title: Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation_expression profiling

city: Montreal

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

department: Genetics

institute: CNRC-IRB

summary:
Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 activates transcription at these loci and is essential. Orthologs of Tbf1 bind TTAGGG telomeric repeats in most eukaryotes, and TTAGGG cis-elements are present upstream of RP genes in plants and fungi, suggesting that Tbf1 was involved in both functions in ancestral eukaryotes. In all Hemiascomycetes, Rap1 substituted Tbf1 at telomeres and in the S. cerevisiae lineage this substitution also occurred independently at RP genes, illustrating the extreme adaptability and flexibility of transcriptional regulatory networks.
Keywords: Expression profiling

overall_design: Expression profiling of tetracycline addition time-course in the tetO-TBF1/tbf1 conditional mutant.

first: Hervé

last: Hogues

first: André

last: Nantel

first: Malcolm

last: Whiteway


title: Transcriptional profiling and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans

status: Public on Mar 11 2008

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

country: Germany

institute: Hans Knoell Institute

summary:
Invasion of host tissue by the human fungal pathogen, Candida albicans is an important step during many forms of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. It is known for example that the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade into host tissue and to cause infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence as compared to SC5314. In this study we compare the in vitro transcriptional profiles and the genotypic profiles of these two widely used laboratory strains in order to determine the principal biological and genetic properties which may govern the different potential for invasiveness and virulence.
Keywords: transcriptional profiling, comparative genomic hybridisation, invasive vs. non-invasive C. albicans strain

overall_design:
Genomic DNA from C. albicans strains SC5314 and ATCC10231 hybridisations were done in duplicate including one dye swap.
Total RNA from C. albicans strains SC5314 and ATCC10231 strains were compared in triplicate including one biological replicate and one dye swap.

first: Sascha

last: Thewes

first: Gary

middle: P

last: Moran

first: Derek

middle: J

last: Sullivan


title: Cell cycle dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes

city: Charlottesville

first: Jie

last: Liu

state: VA

address: 1300 Jefferson Park Avenue

department: Physiology

country: USA

institute: University of Virginia

type: Genome binding/occupancy profiling by genome tiling array

summary:
Nucleosome organization determines local chromatin structure and changes in nucleosome occupancy during the cell cycle are correlated with nuclear functions.
We used oligonucleotide tiling arrays to analyze the cell cycle dependence of nucleosome occupancy at cohesin binding sites in yeast chromosomes.

Processed data included in Series table. Data processing: To improve the signal to noise ratio, the raw data were first processed with dCHIP with its PM/MM difference model and invariant set normalization method, using the entire dataset. 8251 out of the total 92812 probe pairs were excluded from further analysis because they either have multiple hits in the genome or the signal from the genomic hybridization was too weak (cutoff at (PM-MM)/MM < 0.25). After Gaussian smoothing (s =75 bp), the data were normalized by that of the genomic DNA. These values were then converted to log2 scale. The mean was then computed for each array. To facilitate comparisons, the different datasets were rescaled to have the same mean with log2 value of 0. The log2 ratio along the four chromosomes at all the cell cycle stages are included. The ID represents "Chromosome No_chromosomal coordinate".
Keywords: time course

overall_design: Yeast cells were arrested at G1/S boundary with alpha factor, then released for 15 min, 40 min, 65 min and 95 min respectively. Cells were collected at each time points, then mononucleosomal DNA was purified and hybridized to Affymetrix oligonucleotide tiling arrays. Total genomic DNA was hybridized as normalization signal.

first: Daniel

middle: M

last: Czajkowsky

first: Shoudan

last: Liang

first: Zhifeng

last: Shao


title: cyt_aux_balance-Effect of the Auxin/Cytokinin ratio on the transcriptome of stem cells

status: Public on Mar 12 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

summary:
adt05-01_hormon_cells - cyt_aux_balance - Effect of the Auxin/Cytokinin ratio on the transcriptome - Different hormone concentrations were used to grow the cells
Keywords: dose response

overall_design: 6 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Mutations in Multidrug Efflux Pumps of Eshcerichia coli

city: Jefferson

first: Christopher

middle: A

last: Elkins

state: AR

address: 3900 NCTR Drive

department: Microbiology

institute: FDA National Center for Toxicological Research

summary:
The number and overlapping substrate repertoire of multidrug efflux pumps in the E. coli genome suggest a physiological role apart from multidrug resistance.  This role was investigated using transcriptomic analyses of cDNAs labeled from E. coli AG102 mRNA (hyper drug resistant, marR1) and its isogenic major efflux pump mutants.
Keywords: Mutation Analysis

overall_design: For each mutant analysis, at least fivefold redundancy was employed in culture preparation and mRNA isolation.  In addition, each microarray slide contains three complete copies of the array design giving at least 15 data points (5 slides X 3 copies per slide) for each oligonucleotide probe spot.  Respective E. coli mRNA pools were harvested at mid-log phase from cells grown in Luria-Bertani (Miller) medium at 37C.


