 2.

first: Biao

last: Ma


title: Characterization of the SOS response of Pseudomonas fluorescens strain DC454 using whole genome transcript analysis

city: San Diego

first: Hongfan

last: Jin

address: 5501 Oberlin Drive

department: Biotechnology

institute: The Dow Chemical Company

summary:
DNA microarray technology was used to survey changes in gene expression in P. fluorescens after mitomycin C (MMC) treatment.  As expected, genes associated with the SOS response were upregulated.  These include genes coding the recombination involved protein RecA, DNA repair protein RecN, excinuclease ABC subunit A UvrA, and the LexA repressor protein.  The expression profile was similar to that which had been shown for E. coli after MMC treatment.  Interestingly, expression of 33 bacteriophage-like genes was upregulated two hours after MMC treatment. Those genes are clustered in the chromosome.  This result suggests that MMC may induce a prophage resident in the P. fluorescens genome.  However, no phage particles were detected in a preparation of P. fluorescens strain DC454 that had been treated with MMC using transmission electron microscopy, and the same preparation failed to produce phage plaques on lawns of any of 10 different Pseudomonas strains tested, suggesting that the 33 bacteriophage-like gene cluster represents a defective prophage.
Keywords: time course, stress response

overall_design: These are the time points comparisons for 1hs vs 0hs and 2 hr vs 0 hr. The same comparisons were performed for the control strain and MMC treated strain.  Dye swaps were included for each comparison.  Therefore, there are 8 pairs in total.

first: Diane

middle: M

last: Retallack

first: Steven

last: Stelman

first: C

middle: D

last: Hershberger

first: Tom

last: Ramseier


title: H3K4 trimethylation ChIP - ctk1 deletion

status: Public on Dec 01 2006

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary:
Genome-wide location analysis of histone H3 lysine-4 trimethylation in a ctk1 deletion strain
Keywords: repeat

first: Julie

last: Stanton

first: Ali

last: Shilatifard


title: Genomic Resources for Birdsong Research

city: New York

first: XiaoChing

last: Li

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary:
Vocal learning and neuronal replacement have been studied extensively in the songbird brain, but until recently, few molecular and genomic tools have been available for this work.  Here we describe new molecular/genomic resources for songbird research.  We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11000 clones were sequenced from these libraries, representing 5870 unique gene transcripts.  A web-based database has been established for sequence analysis and functional annotations. The cDNA libraries were not normalized. Sequence analysis revealed that a cDNA library made from brains at post-hatching day 30-50, when the song system goes through rapid development and birds learn to sing, shows the highest gene discovery rate.  We grouped genes into functional categories according to the Gene Ontology classification and found that expression of the functional categories changed as the brain developed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species.  We printed cDNA microarrays and profiled gene expression in the HVC of both adult male zebra finches and canaries (Serinus canaria).  Statistical Analysis of Microarrays (SAM) was used for data analysis.  A subset of the differentially regulated genes was validated by in situ hybridization.  The bioinformatic tools EASE and Ingenuity Pathway Analysis were used to identify over-represented functional groups and gene networks among the regulated genes.  These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.
Keywords: HVC, songbird, cDNA microarray, gene expression

sample_organism:
Serinus canaria
Taeniopygia guttata

overall_design: We compared gene expression in HVC and whole-brain samples in adult male zebra finch and canary.  Three birds of each species were used.  For each bird, dye-switching was performed.

first: Xiujie

last: Wang

first: Jonathan

last: Tannenhauser

first: Sheila

last: Podell

first: Piali

last: Mukherjee

first: Moritz

last: Hertel

first: Jeremy

last: Biane

first: Shoko

last: Musuda

first: Fernando

last: Nottebohm

first: Teresa

last: Gaasterland


title: The Bile Response Repressor, BreR, Regulates Expression of the Vibrio cholerae breAB Efflux System Operon

status: Public on Dec 09 2006

city: Lebanon

first: Francisca

middle: A

last: Cerda-Maira

state: NH

address: 16 Cavendish Court

institute: Dartmouth College

summary:
Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene inducing conditions, in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport was increased in the presence of bile, whereas mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis was decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and multidrug efflux pumps from the RND superfamily (vexB and vexD [here renamed breB]) that were induced in response to bile. Further analysis regarding vexAB and breAB expression in the presence of various antimicrobial compounds established that vexAB was induced in the presence of bile, SDS or novobiocin, whereas induction of breAB was specific to bile. BreR is a direct repressor of the breAB promoter and is able to autoregulate its own expression, as demonstrated by transcriptional and electrophoretic mobility shift assays (EMSA). Expression of breR and breAB is induced in the presence of the bile salts cholate, deoxycholate or chenodeoxycholate and EMSA showed that deoxycholate is able to abolish formation of BreR-PbreR complexes. We propose that deoxycholate is able to interact with BreR and induce a conformational change that will interfere with its DNA binding ability resulting in breAB and breR expression. These results provide new insight into a transcriptional regulator and a transport system that likely play an essential role in the ability of Vibrio cholerae to resist the action of bile in the host.

