title: Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- Neutral enrichment

status: Public on Aug 30 2006

first: Jason

last: Lieb

address: 203 Fordham Hall

department: Biology

summary:
Epigenetic modifications of chromatin serve an important role in regulating the expression and accessibility of genomic DNA. We report here a genomewide approach for fractionating yeast chromatin into two functionally distinct parts, one containing RNA polymerase II transcribed sequences, and the other comprising noncoding sequences and genes transcribed by RNA polymerases I and III. Noncoding regions could be further fractionated into promoters and segments lacking promoters. The observed separations were apparently based on differential crosslinking efficiency of chromatin in different genomic regions. The results reveal a genomewide molecular mechanism for marking promoters and genomic regions that have a license to be transcribed by RNA polymerase II, a previously unrecognized level of genomic complexity that may exist in all eukaryotes. Our approach has broad potential use as a tool for genome annotation and for the characterization of global changes in chromatin structure that accompany different genetic, environmental, and disease states.
Keywords: Genomewide mapping of regulatory elements through differential fractionation of crosslinked chromatin based on nucleosome occupancy.

overall_design: Neutral enrichment- All DNA was prepared by glass-bead disruption and standard phenol-chloroform extraction with the modification that the cells were first broken in the absence of phenol-chloroform. The extract was centrifuged for 5 s at 14,000Xg, and the supernatant was sonicated and subsequently phenol-chloroform extracted.

first: Peter

middle: L

last: Nagy

last: Cleary

first: Patrick

middle: O

last: Brown


title: Differentially expressed genes of cir1 mutants in low iron or high iron medium

status: Public on Sep 14 2006

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary:
Iron overload is known to exacerbate many infectious diseases and, conversely, iron withholding is an important defense strategy for mammalian hosts.  The mechanisms by which fungal pathogens sense iron in the mammalian host environment are poorly understood.  The AIDS-associated pathogen Cryptococcus neoformans provides a unique opportunity to explore iron sensing in the context of infection because iron levels control elaboration of the polysaccharide capsule that is the major virulence factor of the fungus.  Additionally, excess iron exacerbates experimental cryptococcosis.  We identified the iron-responsive transcription factor Cir1 that regulates iron acquisition in C. neoformans and discovered that Cir1 also controls the expression of all of the known major virulence factors of the fungus.  In particular, cir1 mutants are defective in capsule formation and avirulent in a mouse model of cryptococcosis.  Thus the ability to sense iron is critical during infection by C. neoformans and may represent a target for antifungal therapy.
Keywords: wt/mutant x low/high iron

overall_design: The following loop design, which includes three biological replicates and consists of four nodes and paths including dye-swap, was adopted for this study: wild-type (low iron) vs wild-type (high iron), wild-type (low iron) vs cir1delta (low iron), wild-type (high iron) vs cir1delta (high iron), and cir1delta (low iron) vs cir1delta (high iron).  A total of 24 arrays were used for the experiment.

first: Wonhee

first: Anita

last: Sham

first: Rick

last: White

first: James

last: Kronstad


title: Gene expression profile of idiopathic thrombocytopenic purpura (ITP)

status: Public on Sep 12 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Five ITP and five control whole blood samples were collected with IRB approval. The age range of ITP patients was 1-54 years, and the range in platelet counts was 2,000-98,000 W 109/L. We examined only one ITP sample for antiplatelet antibodies, and found it to be positive. Total RNA was isolated from 2.5 ml whole blood according to the PAXgene Blood RNA System (PreAnalytix, Switzerland). RNA isolated from ITP patients and controls, along with Human Universal Reference RNA (Stratagene, La Jolla, CA) were linearly amplified using the MessageAmp aRNA amplification kit (Ambion, Austin, TX).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Ruchira

last: Sood


title: Auratus: Goldfish genome project

status: Public on Sep 09 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary:
Muscimol i.p. injection
6 hour treatment
August
female fish 2-3 years of age
Keywords: single pharmacoligical injection of GABA agonist muscimol; effects in neuroendocrine brain

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
Slide 2 and 31 are dye swap
3-4 hypothalami per sample

first: Chris

middle: J

first: Vance

last: Trudeau


title: Responses to P. aeruginosa infection - Shapira

status: Public on Sep 13 2006

city: Palo Alto

first: Michael

last: Shapira

address: 300 Pasteur Dr. Lane Bldg. room L309

department: Genetics

institute: Stanford University

summary:
Synchronized C. elegans cultures were prepared using standard techniques (http://cmgm.stanford.edu/~kimlab/index_methods.html). Live young adult worms were split between NG plates pre-seeded with the non-pathogenic E. coli strain OP50 or the Pseudomonas aeruginosa clinical isolate PA14 and incubated at 25C for 4, 12 or 24 hours before harvesting. This experiment was repeated three times on independent occasions. cDNA probes were prepared from experimental samples and from reference mRNA extracted from mixed stage wild type worms grown at 25C, and were labeled with Cy3 or Cy5, respectively. In the paper corresponding to this experiment set colors were flipped for easier visualization (probes from experimental samples are represented with red, probes from reference RNA are represented with green).
Groups of assays that are related as part of a time series.
Infection: Exposure to the non-pathogenic E. coli strain OP50 or to the pathogenic Pseudomonas aeruginosa strain PA14
Time: Time from the beginning of exposure
Michael Shapira, Brigham J. Hamlin, Jiming Rong, Karen Chen, Michal Ronen, and Man-Wah Tan , A Conserved Role for a GATA Transcription Factor in Regulating Epithelial Innate Immune Responses, Shapira et al. PNAS(in press), 2006-10-01
Keywords: time_series_design

first: Brigham

last: Hamlin

first: Man-Wah

last: Tan


title: High Resolution Mapping and Functional Analysis of the Methylome in Arabidopsis (mCIP, MBD)

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array

summary:
Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. Unexpectedly, over one third of expressed genes contained methylation within transcribed regions, whereas only ~5% of genes contained methylation within promoter regions. Interestingly, genes methylated in transcribed regions were highly expressed and constitutively active, whereas promoter-methylated genes showed a greater degree of tissue-specific expression. Analysis of several DNA methyltransferase mutants revealed widespread epigenetic regulation of protein-coding genes as well as non-coding RNA genes of unknown function.
Keywords: whole genome profiling, DNA methylation, mCIP, MBD

overall_design: All plants used in this study are of the Columbia accession. The met1 and drm1 drm2 cmt3 mutants are previously published. The mutant alleles are: met1-3; drm1-2, drm2-2, cmt3-11. To avoid variability caused by inbreeding, all homozygous mutants were from F1 segregating populations. Plants were grown under continuous light. DNA was extracted from 5 weeks old plants using the Plant DNeasy Kit (QIAGEN) according to manufacturer’s instructions. The entire aerial parts of 2–3 plants were pooled for each 3 biological replicate.

first: Xiaoyu

last: Zhang

first: Junshi

last: Yazaki

first: Ambika

last: Sundaresan

first: Shawn

last: Cokus

first: Simon

middle: W

last: Chan

first: Huaming

last: Chen

first: Ian

middle: R

last: Henderson

first: Paul

last: Shinn

first: Matteo

last: Pellegrini

first: Joseph

last: Ecker


title: Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling

status: Public on Aug 29 2006

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

summary:
We describe the design and evaluate the use of a high density oligonuclotide microarray covering seven sequenced E. coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labelled genomic DNA to query the microarrays and subsequently analyse common virulence genes and phage elements, and perform whole genome comparisons, we observed that O175:H16 D1 is a K-12 like strain and confirmed that its phi3538 phage element originated from the E. coli 3538 strain with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains providing a likely explanation for their capability to transfer phi3538 between them. Analyses of control samples demonstrated that results using our custom designed microarray were representative of the true biology, e.g. by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7 percent of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis.
Keywords: Genomic DNA hybridizations

overall_design: 3 biological replicates of each E. coli strain. 2 biological resplicates of the E. coli phage

first: Anne

last: Petersen

first: David

last: Ussery

first: Camilla

last: Sekse


title: Expression Profiling of Heat Stress Effects on Mice Fed Ergot Alkaloids.