title: HIT analysis of T cells activated in the presence of TGF-β

status: Public on Mar 08 2008

city: Stanford

first: Michael

middle: George

last: Kattah

state: CA

address: 269 Campus Dr., CCSR 2250

department: Medicine

institute: Stanford University

summary:
We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT).  This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode.  After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte.  Here we screened 90 antibodies directed against a panel of cell surface markers as well as 4 isotype controls to compare human naive CD4+ T cells activated in the presence or absence of TGF-β.
Keywords: response to stimulus

overall_design: Two-condition experiment, with or without TGF-β. Biological replicates: 3 normal human donors, each donor served as an internal control.  One replicate per array.  One of the biological replicates was performed as a dye-swap to monitor dye-bias.

middle: G

first: John

last: Coller

first: Neekaan

last: Oshidary

first: Regina

middle: K

last: Cheung

first: Paul

last: Utz


title: Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation_ChIP-CHIP

status: Public on Mar 14 2008

first: Hugo

last: Lavoie

country: Canada

summary:
Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 activates transcription at these loci and is essential. Orthologs of Tbf1 bind TTAGGG telomeric repeats in most eukaryotes, and TTAGGG cis-elements are present upstream of RP genes in plants and fungi, suggesting that Tbf1 was involved in both functions in ancestral eukaryotes. In all Hemiascomycetes, Rap1 substituted Tbf1 at telomeres and in the S. cerevisiae lineage this substitution also occurred independently at RP genes, illustrating the extreme adaptability and flexibility of transcriptional regulatory networks.
Keywords: ChIP-CHIP

overall_design: Two independent biological replicates of ChIP-CHIP of Tbf1-HA and Cbf1-HA.

first: Hervé

last: Hogues

first: André

last: Nantel

first: Malcolm

last: Whiteway


title: A serpin, SAS1, controls hormonal cross talk in the plant defense pathway

status: Public on Mar 10 2008

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
A possible regulatory role for SAS1 was evaluated by examining gene expression patterns of SAS1-HA plants.
Keywords: serpin overexpression

overall_design: Total RNA was extracted from 3 weeks old wt and the over expression SAS1:HA line.  Data in this platform contains 6 repetitions including 2 independent biological experiments.

first: Ofra

last: Budai-Hadrian

first: Olga

last: Davydov


title: Overexpression of the transcription factor GAT201 in Cryptococcus neoformans var. grubii (serotype A, H99)

status: Public on Mar 07 2008

city: San Francisco

first: Oliver

middle: W.

last: Liu

department: Biochemistry and Biophysics

institute: UCSF

summary:
Comparison of transcriptional profiles of WT Cryptococcus neoformans (H99) and strain CM126 (pRPL2b-GAT201) which overexpresses the transcription factor GAT201 using a ribosomal protein promoter
Keywords: Genetic modification

overall_design: WT vs. CM126 competitive hybridization.  4 biological replicates including 2 dye flips.  Cultures grown at 37 degress Celsius in minimal (YNB) medium.  Cultures independently grown and harvested during exponential growth.

middle: W

first: Cheryl

middle: D

last: Chun

first: Eric

last: Chow

first: Changbin

last: Chen

first: Hiten

last: Madhani

first: Suzanne

last: Noble


title: HIT T cell versus B cell line proof-of-principle

first: Michael

last: Kattah

summary:
We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT).  This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode.  After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte.  Here we coupled 44 of the tags to aliquots of an IgG1 isotype negative control antibody and the 4 remaining tags we coupled to anti-CD3, anti-CD4, anti-CD19, and anti-CD20 to create a 48-plex HIT cocktail.  We then used this cocktail to stain 1 x 10^6 T or B cells and during amplification incorporated either cyanine 3-UTP (Cy3-UTP) or Cy5-UTP.  Additionally, we snap froze and thawed an aliquot of the cocktail (FT).
Keywords: protein profiling, cell type comparison

overall_design: Two-condition experiment, T cells versus B cells, including dye-swaps and self-self experiments.  We also tested an array that had been frozen and thawed.