Keywords: Vibrio cholerae response to bile

overall_design: Three independent experiments were performed for the microarray analysis. From each experiment, RNA was obtained from four different time points and was prepared for hybridization, therefore, a total of 3 slides were analyzed per time point. The growth conditions were as follows; C6706 str2 was grown 15 h in LB medium at 30 degrees C with aeration. The cultures were then diluted 100-fold into AKI medium with, or without, 0.4% crude bile (high bile concentration) and were grown at 37degrees C for 3.5 h stationary followed by 2 h with aeration to induce virulence gene expression. Then the cultures were diluted 100-fold into AKI medium with, or without, 0.02% crude bile (low bile concentration) and were grown at 37 degrees C for 2 h stationary. Samples were obtained from 4 different time points: 2, 4, and 5.5 h from the high bile cultures, and at 2 h from the low bile cultures.

first: Carol

middle: S

last: Ringelberg

first: Ronald

last: Taylor


title: Transcriptional changes caused by cpst12 gene disruption in Cryphonectria parasitica

status: Public on Nov 30 2006

city: Rockville

first: Donald

middle: Lee

last: Nuss

address: 9600 Gudelsky Drive

department: Center for Biosystems Research

institute: University of Maryland Biotechnology Institute

summary:
A putative homologue of the Saccharomyces cerevisiae Ste12 transcription factor was identified in a series of expressed sequence tag (EST)-based  microarray analyses as being down regulated in strains of the chestnut blight fungus, Cryphonectria parasitica, infected by virulence-attenuating hypoviruses.  Cloning of the corresponding gene, cpst12, confirmed a high level of similarity to Ste12 homologues of other filamentous fungi.  Disruption of cpst12 resulted in no alterations in in vitro growth characteristics or colony morphology and an increase in the production of asexual spores, indicating that CpST12 is dispensable for vegetative growth and conidiation on artificial medium.  However, the disruption mutants showed a very substantial reduction in virulence on chestnut tissue and a complete loss of female fertility, two symptoms normally conferred by hypovirus infection.  Both virulence and female fertility were restored by complementation with the wild-type cpst12 gene.  Analysis of transcriptional changes caused by cpst12 gene disruption with a custom C. parastica cDNA microaray chip identified 152 responsive genes. A significant number of these putative CpST12-regulated genes were also responsive to hypovirus infection.  Thus, cpst12 encodes a cellular transcription factor, CpST12, that is down-regulated by hypovirus infection and required for female fertility, virulence and regulated expression of a subset of hypovirus responsive host genes.
Keywords: Genetic modification

overall_design: Transcriptional profiles between cpst12 deletion mutant strain cpst-E1 and isogenic wild-type strain EP155 were compared in this experiment. Two sets of RNA samples with dye-swab (total of four hybridizations) were analyzed.

first: Fuyou

last: Deng

first: Todd

last: Allen


title: Expression data from healthy (control) and Staph sureus mastitis cows' mononucle

first: Wenjing

last: Tao

summary:
Analysis of gene expression changes in blood mononuclear cells (BMCs) that occur with Staph Aureus mastitis. We used in house microarrays to indicate the changes that occur in gene expression in the BMCs as a result of mastitis
Keywords: Comparison mastitis animal vs control animal

overall_design: Blood was taken from tail vein of 7 pairs of Holstein cows identified as chronic S. aureus carriers (mastitis susceptible) and the ages, herds, stage of lactation and parity-matched control cows with no evidence or previous history of S. aureus mastitis. Total RNA was extracted and reverse transcripted to cDNA. Labelled cDNA probes (Cy3 and Cy5) derived from BMCs and MSCs) of infected quarters and healthy quarters of controls were hybridised to a bovine immune-endocrine cDNA array containing immune and endocrine related genes and the resulting changes in gene expression were analysed.

first: Bonnie

last: Mallard


title: Differential repression of TLR responses by PPARg and LXRs

first: Christopher

last: Glass

summary:
Transrepression mediated by PPARg and LXRs agonists (GW7845 and GW3965) in primary macrophages stimulated with LPS or poly I:C. Thioglycollate-elicited macrophages were isolated from mice by peritoneal lavage 3 days following peritoneal injection of 2.5 ml 3% thioglycollate (DIFCO). Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after 5 h the medium was removed and cells were fed with fresh medium containing 0.5% fetal bovine serum. Cells were treated with LPS (Sigma) a concentration of 100 ng/ml or poly I:C (100 ng/ml) in the absence or presence of receptor-specific agonists for PPARγ (GW7845) or LXR (GW3965) at 1 µM concentrations. Results suggest signal-dependent nuclear receptors transrepression pathways.

Reference: Molecular Determinants of Crosstalk between Nuclear Receptors and Toll-like Receptors Mediating Counter-regulation of Inflammatory Responses. Sumito Ogawa, Jean Lozach, Chris Benner, Gabriel Pascual, Rajendra K. Tangirala, Stefan Westin, Alexander Hoffmann, Shankar Subramaniam, Michael David, Michael G. Rosenfeld, and Christopher K. Glass. Cell, Vol 122, 707-721, 9 September 2005.
Keywords: PPARg and LXRs agonists

overall_design: Two biological replicates were performed for each experimental condition.