city: Columbia

first: Sachin

middle: S

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

summary:
Fescue toxicosis affects wild and domestic animals consuming ergot alkaloids contained in tall fescue forage infected with the endophytic fungus, Neotyphodium coenophialum. , When animals are consuming infected fescue forage during periods of elevated ambient temperatures (summer), a range of phenotypic disorders collectively called summer slump is observed. It is characterized by hyperthermia, with an accompanying decrease in feed intake, growth, milk yield and reproductive fitness. Laboratory mice also exhibit symptoms of fescue toxicosis a thermoneutral temperature, as indicated by reduced growth rate and reproductive fitness. Our goal was to characterize the differences in gene expression in liver of mice exposed to summer-type heat stress (HS) and infected fescue (E+) when compared to mice fed infected fescue at thermoneutral temperature (TN). Mice were fed E+ diet under HS (34 ± 1°C; n = 13; E+HS) or thermoneutral (TN) conditions (24 ± 1°C; n = 14; E+TN) for a period of two weeks between 47 to 60 d of age. Genes differentially expressed between E+HS versus E+TN were identified using DNA microarrays. Forty-one genes were differentially expressed between treatment groups. Expressions of eight genes were measured using quantitative real-time PCR.
Genes coding for phase I detoxification enzymes were up-regulated in E+HS mouse liver. This detoxification pathway is known to produce reactive oxidative species. We observed an up-regulation of genes involved in the protection against reactive oxidative species. Key genes involved in de novo lipogenesis and lipid transport were also up-regulated. Finally, genes involved in DNA damage control and unfolded protein responses were down-regulated.
Keywords: Stress response

overall_design: Differential gene expression in groups of mice exposed to E+HS, E+TN conditions were studied using Reference design of microarrays. We had six mice (3 males, 3 females) in each group used in microarray analysis. Two/three technical replicates were done per mice out of which one replicate was done in dye-swap design. Mice within each treatment group were hydridized against an universal mouse reference RNA and the differential gene expression between the groups were assessed indirectly.

first: Liu

last: Zhilin

first: Leonard

middle: B

last: Hearne

first: Donald

last: Spiers

first: William

last: Lamberson

first: Eric

last: Antoniou


title: Somatic Activation of KIT in Distinct Subtypes of Melanoma

city: San Francisco

first: Boris

last: Bastian

department: Laboratory Medicine

institute: UCSF Cancer Center

type: Genome variation profiling by genome tiling array

summary:
Melanomas on mucosal membranes, acral skin (soles, palms, and nail bed), and skin with chronic sun-induced damage have infrequent mutations in BRAF and NRAS, genes within the mitogenactivated protein (MAP) kinase pathway commonly mutated in melanomas on intermittently sun-exposed skin. This raises the question of whether other aberrations are occurring in the MAP kinase cascade in the melanoma types with infrequent mutations of BRAF and NRAS.

Oncogenic mutations in KIT were found in three of seven tumors with amplifications. Examination of all 102 primary melanomas found mutations and/or copy number increases of KIT in 39% ofmucosal, 36% of acral, and 28% of melanomas on chronically sun-damaged skin, but not in any (0%) melanomas on skin without chronic sun damage. Seventy-nine percent of tumors with mutations and 53% of tumors with multiple copies of KIT demonstrated increased KIT protein levels.
KIT is an important oncogene in melanoma. Because the majority of the KIT mutations we found in melanoma also occur in imatinib-responsive cancers of other types, imatinib may offer an immediate therapeutic benefit for a significant proportion of the global melanoma burden.
Keywords: melanoma, oncogene, comparative genomic hybridization, KIT

overall_design: We analyzed array comparative genomic hybridization data from 102 primary melanomas (38 from mucosa, 28 from acral skin, and 18 from skin with and 18 from skin without chronic sun-induced damage) for DNA copy number aberrations specific to melanoma subtypes where mutations in BRAF and NRAS are infrequent. A narrow amplification on 4q12 was found, and candidate genes within it were analyzed.

first: John

middle: A

last: Curtin

first: Klaus

last: Busam

first: Daniel

last: Pinkel

middle: C


title: Comparison of gene expression by co-cultured WC1+ gammadelta and CD4+ alphabeta T cells

status: Public on Aug 26 2006

city: Amherst

first: Seth

last: Blumerman

state: MA

address: Paige Laboratory

institute: University of Massachusetts, Amherst

summary:
Vaccination of animals with leptospiral vaccine results in the generation of antigen-responsive CD4 alphabeta T cells and WC1 gammadelta T cells which proliferate and produce effector cytokines following secondary encounter with antigen.  In these studies we compared the gene expression of these antigen-stimulated T cell subsets to each other by microarray.  In addition, each activated T cell population was compared to a reference sample, consisting of unstimulated peripheral blood mononuclear cells.
Keywords: cell type comparison

overall_design:
CD4 T cells from 3 vaccinated animals compared to WC1 T cells from same animals, following in vitro antigen-stimulation.  Each array was repeated for each animal using dye-swapped samples.

CD4 or WC1 T cells from each vaccinated animal were also compared to ex vivo PBMC (unstimulated control). Here sample from antigen-stimulated CD4 or WC1 T cell was always Cy3 labelled, while unstimulated control was always Cy5 labelled.

first: Carolyn

last: Herzig

first: Fei

last: Wang

first: Paul

last: Coussens

first: Cynthia

last: Baldwin


title: anti-H3 Chip-chip in Leu3overexpress or Leu3AD starins

status: Public on Sep 08 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by genome tiling array

summary:
To compare nucleosome distribution between Leu3-overexpressing and Leu3-binding deficient yeast strains
Keywords: ChIP-chip

overall_design:
4 biological replicates of anti-H3 ChIP-chip in Leu3-overexpressing strain
4 biological replicates of anti-H3 ChIP-chip in Leu3-binding deficient strain
2 biological replicates of input/input negative control  in Leu3-overexpressing strain
2 biological replicates of input/input negative control  in Leu3-binding deficient strain

first: Xiao

last: Liu

first: Cheol-Koo

last: Lee

first: Neil

last: Clarke


title: Molecular Basis of Tropheryma whipplei Doxycycline Susceptibility Examined by Transcriptional Profiling

status: Public on Sep 07 2006

city: Marseille

first: My-Van

last: La

address: 27 BD Jean Moulin

country: France

institute: Unité des Rickettsies (CNRS-UMR 6020)

summary:
The suceptibility of T. whipplei to doxycycline was investigated at the transcriptional level using a whole-genome DNA microarray. The microarray data showed good agreement with real-time quantitative PCR (R = 0.969). Exposure of T. whipplei  with the subinhibitory concentration of doxycycline allowed to observe antibiotic-specific primary expression profiles, while indirect effects were detected with a 10 times higher concencentration. In contrast to what was observed for several microorganisms exposed to antibiotics, the heat-shock proteins were not affected by the exposure of T. whipplei to doxycycline. Consistent with the mode of action of this translation inhibitor, genes encoding for ribosomal proteins and translation factors were differentially transcribed. This analysis also evidenced the regulation of genes that should account for the cell growth arrest. Long-term survival of nonreplicating bacteria is likely to be ensured by an increased level of ppGpp, the nucleotide effector of the stringent response. Gene expression profile to the higher concentrations of doxycycline was mainly characterized by the up-regulation of ABC transporters that possibly form efflux and detoxification systems, through which T. whipplei may limit the effects of this bacteriostatic compound. This work represents the first comprehensive genomic approach providing insight into the expression signature triggered by the exposure of this bacterial pathogen to antibiotics.
Keywords: Antibiotic stress with Doxycycline

overall_design:
2 test conditions (Doxycycline MIC and 10xMIC)
1 reference condition (12-day-old culture)
3 biological replicates per condition
4 technical replicates per microarray
Dual-labeling using a reference design: control sample labeled with Cy3-dCTP and test sample labeled with Cy5-dCTP

first: Raoult

last: Didier

first: Patricia

last: Renesto


title: Growth Hormone Doping Detection

status: Public on Aug 31 2006

city: Seibersdorf

first: René

last: Stempfer

address: Reaktorstr.

department: Life Sciences

country: Austria

institute: ARC Seibersdorf research GmbH

summary:
DNA microarray technology was utilised for the identification of potential marker genes for the abuse of human growth hormone (hgh) in athletes.
Keywords: Whole genome gene expression study

overall_design: Three cell lines of leukocyte subsets (THP-1, H9, RA-1) as well as peripheral blood mononuclear cells (PBMC) were challenged with recombinant human growth hormone to elicit specific responses. Suitable doses and incubation times were first tested with THP-1 cells, most effective concentrations were used for the other two cell lines and the PBMC. Tests were carried out in duplicates. For the three cell lines treated and untreated samples (all Cy3) were co-hybridised with reference samples (Cy5). For the PBMC from five donors dye-swaps were carried out for the samples from different sampling days. Treated and untreated control samples were co-hybridised.