first: John

last: Coller


title: Gene expression in the quail MBH under short and long day conditions.

city: Nagoya

first: Takashi

last: Yoshimura

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary:
Various physiological processes and behaviours are controlled by changing daylength.
To dissect genes involved in the photoperiodic changes in physiology and behaviour, global expression analysis was performed using quail kept under short and long day conditions.
Keywords: time course

overall_design: The mediobasal hypothalamus (MBH) of quail kept under short day condition (6h light:18h dark) or long day condition (20h light:4h dark) were collected for RNA extraction. Pooled total RNA from three MBHs was labelled and hybridized on Affymetrix microarrays. Samples were collected from 6 birds every 4h during a 24 h cycle and were analyzed in duplicate set of array (two biological replicates).

first: Nobuhiro

last: Nakao

first: Hiroko

last: Ono

last: Yamamura

first: Tsubasa

last: Anraku

first: Tsuyoshi

last: Takagi

first: Kumiko

last: Higashi

first: Shinobu

last: Yasuo

first: Yasuhiro

last: Katou

first: Sabuo

last: Kageyama

first: Yumiko

last: Uno

first: Takeya

last: Kasukawa

first: Masayuki

last: Iigo

first: Peter

last: Sharp

first: Atsushi

last: Iwasawa

first: Yutaka

last: Suzuki

first: Sumio

last: Sugano

first: Teruyuki

last: Niimi

first: Makoto

last: Mizutani

first: Takao

last: Namikawa

first: Shizufumi

last: Ebihara

first: Hiroki

middle: R

last: Ueda


title: Global gene expression during the photoinduction process.

first: Takashi

last: Yoshimura

summary:
The molecular mechanism of photoperiodic time measurement remains unknown in animals. Japanese quail is an excellent model for studying these phenomena because of their rapid and dramatic response to photoperiod. When quail are transferred from short to long day conditions, increase in plasma gonadotrophin (luteinising hormone: LH) can be observed by the end of the first long day and this phenomenon is called “first day release model”.
To dissect the system dynamics and network structure regulating photoperiodism, we examined global gene expression using high-density oligonucleotide microarray for chicken (Affymetrix Chicken Genome Array).
Keywords: time course

overall_design: The mediobasal hypothalamus (MBH) of quail was collected from 6 birds for each time point during the photoinduction process. Pooled total RNA from three MBHs was labelled and hybridized to each Affymetrix chicken genome array. Samples were analyzed in duplicate set of array (two biological replicate).

first: Nobuhiro

last: Nakao

first: Hiroko

last: Ono

last: Yamamura

first: Tsubasa

last: Anraku

first: Tsuyoshi

last: Takagi

first: Saburo

last: Iwasawah


title: The evolution of spinable cotton fiber entailed prolonged development and a novel metabolism

status: Public on Mar 05 2008

city: Athens

first: Alan

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

summary:
exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium ("cotton fiber"). We have used fiber development in Gossypium as a system to understand how morphology can rapidly evolve.  Fiber has undergone considerable morphological changes between the short, tightly adherent fibers of G. longicalyx and the derived long, spinable fibers of its closest relative, G. herbaceum, that facilitated cotton domestication.  We conducted comparative gene expression profiling across a developmental time-course of fibers from G. longicalyx and G. herbaceum using microarrays with ~ 22,000 genes.  Expression changes between stages were temporally protracted in G. herbaceum relative to G. longicalyx, reflecting a prolongation of the ancestral developmental program.  Gene expression and GO analyses showed that many genes involved with stress responses were up-regulated early in G. longicalyx fiber development.  Several candidate genes up-regulated in G. herbaceum have been implicated in regulating redox levels and cell elongation processes.  Three genes previously shown to modulate hydrogen peroxide levels were consistently expressed in domesticated and wild cotton species with long fibers but expression was not detected by qRT-PCR in wild species with short fibers.  Hydrogen peroxide is important for cell elongation, but at high concentrations it becomes toxic, activating stress processes that may lead to early onset of secondary cell wall synthesis and the end of cell elongation.  These observations suggest that the evolution of long spinable fibers in cotton was accompanied by novel expression of genes assisting in the regulation of reactive oxygen species levels.  Our data suggest a model for the evolutionary origin of a novel morphology through differential gene regulation causing prolongation of an ancestral developmental program.
Keywords: Cotton, fiber, evolution, time-point, comparative genomic hybridization, stress response genes, H2O2