first: Sumito

last: Ogawa

first: Jean

last: Lozach

first: Chris

last: Benner


title: H3K4 trimethylation ChIP - wild-type

first: John

last: Wyrick

summary:
Genome-wide location analysis of histone H3 lysine-4 trimethylation in wild-type strain
Keywords: repeat

first: Julie

last: Stanton

middle: J

first: Ali

last: Shilatifard


title: Comparative genomic hybridization of environmental Escherichia coli isolates indicates highly conserved ecophysiology

status: Public on Dec 05 2006

city: St. Gallen

first: Julian

last: Ihssen

address: Lerchenfeldstrasse 5

country: Switzerland

institute: EMPA

summary:
Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated the variability of important eco-physiological functions such as carbon substrate uptake and breakdown capabilities as well as stress defence mechanisms in the genomes of commensal and pathogenic E. coli strains. Furthermore, eco-physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high affinity substrate uptake systems. Our results indicate that the major eco-physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation.
Keywords: comparative genomic hybridisation

overall_design: Standard approach for comparative genomic hybrisisation, 5 environmental strains were analysed on commercial E. coli MG1655 arrays (MWG), for each strains, biological replicates were done (separate LB cultures)

first: Thomas

last: Egli


title: The Anopheles gambiae midgut transcriptome

status: Public on Nov 23 2006

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary:
The female midgut compartment specifc transcriptomes have been determined with microarray analyses.
Keywords: glass slide microarray analyses

overall_design: 2-dye hubridizations


title: Simultaneous Host and Parasite Expression Profiling Identifies Transcriptional Programs Associated with Cerebral Malaria

status: Public on Nov 24 2006

city: Toronto

first: Fiona

middle: E

last: Lovegrove

address: 1 King's College Circle, MSB Rm 7318

department: Institute of Medical Science

institute: University of Toronto

summary:
The development and outcome of cerebral malaria (CM) reflects a complex interplay between parasite-expressed virulence factors and host response to infection. To simultaneously analyze transcriptional programs in both parasite and host over the course of infection, we created microarrays to concurrently detect transcripts in the genomes of both Plasmodium berghei and mouse.

Analysis of RNA from brain, lung, liver, and spleen of mice infected with P. berghei ANKA showed that parasite gene expression is readily detected in whole organ RNA. Comparison of CM-susceptible (C57BL/6) and CM-resistant (BALB/c) mice showed that both host and parasite display distinct organ-specific transcriptional signatures in susceptible versus resistant animals.

Host genes whose expression differs between CM-resistant and CM-susceptible mice, at either baseline or induced by infection, tend to relate to humoral and immune response, complement activation, or cell-cell interactions, suggesting differences in immune function that may directly underlie protection from or susceptibility to CM.

P. berghei, in contrast, displayed differential expression of genes related to apparent biosynthestic activities, with the majority of transcriptional activity observed in the lung.

These data show that analysis of host and parasite gene expression profiles by hybridizing infected host samples to a single microarray is feasible, and can facilitate dissection of complex host-pathogen interactions.
Keywords: Time course, Disease state analysis

sample_organism:
Plasmodium berghei
Mus musculus

platform_organism:
Plasmodium berghei
Mus musculus

overall_design: 5 mice per group per timepoint;  Compare Brain, Liver, Lung and Spleen of infected (Day 3 and Day 6 post infection) to uninfected resistant (BALB/c) and susceptible (C57BL/6).

first: Lourdes

last: Pena-Castillo

first: Naveed

last: Mohammad

first: Timothy

last: Hughes

first: Kevin

last: Kain


title: Identification of activity-dependent gene expression profiles in cultured rat cortical neurons

status: Public on Nov 25 2006

city: Beijing

first: Guangxin

last: Xiang

address: Tsinghua University

country: China

institute: Medical Systems Biology Research Center

summary:
We report a genome-wide expression analysis of cultured rat cortical neurons treated with specific pharmacological agents, a model with alterations in neuronal activity. Using the microarray approach in combination with microelectrode array (MEA) technology, we ascertained out of approximately 27,000 genes 248 activity-dependent genes, which encompass a large number of members of distinct families, including synaptic vesicle proteins, ion channels, signal transduction molecules, synaptic growth regulators, and others. These genes were further confirmed to be Ca2+-sensitive, largely regulated by Ca2+ influx through N-methyl-D-aspartate (NMDA) receptors, and partly through L-type voltage-gated Ca2+ channels (VGCCs). In addition, the dynamics of gene expression cascades, specifically and temporally regulated, and the pools of those downstream genes, selectively responded to particular routes of Ca2+ entry, were also elucidated, as well as the functional consequences of candidate genes associated with synaptic plasticity.
Keywords: pharmacological agents, cortical neurons

overall_design: pharmacological agents vs control


title: A chromatin-mediated mechanism for specification of conditional transcription factor targets

city: Chapel Hill

first: Jason

middle: D.