title: Regulation of Protein Phosphatase 4 by a MAP Kinase Cascade Controls Chemotaxis

status: Public on Aug 25 2006

city: Houston

first: Ezgi

last: Booth

state: TX

address: S430, One Baylor Plaza

institute: Baylor College of Medicine

summary:
Classical genetics in model organisms has defined many signaling pathways that control cell movement and multicellular morphogenesis. However,these approaches have not succeeded in placing some established chemotaxis regulators, such as the MAP kinase kinase MEK1, in activator/effector pathways. Here, we combined morphological measurements with epistasis analysis of transcriptional phenotypes and found that the protein phosphatase 4 (PP4) signaling pathway controls Dictyostelium chemotaxis and development. PP4 is a phosphatase that regulates recovery from DNA damage. We show that Dictyostelium SMEK functions as the PP4R3 regulatory subunit and may regulate the subcellular localization of PP4 catalytic subunit PP4C. SMEK binds PP4C and the complex functions downstream of MEK1 to regulate chemotaxis and morphogenesis. Microarray analysis of gene expression in mutant strains indicated that PP4 controls leading edge formation and cellular responses to stress. Thus, the MEKPP4C/SMEK pathway has a direct role in regulating chemotaxis, in addition to regulating the DNA repair checkpoint.
Keywords: Developmental time course series from 1 Dictyostelium wildtype and 5 chemotaxis mutants to determine epistatic relationship

overall_design:
6 Dictyostelium strains were analyzed. For each strain, there were 4 developmental time points (0,6,12,18). Each developmental series experiment per strain consisted of 3 biological replicas and 2 technical replications. [6 strain x 4 time point x 3 biologial replica x 2 technical replica]
Each test sample(labeled with Cy5) was co-hybridized with a reference sample (labeled with Cy3) consisting of a pool from vegetative wild type cells and 6 developmental time points (0,3,6,12,17,24 hours)

6 strain x 4 time point x 3 biologial replica x 2 technical replica

first: Michelle

last: Mendoza

first: Gad

last: Shaulsky

first: Richard

last: Firtel


title: A Restricted Role for Sperm-borne MicroRNAs in Mammalian Fertilization

status: Public on Sep 06 2006

city: Kobe

first: Anthony

middle: CF

last: Perry

state: Hyogo-ken

address: 2-2-3 Minatojima-minamimachi

department: Center for Developmental Biology

country: Japan

institute: RIKEN

summary:
Prototypical micro RNAs (miRNAs) are 21~25-base-pair RNAs that regulate differentiation, carcinogenesis and pluripotency by eliminating mRNAs or blocking their translation, processes collectively termed RNA interference (RNAi). RNAi mediated by miRNAs regulates early development in zebrafish, and mouse embryos lacking the miRNA precursor processor, Dicer, are inviable. However, the role of miRNAs during mammalian fertilization is unknown. We here show using microarrays that miRNAs are present in mouse sperm structures that enter the oocyte at fertilization. Sperm contained a broad profile of miRNAs and a subset of potential mRNA targets were expressed in fertilizable, metaphase II (mII) oocytes. Oocytes contained transcripts for the RNAinduced silencing complex (RISC) catalytic subunit, EIF2C3 (formerly AGO3). However, levels of sperm-borne miRNA (measured by quantitative PCR) were apparently low relative to those of unfertilized, mII oocytes, and fertilization did not alter the part of the mII oocyte miRNA landscape that included the most abundant sperm-borne miRNAs. Coinjection of mII oocytes with sperm heads plus anti-miRNAs - to suppress miRNA function - did not perturb pronuclear activation or preimplantation development. Contrastingly, we provide evidence that nuclear transfer by microinjection alters the miRNA profile of enucleated oocytes. These data argue that sperm-borne prototypical miRNAs play a limited role, if any, in mammalian fertilization or early preimplantation development.
Keywords: miRNA profiling

overall_design: Seven samples were analyzed for the study.


title: Small RNA identification in Arabidopsis thaliana using 454 data

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Expression profiling by high throughput sequencing

summary:
The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth.  Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs.  Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.
Keywords: small RNA sequences generated by 454 sequencing

overall_design: Small RNAs identified from inflorescence tissues.

first: Cheng

last: Lu

first: Pamela

last: Green


title: Gene expression in PBMC from Multiple Sclerosis patients undergoing interferon beta therapy.

status: Public on Aug 23 2006

city: Pittsburgh

first: Mandal.

middle: K.

last: Singh

state: PA

address: 3460 Fifth Ave

department: Transplant

institute: Childrens Hospital of Pittsburgh

summary:
We studied the gene expression patterns in PBMC from relapsing remitting MS patients undergoing weekly IFN-ß-1a therapy. On the basis of two fold changes in expression levels and statistical analyses we selected a diagnostic set of 137 genes that were differentially expressed between pretreatment and IFN-ß-1a-treated MS patients.  Some these 137 genes may provide the basis for lack of IFN-ß-1a response.
Keywords: Drug response to Interferon beta therapy in Multiple Sclerosis patients.

overall_design: We studied five RRMS patients with ages ranging from 32 to 46 years naïve to IFN-ß-1a therapy at the outset of the trial. The pretreatment and acute peripheral blood samples respectively were drawn the day before and the day after the start of the therapy.  The chronic samples were drawn one day before the weekly treatment regimen approximately six months following the initiation of therapy. Mononuclear cells were purified from the fresh peripheral blood specimens using Ficoll-Paque density gradient separation. RNA was isolated from the PBMC using the Qiagen column purification procedure (Qiagen, Valencia, CA). We utilized the CodeLink Expression Bioarrays for the analysis of gene expression in PBMC.

first: Mandal

middle: K


title: Aerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses

status: Public on Sep 01 2006

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

summary:
Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers. Equal quantities of RNA from Wild type and norR::Tn5 cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values
Keywords: Mutant Comparison, stress response, nitric oxide, NorR, chemostat, continuous culture

overall_design:
Each strain was grown twice in seperate chemostat runs, exposed to NO.
Samples were hybridised as WT vs NorR::Tn5 and each hybridisation had a corresponding dye-swap performed

first: Steven

middle: T

last: Pullan

first: Jeffrey


title: Transcript Response of Fully Expanding and Growing Soybean to Elevated CO2

city: Urbana

first: Elizabeth

last: Ainsworth

state: IL

address: 147 ERML, 1201 W. Gregory Drive

department: Photosynthesis Research Unit

institute: USDA/ARS

summary:
The transcript responses of both growing, trifoliate 6 and fully expanded, trifoliate 4 soybean leaves to elevated CO2 was investigated. We also compared the transcriptome of fully expanded vs. developing leaves in both ambient and elevated CO2.
Keywords = soybean
Keywords = elevated carbon dioxide
Keywords = global change
Keywords = leaf growth
Keywords = plant
Keywords: soybean leaf comparisons

overall_design: randomized complete block design in SoyFACE, 24 samples, 4 comparisons, 2 technical repeats including dye swaps, 2 biological repeats

first: Alistair

last: Rogers

first: Lila

last: Vodkin

first: Achim

last: Walters

first: Ulrich

last: Schurr


title: Anaerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions.

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added to anaerobic medium at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each, unless otherwise stated. Samples were taken immediately prior to the addition of NOCs and after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Equal quantities of RNA from control and NOC-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

Keywords: Stress Reponse, Continuous culture, Chemostat, NO, Nitric oxide

overall_design: Two biological repeats (ie. two chemostat runs) were grown. Control and exposed samples were taken as described in summary. For each chemostat run 2 hybridisations were performed. One in which the control was Cy3 labelled whilst the exposed was Cy5 labelled, and a dye swap.

first: Jason

last: Barrett


title: Aerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions.

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under
continuous culture (chemostat) conditions. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the

dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen

tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a

Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 was added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each unless stated otherwise. Samples were taken immediately prior to the addition of NOCs and after a period of 5 min exposure to NOCs for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Equal quantities of RNA from control and NOC-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.
Keywords: Stress Reponse, Continuous culture, Chemostat, NO, Nitric oxide


title: Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock

status: Public on Aug 21 2006

city: University Park

first: Frank

last: Pugh

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

summary:
Eukaryotic genes are controlled by sequence-specific DNA-binding proteins, chromatin regulators, general transcription factors, and elongation factors.  Here we examine the genome-wide location of representative members of these groups and their redistribution when the Saccharomyces cerevisiae genome is reprogrammed by heat shock.  As expected, assembly of active transcription complexes are coupled to eviction of H2A.Z nucleosomes, and disassembly is coupled to the return of nucleosomes.  Remarkably, a large number of promoters assemble and disassemble into partial pre-initiation complexes (partial PICs), containing TFIIA, TFIID (and/or SAGA), TFIIB, TFIIE, and TFIIF.  At these promoters, neither TFIIH nor RNA polymerase II are recruited, and nucleosomes are not displaced.  These promoters may be preparing for additional stress that naturally accompany heat stress.  For example, we find that oxidative stress, which often occurs with prolonged exposure of cells to high temperature, coverts partial PICs into full PICs.  Partial PICs therefore represent novel regulated intermediates that assemble in the midst of chromatin.
Keywords: other