sample_organism:
Gossypium herbaceum
Gossypium longicalyx

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: A balanced developmental loop design for microarray analysis was performed. For G. herbaceum (A1) and G. longicalyx (F), four fiber developmental time-points, 5, 10, 20 and 25 DPA were sampled. Within each species, hybridizations were performed between each pair of consecutive developmental stages by labeling one with Cy5 and the other with Cy3, and by closing the loop with a comparison of 25 and 5 dpa. In addition, 2 hybridizations were done between species at each time-point, using a dye swap for each pair. With three biological replications and 16 slides each, we generated gene expression data from a total of 48 microarrays.

first: Ran

last: Hovav

first: Joshua

last: Udall

first: Bhupendra

last: Chaudhary

first: Einat

first: Lex

last: Flagel

first: Guanjing

last: Hu

first: Jonathan

middle: F

last: Wendel


title: Effects of Steroid Treatment on Escherichia coli

first: Christopher

last: Elkins

summary:
Commensal microbes are exposed to enterohepatically circulated steroids such as bile acids and hormones in the gastrointestinal, vaginal, and urinary tracts. Since commensal microbes are exposed to these molecules exclusively in association with their host, we hypothesized that they may serve as effectors to identify and characterize genetic pathways involved in the commensal-host relationship. Host specific and some ingested steroids (phytoestrogens) are enterohepatically circulated through the lumen of the small intestine. Bile acid steroids are present at high concentrations, approximating 4 to 20 mM in the duodenum, and are released in bile from the common bile duct. Steroid hormones are secreted in bile at levels approximating 6 to 13 mg per day once conjugated to glucuronide or sulfate by the liver. Re-absorption of steroids by the terminal ileum is an incomplete process: for example, 200 to 600 mg of bile acid steroids per day in humans escape to the colon where complex microbial populations exist. We have shown that steroid hormones estradiol, progesterone, and hydrocortisone serve as strong substrates for the major RND- and MFS-type (except hydrocortisone) tripartite multidrug efflux systems, AcrAB-TolC and EmrAB-TolC respectively, even though such molecules fail to demonstrate antimicrobial properties in this bacterial background (Elkins and Mullis [2006] J. Bacteriol. 188:1191-1195). Although bile acids are subject to efflux, they are also known to directly interact with intracellular global regulators such as MarR (Prouty et al. [2004] Microbiol. 150:775-783) and Rob (Rosenberg et al., [2003] Mol. Microbiol. 48:1609-1619) consequently altering antimicrobial and bile resistance profiles. In our present study, whole-genome DNA microarrays of E. coli were used to determine what general effect steroids, both bile acid and hormones, may have on the transcriptome in relation to the human commensal environment.
Keywords: Comparative Chemical Class Treatment

overall_design: For each treatment analysis, dimethyl sulfoxide (DMSO)-dissolved steroids were supplied at approximately 1 mM final culture concentration. E. coli mRNA pools were harvested at mid-log phase from cells grown with respective steroid in Luria-Bertani (Miller) broth medium at 37C.


title: Comparative genomic hybridization between chicken and Japanese quail

summary:
Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy.
To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array.
Keywords: comparative genomic hybridization

sample_organism:
Gallus gallus
Coturnix japonica

overall_design: Genomic DNA of female chicken and quail were extracted individually from liver of three birds and hybridized on Affymetrix microarrays. Samples were analyzed in triplicate set of array (three biological replicates).

first: Kumiko

last: Higashi

first: Shinobu

last: Yasuo

first: Yasuhiro

last: Katou

last: Kageyama

first: Yumiko

last: Uno

first: Takeya

last: Kasukawa

first: Masayuki

last: Iigo

first: Peter

last: Sharp

first: Atsushi

last: Iwasawa

first: Yutaka

last: Suzuki

first: Sumio

last: Sugano

first: Teruyuki

last: Niimi

first: Makoto

last: Mizutani

first: Takao

last: Namikawa

first: Shizufumi

last: Ebihara


title: The effects of artificial tethering of chromosomes to the nuclear periphery using LacI/lap2b anchorage constructs, part 2

status: Public on Mar 04 2008

city: Edinburgh

first: Lee

middle: Edward

last: Finlan

state: Lothian

address: Crewe Road South

department: Chromosomes & Gene Expression Laboratory

country: United Kingdom

institute: MRC Human Genetics Unit

summary:
Experiment:   analysis of gene expression changes between J21.c3 (non tethered)  vs J21.c3 lacI-lap2b (lap2b-lacI tethered) that both possess a Chr11 128mer LacO integrant
Keywords: comparative hybridization to access expression profiles between tethered and non tethred cells.