last: Lieb

state: NC

department: Biology

institute: Univeristy of North Carolina at Chapel Hill

summary:
Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered  mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that Rap1, a master regulator of yeast metabolism, binds to an expanded target set upon nutrient depletion despite decreasing protein levels and no evidence of posttranslational modification. Computational analysis predicted that proteins capable of recruiting the chromatin regulator Tup1 acted to restrict the binding distribution of Rap1 in the presence of nutrients. Deletions of TUP1, genes that encode recruiters of Tup1, or chromatin regulators recruited by Tup1, cause Rap1 to bind specifically and inappropriately to low-nutrient targets. These data, combined with whole-genome measurements of nucleosome occupancy and Tup1 distribution, provide evidence for a mechanism of dynamic target specification that coordinates the genome-wide distribution of intermediate-affinity DNA sequence motifs with chromatin-mediated regulation of accessibility to those sites.
Keywords: ChIP-chip

overall_design: ChIP-chip

first: Michael

last: Buck


title: Genomic Analysis of effect of bufalin on HL60 Cells

status: Public on Nov 29 2006

first: Chen

middle: Ai

last: Liang

address: Haidian District

department: Medical  School

institute: Tsinghua University

summary:
Bufalin, a natural toxin isolated from the Chinese toad venom preparation Chan ’su, has been used in leukemia therapy in the mainland China by inducing human leukemia cells to differentiation and apoptosis. In the present study, oligonucleotide microarrays were used to assess profiles of target gene regulation at several points at a 48h period by bufalin at an appropriate concentration in the human promyelocytic leukemia cell line HL60. Data from the gene expression profiles indicated that bufalin altered the expression of 1206 genes which are distributed in multiple profiles of regulation. Results are consistent with bufalin regulating HL60 cells proliferation and differentiation as well as apoptosis.
Keywords: time course

overall_design:
For microarray experiment, the cells in late log phase of growth were seeded in the 100mm flask in fresh medium at a concentration of 1×106/ml and bufalin was added to 12.5 nM concentration with 10 µM stock solution in PBS. Control cultures were maintained in medium supplemented with vehicle (DMSO) at a 1:10,000 dilution. No growth and differentiation effects of DMSO were observed under these culture conditions in HL-60 cells. All cells were grown in the dark.
RNA prepared from bufalin treated cells was used to synthesize fluorescent cDNA probe, followed by hybridization to the human oligonucleotide microarray. We have done double hybridization experiments with fluorescence switch with the same RNA preparation. The fidelity of microarray we used was evaluated with untreated HL60 cells by conducting the self-to-self gene expression profiling with dyeswap strategy. The experimental results indicated that only four genes were found to be altered in their expression level by ≥ 1.5 fold, and no gene was found to be altered in their expression level by ≥ 2 fold. Considering the very low false-positive ratio (4/21,329 for 1.5 fold or 0 for 2 fold), the ratio cut-off value for significant differential expression was chosen at 1.5 fold for 6h, and 2 fold for 12h, 24h, and 48h. The self-to-self gene expression profiling of untreated HL60 cells with dyeswap strategy also serves as the 0h time point experiment.
For microarray analysis with dyeswap strategy experiment, if at least one intensity value of Cy5 or Cy3 on two slides was more than 800, then that gene was selected as an expressed gene. According to this standard, there were 4820, 6318, 6325 and 6710 genes expressed at 6h, 12h, 24h and 48h respectively and total 8050 genes expressed in control and bufalin treated HL60 cells. For identification of differentially expressed genes, if Cy5 and Cy3 intensity value on one slide were both under 800, the Cy5 or Cy3 intensity value on other slide must be more than 3000. There were 21, 272, 461, 659 genes were found to be altered in their expression level by ≥ 2 fold at 6h, 12h, 24h and 48h respectively. Since the cut off 1.5 fold for changed gene expression was often selected and so the changed genes were selected for 6h at such cut off of 1.5 fold. Then there were 102 genes for 6h and was used for analysis below. Then total 1206 genes expression were changed at least one time point.

last: Ailiang

first: Zhang


title: Whole genome mapping of p63 binding sites in ME180 human cervical carcinoma cells

city: Boston

last: Struhl

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

summary:
Using tiled microarrays covering the entire human genome, we identify ~5800 target sites for p63, a homolog of the p53 tumor suppressor essential for stratified epithelial
development and implicated in epithelial stem cell maintenance.
Keywords: ChIP-chip

overall_design:
ME180 cells were grown in the absence (-) or presence (+) of the DNA-intercalating agent Actinomycin D (ActD).
Crosslinked chromatin from ME180 cells was immunoprecipitated with the 4A4 anti-p63 antibody that recognizes all p63 isoforms.

first: Annie

last: Yang

first: Zhou

last: Zhu

first: Philipp

last: Kapranov

first: Frank

last: McKeon

last: Church

last: Gingeras


title: Efficient High-Resolution Discovery in C. elegans by Array Comparative Genomic Hybridization

status: Public on Nov 18 2006

city: Vancouver

first: Donald

last: Moerman

state: British Columbia

address: 301 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

summary:
The Males Experiment:
This experiment was done to test the sensitivity of our array in detecting single copy losses of probes to the X chromosome.  Males (XO) have just one X chromosome, while hermaphrodites (XX) have two.

CB4856 and JU258:
This experiment was done to determine the natural copy number variation that exists in a wild C. elegans isolate.  Extensive natural copy number variation exists in this strain.

gkDf2 (VC100):
This control experiment was done to confirm that we could reliably detect a large 50-kb homozygous deletion on chromosome X using this array.

gk329 (VC766):
This control experiment was done to confirm that we could reliably detect a homozygous 1-kb single-gene deletion on the X chromosome.  This deletion targets the gene ceh-39.

For gk291 (VC615):
This control experiment was done to confirm that we could reliably detect a heterozygous (single copy) single-gene 1-kb deletion on chromsome II.  This deletion targets the gene dab-1.