first: Sara

last: Zanton

first: BFranklin


title: Upf2 loss of function effects

city: Salt Lake CIty

first: Mark

last: Metzstein

state: UT

department: Human Genetics

institute: University of Utah

summary:
RNA was isolated from Upf225G/Y; Btl-GAL4, UAS-GFP/+ and y w FRT19A/ Y; Btl-GAL4, UAS-GFP/+ L3 larvae using Trizol as described in Materials and Methods, cDNA labeled with Cy3 or Cy5 was prepared from each RNA sample and hybridized to microarrays containing ~14,000 gene probes covering the entire Drosophila genome (Gerber et al. 2006). Hybridizations were performed with two independently isolated and labeled RNA samples.  Analysis was carried out using the Stanford Microarray Database (http://genome-www5.stanford.edu/ ).  During analysis we noted that the Upf225G mutants were delayed in development.  To avoid confounding effects of changes in gene expression that result from developmental regulation rather than more direct effects of Upf2 loss of function, we used the available wild- type developmental gene expression time course (Arbeitman et al. 2002) to filter out genes whose transcription changes more than 25% from their maximal value during 72-96 hrs of larval development.  The wild-type data set includes ~33% of genes, and we used just this subset for our analysis.  Furthermore, the wild-type data set is for mixed sex populations, while our microarray was performed only on males.  To compensate for sex differences, we also excluded from analysis genes that differed between males and females by more than 50% based on data from male and female larvae (E. Johnson and M.A.K., unpublished).  Our analysis of genes regulated by NMD is therefore conservative, covering only non-developmentally regulated and non-sex regulated genes whose expression was affected by a hypomorphic Upf2 allele, and thus provides only a lower estimate on genes regulated by NMD.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Stefan

last: Luschnig


title: Gene profiling of spleens of adult protected rats from Plasmodium berghei ANKA

city: Lille

first: Jamal

last: Khalife

address: 1 rue du Prof. Calmette

institute: Inserm U547

summary:
The studies reported here were designed to define in more detail the effector cells responsible for the transfer of protective immunity to young host against P. berghei infection, and to investigate the genes expressed in spleen cells of adult protected rats capable of transferring protection to young rats.
Keywords: age, malaria, protection, rat

overall_design:
In order to investigate the differential gene expression in the spleen of adlut protected rats which are involved in the transfer of immunity to young susceptible rats we profiled the genes from RNA extracted from:
3 healthy control rats (101758, 101760, 101761) and 4 adult protected rats that cleared parasitemia (101762, 101763, 10764, 101765)

first: James

last: George

first: Christine

last: Pierrot

first: David

last: Hot


title: Yeast W303 yox1yhp1 mutant cell cycle

city: Seattle

first: Tata

last: Pramila

state: WA

address: 1100, Fairview Avenue N

department: Basic Sciences

institute: FHCRC

summary:
Two homeodomain proteins, Yox1 and Yhp1, act as repressors at early cell cycle boxes (ECBs) to restrict their activity to the M/G1 phase of the cell cycle in budding yeast. These proteins bind to Mcm1 and to a typical homeodomain binding site. The expression of Yox1 is periodic and directly correlated with its binding to, and repression of, ECB activity. The absence of Yox1 and Yhp1 or the constitutive expression of Yox1 leads to the loss of cell-cycle regulation of ECB activity. Therefore, the cell-cycle-regulated expression of these repressors defines the interval of ECB-dependent transcription. Twenty-eight genes, including MCM2-7, CDC6, SWI4, CLN3, and a number of genes required during late M phase have been identified that are coordinately regulated by this pathway.
Keywords: cell cycle time course

overall_design: Cells were synchronized with alpha factor and sampled every 10 min across 2 cell cycles. A total of 13 samples were analyzed. No replicates were included. cDNA of the cell cycle samples were labelled with Cy5. For Cy3 labelling, asynchronous yeast population was used.

first: Linda

middle: L

last: Breeden


title: Shipyard Creek gene expression in 2005

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

summary:
We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site.   Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs.  Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005).  Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR).  The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000.  As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4.  The magnitude of differential gene expression of the individual genes also decreased during remediation.  The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations.  For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005.  However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop.  Therefore, the number of differentially expressed genes increased to 9.  Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability.
Keywords: Field site

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus

overall_design: Shipyard Creek is a chromium contaminated Superfund site in Charleston, South Carolina (USA) that was added to the NPL list in 1998 because of increasing chromium contaminated in the nearby estuary.  The site began remediation in early 2003.  Mummichogs were collected using baited minnow traps from Shipyard Creek (1) before remediation began in 2000, (2) during remediation in 2003, and (3) as remediation neared completion in 2005.  Mummichogs were also collected from the reference site at North Inlet National Estuarine Research Reserve (NERR) in 2000, 2003, and 2005.  Mummichogs were euthanized immediately after collection, livers excised, and placed in TRI-Reagent« for RNA isolation (Sigma Chemical Co, St. Louis, MO).  Samples were then snap frozen in liquid nitrogen, mailed to UTEP on dry ice, and stored at -80C for array analysis. (n = 7-8)

first: Lisa

last: Bain

first: Pete

last: Key

first: William

last: Baldwin


title: LightResponse

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

summary:
The influence of light on living organisms is critical, not only because of its importance as the main source of energy for the biosphere, but also due to its capacity to induce changes in the behaviour and morphology of nearly all forms of life. The common soil fungus Trichoderma atroviride responds to blue-light in a synchronized manner, in time and space, by forming a ring of green conidia at what had been the colony perimeter at the time of exposure (photoconidiation). The complex putatively formed by the BLR-1 and BLR-2 proteins in T. atroviride appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Expression analyses using microarrays containing 1438 unigenes were carried out in order to identify early light response genes. We found that 2.8% of the genes were light responsive, 2% induced and 0.8% repressed. Exposure of Trichoderma to continuous light allowed us to establish that the light responsive genes are subjected to photoadaptation. Expression analysis in blr deletion mutants allowed us to demonstrate the occurrence of two types of light responses, a blr-independent response in addition to the expected brl-dependent one, as well as a new role of the BLR proteins in repression of transcription. Finally, we show evidence of red light regulated gene expression.
Keywords: Light Response, microarrays

overall_design: Three independent replicates of each mycelial treatment, RNA isolation and labelling, and microarray hybridization were performed. To estimate ‘system noise’ that may be due to differences in Cy-dye labelling between samples, we performed a ‘swap’ hybridization for each biological replicates.

first: T

last: Rosales-Saavedra

first: U

last: Esquivel-Naranjo

first: S

last: Casas-Flores

first: P

last: Martínez-Hernández

first: E

last: Ibarra-Laclette

first: C

last: Cortes-Penagos

first: A

last: Herrera-Estrella


title: Shipyard Creek gene expression in 2000

overall_design: Shipyard Creek is a chromium contaminated Superfund site in Charleston, South Carolina (USA) that was added to the NPL list in 1998 because of increasing chromium contaminated in the nearby estuary.  The site began remediation in early 2003.  Mummichogs were collected using baited minnow traps from Shipyard Creek (1) before remediation began in 2000, (2) during remediation in 2003, and (3) as remediation neared completion in 2005.  Mummichogs were also collected from the reference site at North Inlet National Estuarine Research Reserve (NERR) in 2000, 2003, and 2005.  Mummichogs were euthanized immediately after collection, livers excised, and placed in TRI-Reagent« for RNA isolation (Sigma Chemical Co, St. Louis, MO).  Samples were then snap frozen in liquid nitrogen, mailed to UTEP on dry ice, and stored at -80C for array analysis. (n = 5)


title: Mapping of H4-acetylated chromatin modifications in differentiating human primary myoblasts

status: Public on Aug 28 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

type: Genome binding/occupancy profiling by SNP array

summary:
We assessed the genomic distribution of H4-acetylated chromatin by ChIP using SNP chips and an antibody specific to four acetylated lysine residues of H4.
Keywords: Comparative genomic hybridization

overall_design:
Triplicate Affymetrix 10K ax13339 SNP chips were hybridized to DNA extracted from myoblasts and myotubes.
One replicate set was hybridized to total DNA extracted from myoblasts.
Another replicate set was hybridized to DNA extracted from myotubes after CHiPping with H4-acetylated chromatin.
The final replicate set was hybridized to DNA extracted from myoblasts after CHiPping with H4-acetylated chromatin.


title: Shipyard Creek gene expression in 2003

overall_design: Shipyard Creek is a chromium contaminated Superfund site in Charleston, South Carolina (USA) that was added to the NPL list in 1998 because of increasing chromium contaminated in the nearby estuary.  The site began remediation in early 2003.  Mummichogs were collected using baited minnow traps from Shipyard Creek (1) before remediation began in 2000, (2) during remediation in 2003, and (3) as remediation neared completion in 2005.  Mummichogs were also collected from the reference site at North Inlet National Estuarine Research Reserve (NERR) in 2000, 2003, and 2005.  Mummichogs were euthanized immediately after collection, livers excised, and placed in TRI-Reagent« for RNA isolation (Sigma Chemical Co, St. Louis, MO).  Samples were then snap frozen in liquid nitrogen, mailed to UTEP on dry ice, and stored at -80C for array analysis. (n = 7)


title: Effect of twenty-one different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae

city: gosselies

first: Patrice

last: Godard

address: rue des professeurs Jeener et Brachet, 12

department: IBMM

country: Belgium

institute: Université Libre de Bruxelles

summary:
We have applied whole-genome microarray hybridization to compare the transcriptome of wild-type yeast strain Σ1278b during growth on a minimal medium containing 21 different single nitrogen sources including urea used as a reference condition.
Keywords: growth conditions comparison

overall_design: The 21 compounds were selected from a list of 27 nitrogen sources for their ability to support reproducible growth with a generation time (g) of less than 5 hours. The reference nitrogen source to which the twenty other media were compared in terms of genome expression was urea, chosen because urea catabolism and its regulation are well known, because the generation time of strain Σ1278b on urea is near the middle of the studied g range, and because the major regulations like nitrogen catabolite repression (NCR) and SPS-mediated control are not operational on this medium.