overall_design: Two-condition experiment, stable transfections J21.c3 (non tethered)  vs J21-c3 laci-lap2b (lap2b-lacI tethered) that both possess a Chr11 128mer LacO integrant . Biological replicates = 4 .

first: Duncan

last: Sproul


title: The effects of artificial tethering of chromosomes to the nuclear periphery using LacI/lap2b anchorage constructs, part 1

summary:
Experiment:   analysis of gene expression changes between B49.5 (non tethered)  vs B49.5 74t3 (lap2b-lacI tethered) that both possess a Chr4 128mer LacO integrant
Keywords: comparative hybridization to access expression profiles between tethered and non tethred cells.

overall_design: Two-condition experiment, stable transfections B49.5 (non tethered)  vs B49.5 74t3 (lap2b-lacI tethered) that both possess a Chr4 128mer LacO integrant . Biological replicates = 4 .


title: A. nidulans wild type strain transcriptome analysis upon 100 µM farnesol treatment.

status: Public on Mar 06 2008

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

summary:
Farnesol is a nonsterol isoprenoid produced by dephosphorylation of farnesyl pyrophosphate, a catabolite of the cholesterol biosynthetic pathway. These isoprenoids have been reported to inhibit proliferation and induce apoptosis in neoplastic cell lines as well as to be effective in chemotherapy in several in vivo cancer models. Recently, it was shown that farnesol triggers morphological features characteristic of apoptosis in the filamentous fungus Aspergillus nidulans.
In order to investigate which pathways are involved under Farnesol treatment, we determined the transcriptional profile of A. nidulans wild type strain. Conidia were incubated at 37°C in complete medium for 16 hours and were esposed or not to 100 μM Farnesol for 2 hours. The mycelia were harvested by centrifugation and used for competitive microarray hybridizations. We detected differential regulation of genes involved in a variety of cellular processes whose specific modulation is likely to be implicated with A. nidulans adaptation to farnesol. We observed decreased mRNA abundance of several genes involved in RNA processing and modification, transcription, translation, ribosomal structure and biogenesis, amino acid transport and metabolism. Interestingly, several genes involved in the ergosterol biosynthesis (such as the homologues of erg4/24, 11A, -11B, -13, -25, and –28) have decreased mRNA accumulation and other genes encoding mitochondrial proteins [such as AN9103.3, AN4500.3, and AN5440.3, encoding the Apoptosis Inducing Factor (AIF)-like mitochondrial oxidoreductase, the mitochondrial ATPase inhibitor, and the cytochrome c peroxidase, respectively] have increased mRNA expression when A. nidulans was exposed to farnesol. We also observed as more expressed several genes encoding proteins involved in trehalose metabolism and chaperones.
Keywords: farnesol effect

overall_design:
For the microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks that were incubated in a reciprocal shaker (250 rpm) at 37°C for 12 hours. After this period, the germlings were exposed or not (timepoint 0 min) to 100 µM FOH for 2 hours at 37oC. Germilings were harvested by centrifugation and total RNA was extracted. Hybridization experiments were competitive using probes derived from wild type strain exposed to farnesol for 2 hours using the timepoint zero (control) as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and the flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary file linked below).

middle: H

first: Marcela

last: Savoldi

first: Frederico

last: Soriani

first: Iran

last: Malavazi


title: Self-Self Hybridisation were used to set confidence 99% intervals

summary:
a- Self –Self Hybridisation were used to set confidence 99% interval using RNA from non-tethered cell lines that is both labelled in with cy3 cy5 (theoretically identical cDNA populations) to compared technical errors associated with such experiments
Keywords: comparative hybridization to access expression profiles between Cy3 and Cy5 uniformally labelled template.

overall_design: Two-condition experiment, cells were split in half and labelled with Cy3 or Cy5 respectively,  4 biological replicates were used.


title: Transciptome profiling of small intestinal epithelial crypt and villi in germfree versus conventional neonatal piglets