All other experiments:
This experiment was done in an effort to detect novel balanced single copy losses on chromosome II in mutagenized strains.  Mutants were previously screened for homozygous lethal mutations on chromosome II, and these mutations were then balanced with the mIn1 balancer chromosome to generate the mutant strain screened in this experiment.
Keywords: comparative genomic hybridization

overall_design:
This is a simple Test vs. Reference CGH experiment.  One test sample was cohybridized with a reference sample (the strain N2).  There were no replicates or dye-swaps performed.

For each forward probe on the X:II chip there is also a probe with the reverse complement sequence.


title: Lymphoblastoid cell lines of families with Mitochondrial Myopathy and Sideroblastic Anemia

city: Los Angeles

first: Yelena

last: Bykhovskaya

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary:
We analyzed samples from two affected brothers (Affected 3 and 4) and their two affected female cousins (Affected 7 and 9) homozygous for the MLASA ? associated C656T mutation in the PUS1 gene; four parents ? heterozygous carriers of the C656T mutation (Parents 1, 2, 5, 6), and an unaffected female carrying wild-type genotype at the PUS1 gene (Control 8). In addition, two females and one male with normal hearing from Arab-Israeli family with nonsyndromic deafness carrying wild-type PUS1 sequence were used as controls (Controls 10, 11, 12).
Keywords: Comparison of genome-wide expression in cell lines of patients and controls

overall_design: Lymphoblastoid cell lines established from peripheral blood lymphocytes of study participants and immortalized with Epstein-Barr virus, were grown in suspension in T flasks in RPMI-1640 medium (Invitrogen, Inc., Carlsbad, CA), containing 2 mmol/L L-glutamine, 100 ug/ml streptomycin, and 10% fetal calf serum. Total RNA was extracted using Trizol reagent (Invitrogen, Inc.) according to the manufacturer?s protocol. cRNA amplification and labeling with biotin were performed using Illlumina® TotalPrep RNA amplification kit, manufactured by Ambion, Inc (Austin, TX) according to the manufacturer?s protocol using 100 ng of total RNA as input material. 1ug of labeled cRNAs were hybridized to the three ?whole genome? Sentrix Human-6 Expression BeadChips (Illumina, San Diego, CA). RNA sample from patient Affected 4 was duplicated on the same chip, RNA samples from Affected 7 and Control 8 were duplicated on different chips. All hybridization and scanning steps were performed according to the manufacturers? instructions using reagents and equipment purchased from Illumina, Inc.

first: Y

first: E

last: Mengesha

first: N

last: Fischel-Ghodsian


title: Candidate genes correlated with progression to androgen-resistant stage in the LuCaP 23.1 xenograft model.

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

institute: Institut Paoli-Calmettes

summary:
Androgen-independent prostate adenocarcinomas are responsible for about 6% of overall cancer deaths in men. We used DNA microarrays to identify genes related to the transition between androgen-dependent and androgen-independent stages in the LuCaP 23.1 xenograft model of prostate adenocarcinoma.
Keywords: Prostate cancer, cDNA array

overall_design: We used DNA microarrays to compare the mRNA expression profiles of ~1.000 selected genes between primary, HS, and HR tumors in the LuCaP 23.1 xenograft model of prostate carcinoma. RNA extracts were pooled according to the three distinct stages of tumor progression in the LuCaP 23.1 model (4 samples / tumor stage). DNA microarray hybridizations were done as previously described (14, 15) on home-made nylon DNA microarrays (TAGC, Marseille-Luminy, France), which contained spotted PCR products from 945 human cDNA clones. Most genes were selected for a proven or putative implication in cancer and/or in immune reactions (the list is available on the web site: http:/tagc.univ-mrs.fr/pub/Cancer/).

first: Elisabeth

last: Devilard

first: Franck

last: Bladou

first: Olivier

last: Ramuz

first: Gilles

last: Karsenty

first: Jean-Philippe

last: Dales

first: Gwenaelle

last: Gravis

first: Cathy

last: Nguyen

first: Francois

last: Bertucci

first: Luc

last: Xerri

first: Daniel

last: Birnbaum


title: Transcripts associated with cell wall metabolism and development in the sugarcane stem by GeneChip expression profiling

status: Public on Nov 19 2006

city: St Lucia

first: Rosanne

middle: Elena

last: Casu

state: QLD

address: Queensland Bioscience Precinct, 306 Carmody Rd

institute: CSIRO Agriculture Flagship

summary:
Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem.
Keywords: stem development profile