first: Antonio

last: Urrestarazu

first: Stephan

last: Vissers

first: Bruno

last: André


title: Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

status: Public on Aug 10 2006

first: Andrew

last: Sharp

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

summary:
Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome we investigated 130 regions which we hypothesized as candidates for novel genomic disorders 1. We tested 290 patients with mental retardation by BAC array CGH, identifying sixteen pathogenic rearrangements, including four patients with de novo microdeletions of 17q21.31. Using oligonucleotide arrays we refined the breakpoints of this microdeletion, defining a 478 kb critical region containing six genes that were deleted in all four cases. The breakpoints of this deletion, and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 were mapped to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are also sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions.
Keywords: BAC comparative genomic hybridization of individuals with mental retardation and congenital anomalies

overall_design: 290 individuals were analysed using a custom BAC array (Sharp et al. 2005, Am J Hum Genet. v77, p78). Each individual was analysed using dye-swap replicate hybs. 316 normal control individuals were analysed using identical methods, and have been reported previously (Sharp et al. 2005, Am J Hum Genet. 77, 78-88 and Locke et al. 2006, Am J Hum Genet, v79 p275). All hybridizations used a single male reference DNA (Coriell ID NA15724).

first: Sierra

last: Hansen

first: Rebecca

last: Selzer

first: Ze

last: Cheng

first: Regina

last: Regan

first: Jane

last: Hurst

first: Helen

last: Stewart

first: Sue

middle: M

last: Price

first: Edward

last: Blair

first: Raoul

last: Hennekam

first: Carrie

last: Fitzpatrick

first: Rick

last: Segraves

first: Todd

last: Richmond

first: Cheryl

last: Guiver

first: Donna

middle: G

last: Albertson

first: Daniel

last: Pinkel

first: Peggy

last: Eis

first: Stuart

last: Schwartz

first: Samantha

last: Knight

first: Evan

last: Eichler


title: Comparison of Gene Expression from Day 6 In Vivo- and In Vitro-Produced Porcine Blastocysts

city: Clay Center

first: Jeremy

last: Miles

state: NE

address: State Spur 18A

institute: USDA-ARS

summary:
Production of embryos in vitro has enormous potential for research and commercial applications.  Unfortunately, in vitro production of porcine embryos is extremely inefficient.  Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development.  The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE.  Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries.  Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively.  A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively.  Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively.  Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs.  Annotated tags were categorized into functional groupings according to gene ontology annotations.  Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts.  These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods.
Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos)

overall_design: Whole-cell RNA from pools of Day 6 in vivo- and in vitro-produced blastocysts was used to construct small amplified RNA (SAR)-SAGE libraries.

first: J

first: L

last: Blomberg

first: R

last: Krisher

middle: E

last: Everts

first: T

last: Sonstegard

first: C

middle: P

last: Van Tassell

first: K

last: Zuelke


title: Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration

status: Public on Aug 11 2006

city: Indianapolis

first: Matthew

last: Grow

state: IN

institute: Indiana University

summary:
Xenopus laevis tadpoles are capable of limb regeneration following amputation, in a process which initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages.  We have used the Affymetrix Xenopus laevis Genome Genechip® microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days post-amputation.  Through an exhaustive reannotation of the Genechip® and a variety of comparative bioinformatic analyses, we have identified genes that are differentially expressed between the regeneration-complete and –incomplete stages, detected the transcriptional changes associated with the regenerating blastema, and compared these results with those of other regeneration researchers.  We focus particular attention on striking transcriptional activity observed in genes associated with patterning, stress response, and inflammation.  Overall, this work provides the most comprehensive views yet of a regenerating limb and different transcriptional compositions of regeneration-competent and deficient tissues.
Keywords: Expression profiling

overall_design: This experiment measures gene expression in regeneration competent stage 53 and regeneration non-competent stage 57 Xenopus laevis hindlimbs, at 1 and 5 days post-amputation. Four replicates for each condition were used.  Hindlimbs at either st53 or st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One (1dPA) and 5 days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).  One microgram of total RNA was amplified with the the Affymetrix 2 cycle kit and assayed per Genechip using standard Affymetrix protocols.

middle: W

first: Anton

last: Neff

first: Anthony

last: Mescher

first: Michael

last: King


title: Transcriptional profile of thermophilic bacteriophage GVE2 genes

city: xiamen

first: xiaobo

last: zhang

address: No. 178 Daxue Rd.,

country: China

institute: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration,China

summary:
To investigate the transcriptional profile of GVE2 genes, the viral genes were identified by DNA microarray with Cy5- or Cy3-dUTP-labeled cDNAs prepared from uninfected and GVE2-infected Geobacillus sp. E263 at 4 h p.i.. After hybridization with the Cy3-dUTP-labeled cDNAs from GVE2-infected Geobacillus sp. E263 at 4 h p.i., Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263 as well as Cy3- dUTP-labeled yeast cDNAs and Hex DNA, many spots produced positive signals significantly above the background, while no signal appeared for the Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263., indicating that the positive signals represented the GVE2 gene transcripts detectable by DNA microarray. The DNA fragments, detected to be positive in the reverse transcripts at 4 h p.i., contained 74.2% of the presumptive GVE2 ORFs.
Keywords: Transcriptional profile of thermophilic bacteriophage at 4 h p.i.

overall_design: A DNA microarray containing 82 DNA fragments of the viral genome was constructed following a PCR-based microarray method. Briefly, specific primer sets were designed to amplify approximately 500-bp fragment each using viral genome as template. All PCR products showing a single band of the appropriate size by gel electrophoresis were purified, and reconstituted in TE buffer at a final concentration of about 500 μg/ml for spotting in triplicates onto the silylated-glass slides (CEL Associates, Inc. USA) using a microarrayer (Smart Arrayer 48, CapitalBio). Eight DNA fragments from yeast genome and a randomly synthesized DNA fragment (Hex) were included as exogenous positive controls to normalize the microarry date. Distilled water was used as negative controls. Total RNAs were isolated from the uninfected and phage-infected Geobacillus sp. E263 cells at 4 h postinfection. The cDNAs from uninfected Geobacillus sp. E263 were labeled with Cy5 and the cDNAs from phage-infected Geobacillus sp. E263 labeled with Cy3. At the same time, the cDNAs from yeast and the Hex DNA were labeled with Cy3. The Cy5- or Cy3-dUTP-labeled cDNAs were resuspended in hybridization solution and hybridized with the microarrays for 16 to 18 h at 42°C. Then the microarrays were rinsed several times following the standard method. Following the washing steps, the microarrays were dried by low-speed centrifugation (500 g for 5 min), and immediately scanned using a GenePix 4000B array scanner (Axon Instruments, Inc.). Images obtained from scanning were analyzed by GenePix Pro 4.0 array analysis software (Axon Instruments, Inc.)


title: Transcriptional analysis of carbohydrate utilization by Lactobacillus acidophilus using whole-genome microarrays

status: Public on Aug 07 2006

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary:
L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005).
Keywords: other

first: Rodolphe

last: Barrangou

first: Maria

last: Azcarate-Peril


title: Auratus goldfish genome project: effects of fluoxetine on female goldfish

status: Public on Aug 04 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary:
A goldfish brain enriched cDNA combined with a carp microarray (Gracey et al., 2004). Female adult goldish were treated twice a week for 17 days, for a total of five injections.  Each of the injections consisted of 5 μg fluoxetine/g of body weight with an injection volume of 1μl/g.  The telencephalon was tissue used.
Keywords: i.p.injection of muscimol, 6 hours, pharmacological

overall_design:
4 slides (n=3 treatment samples and common control pool)
slide 19 = treatment sample 1
slide 30 = treatment sample 2
slide 36 = treatment sample 3 (dye swap)
slide 39 = treatment sample 3 (dye swap)

first: Jan

last: Mennigen

first: Chris

first: Vance

last: Trudeau


title: Auratus goldfish genome project: Muscimol experiment (6 hour)

summary:
A goldfish brain enriched cDNA combined with a carp microarray (Gracey et al., 2004). Female goldfish were i.p. injected with 1 ug/g muscimol once and after 6 hours, telencephalon dissected and used in microarray analysis. More details on microarray hybridizations and technique used in our laboratory in Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17α-EE2(paper under review)
Keywords: muscimol, GABA, goldfish, brain

overall_design:
4 arrays using a common control pool and 3 treatment samples.
Slides 16, 22, 33, and 50
Slides 22 and 33 are dye swap.