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory Dr

department: Animal Sciences

institute: UIUC

summary:
To gain insight into host-microbe interactions in a piglet model, a functional genomics approach has been applied to address the working hypothesis that transcriptionally regulated genes associated with promoting epithelial barrier function evolved as a defensive response to the intestinal microbiota. Cesarean-derived germfree (GF) newborn piglets were colonized with adult swine feces, and villus and crypt epithelial cell transcriptomes from colonized and GF neonatal piglets were compared using laser-capture microdissection and high-density porcine oligonucleotide microarray technology. Consistent with our hypothesis, results revealed that resident microbiota induces the expression of genes encoding proteins involved in promoting intestinal epithelial cell turnover and mucus biosynthesis and priming of the immune system. Furthermore, differential expression of genes associated with antigen presentation (SLA-7, B2M, TAP1 and TAPBP) demonstrates that microbiota induced immune responses using a distinct regulatory mechanism common for these genes. Intestinal microbiota stimulated interferon (IFN) receptor-mediated signaling cascade using signal transducer and activator of transcription-1 (STAT1), STAT2 and IFN regulatory factor-7 transcription factors to activate IFN-inducible genes. In addition, excessive inflammatory responses were prevented by activating RNA expression of inhibitory-kappa-B and Toll-interacting protein, along with downregulating the expression of a gene encoding GATA binding protein-1 consistent with the maintenance of intestinal homeostasis. This study supports the concept that the intestinal epithelium has evolved to maintain a physiological state of inflammation with respect to continuous microbial exposure, which serves to maintain tight intestinal barrier but prevent overt inflammatory responses that would compromise barrier function.

Keywords: oligonucleotide array

overall_design: Four piglets from one isolator were maintained germfree and four piglets in other isolator were conventionalized by fecal slurry. Laser capture microdissection was used to recover epithelial villus and crypt cells from frozen ileal sections. Porcine oligonucleotide set represents 13,297 porcine cDNAs and ESTs. A reference design was used in which each of the experimental samples was cohybridized with the reference sample that contained equal amounts of all the RNA samples used in the experiment, which allowed the treatment of fluorescence ratios as measurements of relative expression.

first: Shankar

last: Chowdhury

first: Dale

middle: E

last: King

first: B

last: Willing

first: M

last: Band

first: A

middle: B

last: Lane

first: J

middle: C

last: Marini

first: L

last: Rund

last: Beever

last: Schook

last: Loor

last: Van Kessel


title: HIT: a new versatile protein array platform for multi-analyte phenotyping of surface molecules

status: Public on Mar 03 2008

first: Michael

last: Kattah

summary:
We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT).  This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode.  After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte.  Here we screened 90 antibodies directed against a panel of cell surface markers as well as 4 isotype controls to compare resting human naive CD4+ T cells versus CD4+ T cells activated for 48 h with anti-CD3/anti-CD28 coated beads.
Keywords: protein profiling, response to stimulus

overall_design: Two-condition experiment, activated versus resting cells. Biological replicates: 3 normal human donors, each donor served as an internal control.  One replicate per array.  One of the biological replicates was performed as a dye-swap to monitor dye-bias.  We also performed a self-self comparison between activated cells from two different donors.

first: John

last: Coller

first: Neekaan

last: Oshidary

first: Regina

last: Cheung

first: Paul

middle: J

last: Utz


title: Changes in Prostate Gene Expression in a Cohort Undergoing an Intensive Nutrition and Lifestyle Intervention

status: Public on Mar 01 2008

first: Scot

middle: M

last: Federman

address: 499 Illinois St

department: Biochemistry

summary:
The GEMINAL Study- Gene Expression Modulation by Intervention with Nutrition and Lifestyle