overall_design: Three tissue samples were harvested from four biological replicates of field-grown Q117 sugarcane plants (12 tissue samples in all). The plants were grown as a commercial crop and were harvested in late March, 2005, 11 months after planting at Kalamia Mill estate in the Burdekin River region (North Queensland, Australia, Lat.: 19° 32’ S; Long.: 147° 25’ E). The tissue samples comprised (i) young stem (meristem and internodes 1-3; M,I1-3); (ii) maturing stem (internode 8; I8) and mature stem (internode 20; I20). Internodes were numbered from the apex down according to the method of Moore (1987). All samples were immediately frozen in liquid nitrogen and stored at -80ºC until required, then ground to a fine powder in liquid nitrogen using a coffee grinder followed by a mortar and pestle, and then stored again at -80ºC. Total RNA was isolated from each tissue using a modification of the method devised by Chomczynski and Sacchi (1987). Each RNA sample was subjected to DNase digestion (QIAGEN) to remove any remaining DNA and purified through an RNeasy column according to the manufacturer’s directions (QIAGEN). Labelled cRNA target for use in hybridisations was generated from 15 µg of total RNA using the One-Cycle Eukaryotic Target Labeling Assay, and hybridized to an Affymetrix Sugarcane Genome Array with washing, staining and scanning beingperformed as specified in the manufacturer’s protocol (Affymetrix, Inc.). The scanner operating software, GCOS, converted the signal on each array into a DAT file, which was then used to generate CEL and CHP files for analysis. GeneSpring 7.3 (Agilent Technologies) was used for data analysis. A “Sugarcane Genome” text file describing the probe sets present on the array was developed from the Sugar_Cane.gin file provided by Affymetrix as part of the GeneChip Sugarcane Genome Array Library Files. The CHP file was imported into GeneSpring running the Sugarcane Genome. A final normalised ratio was obtained by applying an additional “per probe set” normalisation. This was achieved by dividing the raw value for each probe set by the median value for that probe set in the whole experiment. This centred the data near a value of 1 and ensured ease of identification of differentially expressed probe sets.

first: Janine

last: Jarmey

first: Graham

last: Bonnett

first: John

last: Manners


title: Expression data from barley under salinity stress and JA treatment

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary:
Expression Data of Barley Crown and Growing Point Tissue Under Salt Stress abd JA treatment
Keywords: treatments (control, salt stressed, JA and JA plus salt stress)

overall_design: Barley genotype Golden Promise was used for expression anlaysis using the tissue from crown and growing point under control, salt stressed, JA treatment and JA pretreatment followed by salt stress

first: Timothy

last: Close


title: Mouse cerebellar libraries:Ethanol-treated and controls

status: Public on Nov 22 2006

city: Columbus

first: Magdalena

last: Popesco

state: OH

institute: The Ohio State Universiy

summary:
P300 and P720 C57BL6/J male mice were exposed to ethanol vapor (95% w/v) for 3 hours each day for a total of 5 days. Blood alcohol levels in the ethanol treated animals was 3.0mg/ml. Controls at P300 and P720 were included.
Keywords: SAGE-dose response

overall_design:
All C57BL/6 male mice were sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the libraries, 40micrograms of total RNA was used. cDNA was synthesized on oligo dt beads.
Enzyme: NlaIII
Vector: pZERO-I

first: Andrej

last: Rotter

first: Adrienne

last: Frostholm


title: Regulatory Network of Inflammation Downstream Proteinase-Activated Receptors

city: Oklahoma City

first: Ricardo

last: Saban

state: OK

institute: University of Oklahoma Health Sciences Center

summary:
Here, cDNA array experiments determined inflammatory genes whose expression is dependent on PAR1 activation. For this purpose, we compared the alteration in gene expression in wild type and PAR1-/- mice induced by classical pro-inflammatory stimuli (LPS, SP, and antigen). 75 transcripts were considered to be dependent on PAR-1 activation and further annotated in silico by Ingenuity Pathways Analysis and gene ontology (GO). Selected transcripts were target validated by real-time PCR.  Among PAR1-dependent transcripts, the following have been implicated in the inflammatory process: b2m, ccl7, cd200, cd63, cdbpd, cfl1, dusp1, fkbp1a, fth1, hspb1, marcksl1, mmp2, myo5a, nfkbia, pax1, plaur, ppia, ptpn1, ptprcap, s100a10, sim2, and tnfaip2. However, a balanced response to signals of injury requires a transient cellular activation of a panel of genes together with inhibitory systems which temper the overwhelming inflammation.  In this context, the activation of genes such as dusp1 and nfkbia seems to counter-balance the inflammatory response to PAR activation by avoiding prolonged activation of p38 MAPK and increased cytokine production. In contrast, transcripts such as arf6 and dcnt1 that are involved in the mechanism of PAR re-sensitization would tend to perpetuate the inflammatory reaction in response to common pro-inflammatory stimuli.
Keywords: time course, stress response, genetic modification

overall_design:
To determine the time course of gene-expression in urinary bladders in response to saline, SP, or LPS, challenge of wild type control and PAR1-/- mice.

We analyzed two animal strains:
C57bl6 (WT): GSM144550, GSM144556, GSM144557, GSM144558, GSM144559
PAR1ko: GSM144551, GSM144552, GSM144553, GSM144554, GSM144555

We used the following agents:
Saline: GSM144550; GSM144551
LPS: GSM144552, GSM144553, GSM144556, GSM144557
SP: GSM144554, GSM144555; GSM144558; GSM144559

The following time points:
4 hours: GSM144552; GSM144554; GSM144556; GSM144558
24 hours: GSM144550; GSM144551; GSM144553; GSM144555; GSM144557; GSM144559

No replicate is included. No dye-swaps.