middle: J


city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2142

department: Dermatology

institute: Stanford University

summary:
Data set to accompany :  Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2006 Jul;2(7):e119.  PMID: 16895450  Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal), proximal-distal, and dermal versus nondermal. A set of 337 genes that varied according to these positional divisions was able to group all 47 samples by their anatomic sites of origin. Genes involved in pattern formation, cell-cell signaling, and matrix remodeling were enriched among this minimal set of positional identifier genes. Many important features of the embryonic pattern of HOX gene expression were retained in fibroblasts and were confirmed both in vitro and in vivo. Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: John

last: Rinn


title: Designing siRNA that distinguish between genes that differ by a single nucleotide

city: Boston

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

summary:
Small interfering RNAs (siRNAs), the guides that direct RNA interference (RNAi), provide a powerful tool to reduce the expression of a single gene in human cells. Ideally, dominant, gain-of-function human diseases could be treated using siRNAs that specifically silence the mutant disease allele, while leaving expression of the wild-type allele unperturbed.  Previous reports suggest that siRNAs can be designed with single-nucleotide specificity, but no rational basis for the design of siRNAs with single nucleotide discrimination has been proposed.
Keywords: siRNA, single-nucleotide discrimination, SOD1, allele-specific

overall_design:
We transfected the siRNAs into cultured human HeLa cells at 100 nM final
concentration.  Amplified cRNA from siRNA-transfected cells was hybridized against cRNA from mock-transfected cells (treated with transfection reagent in the absence of RNA duplex). Ratio hybridizations were performed with fluorescent label reversal to eliminate dye bias.

first: Dianne

middle: S

last: Schwarz

first: Hongliu

last: Ding

first: Lori

last: Kennington

first: Jessica

last: Moore

first: Janell

last: Schelter

first: Peter

last: Linsley

first: Neil

last: Aronin

first: Zuoshang

last: Xu

first: Phillip

last: Zamore


title: Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary:
The meiotic cohesin Rec8 is required for the stepwise segregation of chromosomes during the two rounds of meiotic division. By directly measuring chromosome compaction in living cells of the fission yeast Schizosaccharomyces pombe, we found an additional role for the meiotic cohesin in the compaction of chromosomes during meiotic prophase. In the absence of Rec8, chromosomes were decompacted relative to those of wild-type cells. Conversely, loss of the cohesin-associated protein Pds5 resulted in hyper-compaction. While this hyper-compaction requires Rec8, binding of Rec8 to chromatin was reduced in the absence of Pds5, indicating that Pds5 promotes chromosome association of Rec8. To explain these observations, we propose that meiotic prophase chromosomes are organized as chromatin loops emanating from a Rec8-containing axis; the absence of Rec8 disrupts the axis, resulting in disorganized chromosomes, whereas reduced Rec8 loading results in a longitudinally compacted axis with fewer attachment points and longer chromatin loops.
Keywords: ChIP-chip analysis

overall_design: ChIP analysis of Rec8: In all cases, hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Pombe chromosome II, III array was used.

first: Da-Qiao

first: Nobuko

last: Sakurai

first: Yuki

last: Katou

first: Takehiko

last: Itoh

first: Yasushi

last: Hiraoka


title: Small RNAs from the moss Physcomitrella patens

status: Public on Aug 15 2006

first: Michael

last: Axtell

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

type: Non-coding RNA profiling by high throughput sequencing

summary:
High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens.  This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens.
SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME
Keywords: High throughput small RNA sequencing

overall_design:
Small RNA cDNA libraries derived from polyacrylamide gel electrophoresis (PAGE) fractionated total RNA, adapter ligation, reverse transcription, and pyrosequencing was used for microRNA and endogenous siRNA discovery in wild-type tissues of the moss Physcomitrella patens.  See

Axtell et al. (2006) A two-hit trigger for siRNA biogenesis in plants.  Cell 127: 565-577.

for details.

first: David

last: Bartel


title: High Resolution Mapping and Functional Analysis of the Methylome in Arabidopsis (polyA RNA)

status: Public on Aug 17 2006

city: La Jolla

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

type: Expression profiling by genome tiling array

summary:
Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. Unexpectedly, over one third of expressed genes contained methylation within transcribed regions, whereas only ~5% of genes contained methylation within promoter regions.  Interestingly, genes methylated in transcribed regions were highly expressed and constitutively active, whereas promoter-methylated genes showed a greater degree of tissue-specific expression. Analysis of several DNA methyltransferase mutants revealed widespread epigenetic regulation of protein-coding genes as well as  non-coding RNA genes of unknown function.
Keywords: whole genome profiling, poly(A)RNA, DNA methylation

overall_design: All plants used in this study are of the Columbia accession. The met1 and drm1 drm2 cmt3 mutants are previously published. The mutant alleles are: met1-3; drm1-2, drm2-2, cmt3-11. To avoid variability caused by inbreeding, all homozygous mutants were from F1 segregating populations. Plants were grown under continuous light. RNA was extracted from 5 weeks old plants using the Plant RNeasy Kit (QIAGEN) according to manufacturer’s instructions. The entire aerial parts of 2–3 plants were pooled for each 3 biological replicate.

first: Xiaoyu

last: Zhang

first: Junshi

last: Yazaki

first: Ambika

last: Sundaresan

first: Shawn

last: Cokus

first: Simon

last: Chan

first: Huaming

last: Chen

first: Ian

middle: R

last: Henderson

first: Paul

last: Shinn

first: Matteo

last: Pellegrini

first: Steve

last: Jacobsen


title: Time evolution study of sepsis in patients at D1, D7 and D28 post-inclusion

status: Public on Aug 01 2006

city: Paris

first: Didier

last: Payen de la Garanderie

address: 2 rue Ambroise Pare

department: DAR-ICU

institute: Hopital Lariboisiere

summary:
Microarray was performed on PBMC with an inflammatory dedicated slide of 340 genes, and target samples labelled with Cy3 for day 0 (reference) and with Cy5 for the other days. Changes in expression levels were evaluated by the ratio Dx/D0. According to time evolution, a two-dimensional clustering was performed.
Keywords: time evolution of sepsis in patients at D1, D7 and D28 post-inclusion

overall_design: The day of inclusion corresponded to the first blood sampling (15 ml) quoted day 0. The following blood samples were performed at days 1, 7, and 28. Since the pre-sepsis expression of the genes as a control cannot be obtained, the day 0 sample was used patient per patient as a reference value for the next days samples for micro-array study. Patients evolution was considered.

first: Yulia

last: Belikova

first: Anne-Claire

last: Lukasciewicz

first: Nicolas

last: Sevenet

last: Payen


title: Expression profile of the first 24 hrs of Drosophila embryonic development using tiling arrays

status: Public on Aug 14 2006

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

summary:
Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. To begin to address this question, we have generated a series of transcription maps at an interrogation resolution of 35 base pairs (bp) across the Drosophila genome for the first 24 hrs of development in 2 hour increments, similar to maps we have created for regions of the human genome. Using a single tiling array, 3,075,693 probe pairs of twenty-five nucleotides (nts) in length were used to interrogate 105,897,358 non-repeat bp of the fly genome.  Maps of the sites of transcription were made using total RNA greater than 200 nts. Approximately 7% and 23% of the detected transcribed nucleotides during D. melanogaster embryogenesis map to unannotated intergenic and intronic regions, respectively.  Based on computational analysis of coordinated transcription, we conservatively estimate that 29% of all unannotated transcribed sequences function as missed or alternative exons of well-characterized protein coding genes. 15.6 % of intergenic transcribed regions function as missed or alternative transcription start sites utilized by 11.4% of the expressed protein-coding genes. Identification of P element mutations within or near newly identified 5' exons provides a strategy for mapping previously uncharacterized mutations to their respective genes.  Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome.
Keywords: time course, Drosphila embryonic development, tiling array, expression profile

overall_design: Total RNA was extracted from dechorionated whole embryos collected in 2hr intervals (0-2 hr, 2-4hr..etc)for 12 time points (first 24hr of development). RNA was then converted to cDNA using standard protocols. 3 replicate chips were used for each sample (time point).

first: John

last: Manak

first: Sujit

last: Dike

first: Victor

last: Sementchenko

first: Philipp

last: Kapranov

first: Frederic

last: Biemar

first: Jeff

last: Long

first: Jill

last: Cheng

last: Bell

first: Srinka

last: Ghosh

first: Antonio

last: Piccolboni


title: Transcriptional Response of Human Macrophages to Legionella pneumophila Infection

first: Ralph

last: Isberg

address: 150 Harrison Ave.