We conducted a pilot study to examine changes in gene expression in men diagnosed with low risk prostate cancer who participated in an intensive nutrition and lifestyle intervention. We profiled gene expression in morphologically normal tissues from prostate biopsies of all 30 participants before and after the intervention.
Keywords: Differential gene expression analysis


title: Divergent genome expression profiles during hepatic ischemia in young and adult mice

city: Cincinnati

first: Bhuvaneswari

last: Sakthivel

state: OH

address: 3333 Burnet Ave

department: Biomedical Informatics

institute: CCHMC

summary:
Experimental Design:
1. The goal of the experiment:
Age-Related Genome Expression Profiles During Hepatic Ischemia
2. Brief description of the experiment:
Hepatic ischemia/reperfusion (I/R) injury is a complication of liver surgery, transplantation and shock and differs with age.  In the present study, we sought to determine if the age-dependent response to I/R injury was related to differential gene expression during the ischemic period.  Total RNA of young (4-5 weeks) and adult (12-14 months) mice undergoing sham surgery or partial hepatic ischemia for 30, 60, or 90 minutes was analyzed by Affymetrix microarray.  Gene expression was filtered based on a change in expression of 1.5-fold relative to respective controls and then analyzed by ANOVA.  Significant differences in gene expression were observed between age groups.  In young mice, 169 genes were down-regulated, whereas adult mice had 1167 genes down-regulated.  Of these, only 28 genes were down-regulated in both young and adult mice.  Far fewer genes had increased expression during ischemia.  Sixty genes in young mice and 51 genes in adult mice were up-regulated.  Of those, none were up-regulated in both young and adult mice.  There were no distinct functional patterns of gene regulation in either age group.  The data demonstrate significant and widespread changes in hepatic gene expression during the ischemic period that may be important to the age-dependent response to I/R injury.
Keywords: treated vs non treated

overall_design:
2 age groups of 12 young and 12 adult mice that underwent either 30, 60 or 90 minutes of partial ischemia (n=3) or sham operation (n=3)
We used microarray to uncover the genomic response during different time points of ischemia

first: Nadine

last: Huber

first: Thorsten

last: Eismann

first: Thomas

last: Shin

first: Satoshi

last: Kuboki

first: Elizabeth

last: Galloway

first: Rebecca

last: Schuster

first: Hector

last: Wong

first: Alex

last: Lentsch


title: Expression profiling basal and luminal prostate epithelial cells

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
Immuno-stained (keratin 14+ basal marker) frozen prostate sections were subjected to laser-guided microdissection to isolate basal and luminal epithelial prostate cells for expression profiling. RNA was amplified using the AmpTec TRinucleotide kit (AmpTec GmBH). Expression profiling performed using the Invitrogen post-labelling kit and the CRUK whole genome array (WGA) gene set.
Keywords: repeat sample

overall_design: 10 samples  - All samples compared to universal reference RNA


title: Bovine trophoblasts: control vs. infected with Brucella abortus

city: Belo Horizonte

first: Renato

middle: L.

last: Santos

state: MG

address: Av. Antonio Carlos, 6627

department: Dept. Clinica e Cirurgia Vet.

institute: Escola de Vetreinaria da Universidade Federal de Minas Gerais

summary:
Brucellosis is still a widespread zoonotic disease. Very little is known about the interaction between B. abortus and trophoblastic cells, which is essential for better understanding the pathogenesis of the Brucella-induced placentitis and abortion, a key event for transmission of the disease. The goal of this study was to evaluate the profile of gene expression by bovine trophoblastic cells during infection with B abortus. Explants of chorioallantoic membranes were inoculated with B. abortus strain 2308. Microarray analysis was performed at 4 h after infection, and expression of cytokines and chemokines by trophoblastic cells was assessed by real time RT-PCR at 6 and 12 h after inoculation. In addition, cytokine and chemokine expression was evaluated in placentomes from experimentally infected cows. Expression of pro-inflammatory genes by trophoblastic cells was suppressed at 4 h after inoculation, whereas a significant up-regulation of CXC chemokines, namely CXCL6 (GCP-2) and CXCL8 (IL-8), was observed at 12, but not at 6 h after inoculation. Placentomes of experimentally infected cows had a similar profile of chemokine expression, with upregulation of CXCL6 and CXCL8. Our data indicate that B. abortus modulates the innate immune response by trophoblastic cells, suppressing expression of pro-inflammatory mediators during the early stages of infection that is followed by a delayed and mild expression of pro-inflammatory chemokines, which is similar to the profile of chemokine expression in the placentomes of experimentally infected cows. This trophoblastic response is likely to contribute to the pathogenesis of B. abortus-induced placentitis.
Keywords: trophoblast response to Brucella

overall_design: Total RNA used for microarray analysis was obtained from 6 placentas with 12 infected and 12 control explants from each placenta. At 4 h after inoculation, total RNA was isolated from the trophoblastic surface of the explants. Three RNA pools from two placentas each were generated prior to cDNA synthesis.