title: Gene expression profiles of starved mice and mice treat with TNF alpha

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

summary:
Pathogenesis of atherosclerosis results from the interactions between disrupted lipid homeostasis and immune response but the molecular bridges between the major players are still a matter of controversy. We investigated the systemic effect of inflammatory cytokine tumor necrosis factor alpha (TNF-α), a well established anorexia agent, in livers
of mice exposed to 24h-cytokine/starvation. 10% of genes of the Agilent 10kb cDNA array is detected above level of detection in the mouse liver. 12% of these is modulated upon starvation while 22% is altered by TNF-α.
Keywords: Disease state analysis

overall_design:
Twelve mice (C57BL/6, Harlan) were randomly assigned into three groups. Three animals were i.v. injected by human recombinant TNF-α (30 µg/animal), a dose that is known to have a significant effect in
mice without leading to mortality. Food was withdrawn after application of TNF-alpha (TNF/starvation group). Further, for three animals which were treated with corresponding volume (200µl) of saline a food was withdrawn (starvation group). Three animals from control group had free access to food throughout the study. Mice were sacrificed 20 hours later. Livers for RNA analysis were stored in RNAlater (Quiagen) according to manufacture's instruction. RNA of individual treated mouse was hybridized versus control sample which is obtained by pooling of control RNAs.

first: Klementina

last: Fon Tacer

first: Matej

last: Seliskar

first: Denis

last: Pompon

first: Damjana

last: Rozman


status: Public on Nov 17 2006

city: Stanford

first: Andrew

last: Fire

state: CA

address: 300 Pasteur Drive RML235 M5324

department: Pathology and Genetics

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary:
RNA interference (RNAi) is a phylogenetically widespread gene silencing process triggered by doublestranded RNA (dsRNA). In plants and C. elegans, two distinct populations of small RNAs have been proposed to participate in RNAi : "Primary siRNAs" (derived from Dicer nuclease-mediated cleavage of the original trigger) and "Secondary siRNAs" (additional small RNAs whose synthesis requires an RNA-directed RNA polymerase [RdRP]). Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found secondary siRNAs to comprise the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode where each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular mRNAs by RdRP activity may have key roles in cellular regulation.
Keywords: C. elegans small RNA sequences from wild type animals fed on sel-1 dsRNA producing bacteria

first: Julia

last: Pak


title: Tup12-GFP ChIP-CHIP

status: Public on Nov 15 2006

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

summary:
We have performed a genome wide investigation for the binding locations of the transcriptional co-repressor proteins Ssn6, Tup11 and Tup12 in the fission yeast Schizosaccharomyces pombe. We have used a ChIP protocol described previously (Robyr et al, 2003) with microarrays containing ORF and IGR fragments representing the complete fission yeast genome (Wiren et al, 2005).
Keywords: ChIP-CHIP

overall_design:
Chromatin Immunoprecipitations.
Chromatin immunoprecipitations were essentially performed as described previously (Robyr et al, 2003, Wiren et al, 2005). Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking. The lysate was subjected to sonication 3x60 sec for generation of chromatin fragments with appropriate length. The lysate from the two sonications was pooled, aliquoted and subjected to immunoprecipiation with a polyclonal a-GFP antibody 1:100 (Applied Biosciences 8372-2) and protein A sepharose beads (Amersham 17-5280-01). Chromatin bound beads were washed and eluated fromm beads. DNA was purified with phenol-chloroform extraction and ethanol-sodium acetate precipitation. Precipitated chromatin and input DNA fragments from three individually separated experiments were subjected to a two step linear amplification. Round A was performed with Sequenase (USB 70775Y) and TPCRA priming. Round B was performed with Amplitaq (Roche) with TPCRB priming. Amplified material (500-1000ng) was subjected to Klenow labelling (Invitrogen 18094-011) with Cy3 and Cy5 (Amersham 53021 and 55021). Generally the input fragments was labelled with Cy3 and precipitated material was labelled with Cy5. Reportedly minimal dye swap bias has previously been observed (Robyr et al, 2003) and labelling was therefore not carried out in dye swap. Labelled fragments were hybridized to IGR+ORF microarrays from Eurogentech SA, Seraing, Belgium. Microarray signals were visualized with ScanExpress laser scanner and quantified with the TIGR spotfinder quantification software. Data was analysed and median normalized to the 50th percentile with the GeneSpring software (Silicon Genetics) to generate six data points for each binding map. Flag values were subtracted from the data set and ratios were subjected to median percentile ranking analysis described (Buck et al, 2004). Cutoff values for the generation of binding lists were set to the 85th percentile.

first: Fredrik

last: Fagerström-Billai

middle: P


title: Complementation

status: Public on Nov 28 2006

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

summary:
To better understand effects of iron starvation on A. pleuropneumoniae and to identify new potential vaccine targets, we conducted transcript profiling using a DNA microarray containing all 2025 ORFs of the genome of A. pleuropneumoniae serotype 5b strain L20. Upon comparing growth of this pathogen in iron-sufficient versus iron-depleted medium, 210 genes were identified as being differentially expressed. Some genes (92) were identified as being up-regulated; many have confirmed or putative roles in iron acquisition, such as the genes coding for two TonB energy-transducing proteins and the hemoglobin receptor HgbA. Transcript profiling also led to identification of some new iron acquisition systems of A. pleuropneumoniae.
Keywords: stress response

overall_design:
The bacteria was grown in BHI broth with or without 50 ug/ml EDDHA to generate iron restriction. In the iron-restricted medium, 50 ug/ml FeCl3 was added to the medium 5 min. after the addition of EDDHA.  RNA extractions were performed on three different days using the QIAGEN RNeasy Kit, and a total of four hybridization were performed.