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary:
Abstract
Legionella pneumophila, the causative agent of Legionnaire’s disease, grows within macrophages and manipulates target cell signaling.  Formation of a Legionella-containing replication vacuole requires the function of the bacterial type IV secretion system (Dot/Icm), which transfers protein substrates into the host cell cytoplasm.  A global microarray analysis was used to examine the response of human macrophage-like U937 cells to low dose infections with L. pneumophila. The most striking change in expression was the Dot/Icm-dependent up-regulation of anti-apoptotic genes positively controlled by the transcriptional regulator NF-?B.  Consistent with this finding, L. pneumophila triggered nuclear localization of NF-?B in human and mouse macrophage in a Dot/Icm-dependent manner.  The mechanism of activation at low dose infections involved a signaling pathway that occurred independently of the TLR adaptor MyD88, and cytoplasmic sensor Nod1.  In contrast, high MOI conditions caused a host cell response that masked the unique Dot/Icm-dependent activation of NF-?B.  Inhibition of NF-?B translocation into the nucleus resulted in premature host cell death and termination of bacterial replication.  In the absence of one anti-apoptotic protein, PAI-2, host cell death increased in response to L. pneumophila infection, indicating that induction of anti-apoptotic genes is critical for host cell survival.
Keywords: time course, dose response

overall_design:
To identify host cell genes that may modulate intracellular growth of L. pneumophila, we compared the transcriptional profile of U937 cells incubated with either WT L. pneumophila or a dotA- mutant lacking a functional Dot/Icm type IV translocator.  The isolation of a homogenously infected cell population was a prerequisite for this study.  Unlike other pathogens, L. pneumophila causes rapid Dot/Icm-dependent cytotoxicity at the high multiplicities of infection (MOI) that are required to infect the majority of cells in the monolayer.   To bypass cytotoxicity, incubations unless indicated were performed at MOI=1 (1 bacterium per macrophage), which results in a approximately 30%the cultured cells having associated bacteria.  To specifically analyze this population, U937 cells having associated bacteria were sorted away from the vast excess of uninfected cells using the GFP marker. Samples were collected 1 or 8 hours post infection, sorted for the cell population harboring GFP bacteria, and total RNA was isolated from these sorted populations.  These two time points were chosen because the Dot+ strain initiates biogenesis of the replication vacuole at 1 hpi, with clear recruitment of ER-derived vesicles at this time point, and has completed one round of division by 8 hpi.  In contrast, the type IV secretion-defective strain dotA-GFP strain fails to establish an ER-like vacuole and to replicate. To confirm that any changes in expression patterns were a result of a response to functions performed by the type IV translocation system, the mutant strain dimB- was included in this study.  The dimB- mutant has an intact Dot/Icm translocator and shows proper formation of a replication vacuole, but is defective for intracellular growth and stalls after one intracellular doubling.

A total of 27 microarrays were used in this study. For each condition three independent microarrays were performed on cells isolated from three independent infections. The conditions were sorted U937 infected with WT, dimB, dotA at MOI=1 for 1 or 8 hours, as well as U937 cells infected with dotA at MOI=10.   As control of gene expression changes due to sorting alone sorted uninfected U937 cells were included.  No dye swaps were used. cDNA isolated from uninfected, unsorted U937 cells was always labeled with Cy3, and the sorted sample or high moi sample was always labeled with Cy5.  The same reference total RNA preparation was used with each microarray experiment.

first: Vicki

last: Losick


title: Sall4: -/- NT1 vs TBV

status: Public on Aug 02 2006

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
Sall genes are expressed early in development and in diversity of embryonic and adult structures. Sall4 plays a crucial role during the development of a number of systems. Mutations in the SALL4 gene have been linked to Okihiro/acro-renal-ocular syndrome, in which patients exhibit forearm malformations and eye movement deficits.
Homozygote and heterozygote Sall4 cells from mouse blastocysts were collected and used to design a genetrap mouse mutant line.
The homozygote Sall4 ES cells form mouse blastocyst were hybridizised versus TBV wildtype cells to detect changes in gene expression. Three biological samples of different passages of the same clone of NT1 and TBV were analyzed in 13 chip hybridizations; each sample was analyzed in 2-5 experimental replicates including dye swap experiments.
Keywords: others

overall_design: 13 dual-color DNA-chip hybridizations including 6 dye swap experiments of cDNAs were performed

last: Floss

first: Nikolas

last: Uez

first: Marion

last: Horsch

first: Johannes

last: Beckers


first: Tristan

last: Coram

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

summary:
Using microarray technology and a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, the ascochyta blight (Ascochyta rabiei (Pass.) L.) resistance response was studied in four chickpea genotypes, including resistant, moderately resistant, susceptible and wild relative (Cicer echinospermum L.) genotypes.  The experimental system minimized environmental effects and was conducted in reference design, where samples from mock-inoculated controls acted as references against post-inoculation samples.  Robust data quality was achieved through the use of three biological replicates (including a dye-swap), the inclusion of negative controls, and strict selection criteria for differentially expressed genes including a fold change cutoff determined by self-self hybridizations, Students t test and multiple testing correction (P<0.05).  Microarray observations were also validated by quantitative RT-PCR.  The time-course expression patterns of 756 microarray features resulted in differential expression of 97 genes in at least one genotype at one time-point.  K-means clustering grouped the genes into clusters of similar observations for each genotype, and comparisons between A. rabiei-resistant and susceptible genotypes revealed potential gene 'signatures' predictive of effective A. rabiei resistance.  These genes included several pathogenesis-related proteins, SNAKIN2 antimicrobial peptide, proline-rich protein, disease resistance response protein DRRG49-C, environmental stress-inducible protein, leucine-zipper protein, polymorphic antigen membrane protein, as well as several unknown proteins.  The potential involvement of these genes and their pathways of induction are discussed.  This study represents the first large-scale gene expression profiling in chickpea, and future work will focus on functional validation of the genes of interest.
Keywords: time course disease state analysis

platform_organism:
Cicer arietinum
Lathyrus sativus
Lens culinaris

overall_design:
Total RNA was extracted from pooled stem and leaf samples for each genotype (FLIP94-508C, ICC3996, ILWC245 and Lasseter) at each time-point (including control samples) using the RNeasy® Plant Mini Kit (Qiagen, Valencia, CA).  The quantity and quality of the total RNA samples were assessed by OD260/OD280 ratios and gel electrophoresis respectively.  Fluorescent-labeled targets were prepared and hybridized to array slides according to [Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Published in Plant Biotechnology Journal].  All hybridizations were performed with six technical replicates and three biological replicates, incorporating dye-swapping (i.e. reciprocal labelling of Cy3 and Cy5) to eliminate any dye bias.  Overall, 360 images were analyzed from 60 slides, resulting in 18 data points for each time-point of each genotype.

Slides were scanned at 532 nm (Cy3 green laser) and 660 nm (Cy5 red laser) at 10 µm resolution using an Affymetrix® 428 array scanner (Santa Clara, CA), and captured with the Affymetrix® Jaguar software (v. 2.0, Santa Clara, CA).  Image analysis was performed using Imagene 5 (BioDiscovery, Marina Del Rey, CA) software.  Quantified spot data was then compiled and transformed using GeneSight 3 (BioDiscovery, Marina Del Rey, CA).  Data transformations consisted of a local background correction (mean intensity of background was subtracted from mean signal intensity for each spot), omitting flagged spots, Lowess normalisation of the entire population, creating a Cy5/Cy3 mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data.  To identify differentially expressed (DE) genes, expression ratio results were filtered to eliminate genes whose 95% confidence interval for mean fold change (FC) did not extend to 1.8-fold up or down, followed by Students t test with False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression changes versus untreated control were significant at P < 0.05.

first: Edwin

middle: C

last: Pang

first: Nitin

last: Mantri

first: Barkat

last: Mustafa


title: A computational genomics approach to identify cis-regulatory modules - a case study using E2F1

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

summary:
We first trained a set of experimentally identified E2F1 targets by a ChIPModules approach, the identified module of E2F1 and AP-2alpha was validated by ChIP-chip assays.
Keywords: ChIP-chip

overall_design: We have performed 3 sets of ChIP-chip experiments in MCF-7 for E2F1 and AP-2alpha respectively. The common genes bound by both E2F1 and AP-2alpha were then identified as a co-localized set of genes. We also performed ChIP-PCR conformation for randomly selected 10 targets.

first: Alina

last: Rabinovich

first: Sharon

last: Squazzo

first: Roland

last: Green

first: Peggy

last: Farnham


title: High resolution analysis of early lobular neoplastic breast lesions (ALH and LCIS) by whole genome tiling path array CGH

city: Toronto

first: Teresa

last: Mastracci

address: 600 University Ave., room 984

department: Mount Sinai Hospital

institute: Samuel Lunenfeld Research Institute

summary:
The identification of genomic alterations occurring in neoplastic lesions provides insight into both lesion occurrence and disease progression.  In this study we used microarray comparative genomic hybridization (CGH) to investigate genetic changes in atypical lobular hyperplasia (ALH) and lobular carcinoma in situ (LCIS), as the presence of these lobular neoplastic lesions is an indicator of risk in the development of invasive breast cancer.  DNA was extracted from microdissected archival breast tissue containing ALH or LCIS, lacking adjacent invasive carcinoma, and subjected to whole-genome tiling path microarray-CGH using the submegabase resolution tiling set (SMRTr)-array platform.  Twelve ALH and 13 LCIS lesions were examined.  Copy number alterations were identified using statistical criteria and validated with Real-Time PCR and fluorescence in situ hybridization.  From statistical analysis, a greater number of alterations were observed in ALH compared to LCIS.  Alterations common to ALH include gain at 2p11.2 and loss at 7p11.2-p11.1 and 22q11.1.  Alterations common to LCIS include gain at 20q13.13 and loss at 19q13.2-q13.31.  In both ALH and LCIS, we observed loss of 16q21-q23.1, an altered region previously identified in lobular neoplasia and invasive carcinoma.  The validation of select alterations reinforces the genomic signature.  This study represents the first whole-genome investigation of lobular neoplastic breast lesions using clinical archival specimens.  The identified genomic signature includes copy number alterations not previously identified for lobular neoplasia.  This genomic signature, common to ALH and LCIS, suggests a role for the acquisition of novel genomic alterations in the aberrant cellular proliferation that defines lobular neoplasia.
Keywords: comparative genomic hybridization, high resolution analysis of atypical lobular hyperplasia (ALH) and lobular carcinoma in situ (LCIS) human archival breast lesions by whole genome tiling path array CGH

overall_design: 25 early lobular neoplastic breast lesions (atypical lobular hyperplasia, ALH; lobular carcinoma in situ, LCIS) were differentially labeled and each competitively hybridized against female genomic DNA using the (27K) SMRTr tiling array

first: Ashleen

last: Shadeo

first: Sarah

last: Colby

first: Alan

middle: B

last: Tuck

first: Frances

last: O'Malley

first: Shelley

last: Bull

first: Wan

last: Lam

first: Irene

last: Andrulis


title: MEF cell study

city: New Havem

first: Nyam-Osor

last: Chimgee

state: CT

address: 266 Whitney Ave

department: MCDB

institute: Yale University

summary:
overexpression of Gtf2iRD1 or TFII-I in MEF cells
Keywords: treated vs.untreated

overall_design:
2 biological replicates of Gtf2iRD1 transfected vs mock transfected
2 biological replicates of TFII-I transfected vs mock transfected


title: Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

city: Berkeley

first: Frederic

last: Biemar

address: 142 LSA

department: Molecular & Cell Biology

institute: UC Berkeley

summary:
Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence specific transcription factor distributed in a broad nuclear gradient in the precellular embryo.Previous studies have identified as many as 70 protein-coding  genes and one microRNA gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit  diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation.  Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30  protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5' exons were identified for at least 10 of the ~100 protein-coding genes that  were missed in earlier annotations. As many as 9 intergenic, uncharacterized transcription units  were identified, including two that contain known microRNAs, miR-1 and miR-9a. We discuss the potential functions of these newly identified genes, and suggest that intronic enhancers are a common feature of the DV gene network.
Keywords: gene expression, dorsal-ventral pattern genes, tiling array

overall_design: 3 samples where analyzed (Tollrm9/Tollrm10, pipe386/pipe664, Toll10B/+), 3 technical replicates

first: Fred

first: John

last: Manak

first: David

last: Nix

first: Mike

last: Levine


title: Analysis of Hepatic Gene Expression in Chickens with Hormonally-Induced Lean and Fat Phenotypes

status: Public on Aug 09 2006

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary:
Obesity is a growing health concern in the United States and has been linked to a global epidemic--the metabolic syndrome.  The purpose of this project was to use microarray analysis to unravel the genetic circuits controlling deposition and metabolism of fat in a hormonally-induced obesity model.  Glucose, triglyceride, and free fatty acid levels of four-week-old chickens were dramatically altered after acute infusion (six days) of exogenous corticosterone (CS), effectively producing a fat phenotype.  A lean phenotype was induced by thyroid hormone (T3), and the interaction of both hormones (CS+T3) was also examined.  The Del-Mar 14K Chicken Integrated Systems Microarray (Geo Platform GPL1731) was used to identify differentially expressed hepatic genes (false discovery rate, P < 0.05).  In the contrast of fat (CS) and lean (T3) phenotypes, 231 genes were up-regulated by CS, whereas 532 genes were up-regulated by T3.  This study revealed several transport proteins, transcription factors, and metabolic enzymes that control lipogenic (CS induced) and lipolytic (T3 induced) pathways.  Also, the divergent expression of three genes belonging to the β-defensin family (DEFB9, DEFB10, and DEFB11) suggests a novel role for these antimicrobial peptides in adiposity.  This project provides new insight into genetic control of metabolic disorders, such as diabetes and obesity.
Keywords: Hormonal treatment on hepatic gene expression levels

overall_design: Six biological replicates each of the four treatment groups (except for five biological replicates for CS+T3) from four-week-old chickens given six days of hormonal treatment were analyzed for hepatic gene expression.  Each of the 23 experimental samples was labeled with Alexa Fluor 555 and hybridized with an aliquot of the Alexa Fluor 647 reference RNA pool in a reference hybridization design.

first: Jessica

middle: A

last: Hall

first: Nares

last: Trakooljul


title: Genome-based approaches to understanding phosphorus deprivation responses and PSR1 control in Chlamydomonas reinhardtii.

status: Public on Aug 18 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
The Chlamydomonas reinhardtii transcription factor PSR1 is required for the control of activities involved in scavenging phosphate from the environment during periods of phosphorus limitation. Increased scavenging activity reflects the development of high-affinity phosphate transport and the expression of extracellular phosphatases that can cleave phosphate from organic compounds in the environment. A comparison of gene expression patterns using microarray analyses and quantitative PCRs with wild-type and psr1 mutant cells deprived of phosphorus has revealed that PSR1 also controls genes encoding proteins with potential "electron valve" functions--these proteins can serve as alternative electron acceptors that help prevent photodamage caused by overexcitation of the photosynthetic electron transport system. In accordance with this finding, phosphorus-starved psr1 mutants die when subjected to elevated light intensities; at these intensities, the wild-type cells still exhibit rapid growth. Acclimation to phosphorus deprivation also involves a reduction in the levels of transcripts encoding proteins involved in photosynthesis and both cytoplasmic and chloroplast translation as well as an increase in the levels of transcripts encoding stress-associated chaperones and proteases. Surprisingly, phosphorus-deficient psr1 cells (but not wild-type cells) also display expression patterns associated with specific responses to sulfur deprivation, suggesting a hitherto unsuspected link between the signal transduction pathways involved in controlling phosphorus and sulfur starvation responses. Together, these results demonstrate that PSR1 is critical for the survival of cells under conditions of suboptimal phosphorus availability and that it plays a key role in controlling both scavenging responses and the ability of the cell to manage excess absorbed excitation energy.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed

first: Jeffrey

last: Moseley


title: Effect of Cyclic stretching on the gene expression in human spinal ligament cells

city: Hirosaki

first: Ken-Ichi

last: Furukawa

address: Zaifucho 5

department: Pharmacology

institute: Hirosaki University School of Medicine

summary:
Ossification of the posterior longitudinal ligament (OPLL) of the spine is characterized by progressive ectopic bone formation in the spinal ligament. To identify the genes related to ectopic ossification of human spinal ligament affected by mechanical stress, analyses using cDNA microarray were carried out using cultured human spinal ligament cells that had been subjected to uniaxial cyclic stretching. cDNA microarrays revealed that ranges of distribution of both up- and down-regulated genes evoked by cyclic stretching were significantly wider in cells from than in non-OPLL cells.
Keywords: mechanical-stress response

overall_design: Cells were cultured in deformable silicon chamber which were exposed to cyclic stretching (120% extension ratio) for up to 9 hr. After cyclic stretching, total RNA was extracted from each cell monolayer. Target cDNAs transcribed from non-stretched control cells and stretched cells were labeled with Cy3 and Cy5, respectively, and then hybridized with an Agilent Human 1 cDNA Microarray. The microarrays were scanned in both the Cy3 and Cy5 channels with an Affymetrix 428 Array Scanner, and then analyzed using the ImaGene and GeneSight-Lite Software packages.

first: Tomohiro

last: Iwasawa

first: Koei

last: Iwasaki

first: Toshitada

last: Sawada

first: Akihiro

last: Okada

first: Kazumasa

last: Ueyama

first: Shigeru

last: Motomura

first: Seiko

last: Harata

first: Itsuro

last: Inoue

first: Satoshi

last: Toh