Data were acquired using a Perkin-Elmer ScanArray Express scanner, and were quantified, normalized and analysed using the SpotFinder, MIDAS and TMEV software from TIGR's TM4 Suite of Microarray Analysis softwares.

first: Nash

middle: H

last: John

first: Harel

last: Josée

first: Coulton

middle: W

last: James

first: Jacques

last: Mario


title: Identification of candidate genes involved in fructooligosaccharides (FOS) utilization by Lactobacillus paracasei

first: Yong Jun

last: Goh

address: 332 Food Industry Complex

department: Food Science and Technology

summary:
A shotgun microarray-based approach was used to identify candidate genes encoding the FOS utilization pathway in L. paracasei 1195.  Differential expression profiles between cells grown on FOS and glucose provided a basis for identifying genes specifically induced by FOS.  In addition, transcriptional analysis of cells grown on FOS or FOS + glucose allowed us to investigate the effect of catabolite repression on the expression of the FOS-induced genes.
Keywords: gene identification

overall_design: For sugar induction experiment (FOS vs. glucose; FOS vs. fructose), L. paracasei were grown in modified MRS (mMRS) basal medium to a final OD625 nm of ca. 0.3, at which point all of the residual sugars in the medium were consumed (based on HPLC analysis of the supernatants).  The culture was then divided into equal portions, where FOS or glucose was added to a 1% final concentration.  Cells were collected for total RNA isolation after 30 min (OD625 nm ca. 0.3 – 0.4).  For glucose repression experiment (FOS vs. FOS + glucose), cells were grown in mMRS supplemented with 2% FOS to an OD625 nm 0.6.  The culture was split into equal portions, and glucose was added to one of the portions at a 2% final concentration.  Both cultures were grown for another 60 min (OD625 nm ca. 1.0) before harvested for total RNA isolation.  Both experiments were performed in independent replicates (two biological replicates per experiment) with incubation at 37 degree celsius in ambient atmosphere.

first: Yong-Jun

first: Chaomei

last: Zhang

last: Benson

first: Robert

last: Hutkins


title: Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to MMS and IR

city: Madison

first: Michael

middle: G

last: Benton

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

summary:
Wt S. cerevisiae cells from a W303 background were exposed to multiple doses of MMS and Gamma Radiation and their global transcriptional response was measured
Keywords: dose response

overall_design: We analyzed 3 doses of MMS and a control no-dose array and 3 doses of Gamma radiation and control no-dose array in triplicate for 24 arrays total

first: Swetha

last: Somasundaram

first: Jeremy

last: Glasner

first: Sean

last: Palecek


title: Ssn6HA-ts VS WT @ 36 Deg

summary:
We have performed a genome wide expression profile study of the transcriptional co-repressor proteins Ssn6 in Schizosaccharomyces pombe. The expression of a conditional Ssn6HA-ts strain was compared against the expression in a WT strain as described before (Xue et al, 2004), except that cells were shifted to 36 deg 1 h prior to RNA extraction.
Keywords: Conditional mutant

overall_design: Gene expression profiling experiment in which gene expression in logarithmically growing cultures of Ssn6HA-ts mutant was compared to that in wt controls. Wt and Ssn6HA-ts cells were grown in rich medium, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004), except that cells were shifted to 36 deg 1 h prior to RNA extraction. Two independent RNA preparations were used to hybridise to two microarrays one on which wildtype was labelled with Cy5 and with Cy3 and the other with dye swap. Data normalized with 'Lowess' per chip per spot normalization.


title: Tup11D,12D/WT

summary:
We have performed a genome wide expression profile study of the transcriptional co-repressor proteins tup11,12 in Schizosaccharomyces pombe. The expression of a double knock out strain (tup11,12D) was compared against the expression in a WT strain under normal conditions YES-media at 30 degrees (Xue et al, 2004).
Keywords: DeletionMutant/WT

overall_design: Gene expression profiling experiment in which gene expression in logarithmically growing cultures of tup11,12D mutants was compared to that in wt controls. Wt  and tup11,12D cells were grown in rich medium, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Two independent RNA preparations were used to hybridise to two microarrays one on which wildtype was labelled with Cy5 and with Cy3 and the other with dye swap. Data normalized with 'Lowess' per chip per spot normalization.


title: Ssn6 Overexpression

summary:
We have performed a genome wide expression profile study of the essential transcriptional co-repressor protein Ssn6 in Schizosaccharomyces pombe. Ssn6 affected targets were identified by over expression of Ssn6 protein in a WT strain. A WT strain holding a plasmid expressing Ssn6 (pDUAL-Ssn6) was compared against the expression in a WT with the empty plasmid (pDUAL-EMPTY) strain.
Keywords: Overexpression/WT

overall_design: Gene expression profiling experiment in which gene expression in logarithmically growing cultures of cells expressing the Ssn6 plasmid was compared to that in wt controls expressing the empty plasmid. Wt and Ssn6 overexpressing cells were grown in MM-URA media, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Two independent RNA preparations were used to hybridise to two microarrays one on which wildtype was labelled with Cy5 and with Cy3 and the other with dye swap. Data normalized with 'Lowess' per chip per spot normalization.


title: Microarray analysis of gene expression in wt, rpoS and hapR mutants in stationary phase

status: Public on Nov 03 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Alex

last: Nielsen

first: Nadia

last: Dolganov