first: Alcina

middle: V

last: CarvalhoNeta

first: Ana

last: Steynen

first: Tatiane

middle: A

last: Paixão

first: Karina

middle: L

last: Miranda

first: Fabiana

last: Silva

first: Christelle

last: Roux

first: Renee

last: Tsolis

first: Robin

last: Everts

first: Harris

last: Lewin

first: L

last: Adams

last: Carvalho

first: Andrey

middle: P

last: Lage


title: Age-dependent gene expression profiles after hepatic ischemia/reperfusion in mice

first: Bhuvaneswari

last: Sakthivel

summary:
Experimental Design:
1. The goal of the experiment:
Age-Dependent Gene Expression Profiles After Hepatic Ischemia/Reperfusion: Implications for the AP-1 and Ubiquitin-Proteosome Pathways
2. Brief description of the experiment:
Hepatic ischemia/reperfusion (I/R) injury is a complication of liver surgery, transplantation and shock.  Our previous studies have suggested there is an age-dependent response to I/R.  In the present study, we examined global gene expression after liver I/R in young (4-5 weeks) and adult (12-14 months) mice using Affymetrix microarray.  Gene expression was filtered based on a change in expression of 1.5-fold relative to respective controls and then analyzed by ANOVA.  Seventy-two genes in young mice and 56 genes in adult mice had significantly increased expression.  Of these, only 18 were up-regulated in both age groups.  In young mice, 289 genes were down-regulated whereas in adult mice, 874 genes were decreased.  Of these genes, 175 genes were decreased in both groups.  Pathway and network analyses of up- and down-regulated gene lists revealed a number of notable differences between young and adult mice.  Of these, we found that genes related to the activating protein-1 (AP-1) pathway were upregulated preferentially in young mice.  This corresponded with an increase in AP-1 activation in young versus adult mice.  Finally, we found that genes related to the ubiquitin-proteasome pathway were selectively down-regulated in adult mice.  This was accompanied by reduced degradation of the inhibitory protein, I?B?, in adult mice.  The data demonstrate specific, pathway- and network-related differences in gene expression profiles between young and adult mice in the response to I/R.  More specifically, we have identified two pathways that may contribute to the superior response to I/R in young mice which represent potential therapeutic targets.
Keywords: treated vs non treated

overall_design:
2 age groups of 6 young and 6 adult mice that underwent either  90 minutes of partial ischemia followed by 1 hour of reperfusion (n=3) or sham operation (n=3)
We used microarray to uncover the genomic response after ischemia reperfusion in 2 different age groups

first: Nadine

last: Huber

first: Thorsten

last: Eismann

first: Satoshi

last: Kuboki

first: Thomas

last: Shin

first: Elizabeth

last: Galloway

last: Schuster


title: CD133+ and CD133- expression profiles of benign and HRPC cells

first: Ian

last: Giddings

summary:
Epithelial cell cultures derived from benign and HRPC tissue biopsies were expanded in culture for 2-3 weeks. CD133+ and CD133- cells were isolated using the miltenyi magnetic bead system after adherence to collagen. CD133+ and CD133- RNA was isolated and amplified using the RiboAmp HS kit and expression profiling performed using the CRUK WGA gene set.
Keywords: Tumour vs normal comparison

overall_design: 28 samples  - All samples compared to universal reference RNA


title: Benign Uncultured CD133+ vs CD133-

summary:
6 benign TURP samples taken directly from patients were subjected to collagen digestion overnight. Epithelial cells isolated were adhered to collagen for 15 minutes. Adherent cells were passed through a magnetic bead column and cells positive for CD133 antibody were double selected. RNA was extracted from CD133+ and CD133- cells from each patient and amplified using the RiboAmp HS RNA amplification system. CD133+ (Cy5) and CD133- (Cy5) cDNA was hybridised to 30K cDNA array (CRUK facility) using the Invitrogen post labelling system. In each case that RNA was co-hybridised to a human pooled universal reference cDNA (Cy3).
Keywords: repeat sample

overall_design: 12 samples  - All samples compared to universal reference RNA


title: Gene expression in Maize root region 2 at low water potential-developmental control

city: Columbia

first: William

middle: G.

last: Spollen

state: MO

address: 113 Bond Life Sciences Center

department: Informatics Research Core Facility

institute: University of Missouri-Columbia

summary:
Previous work showed that the maize primary root adapts to low water potential (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low water potential. To identify mechanisms that determine these responses to low water potential, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation. Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit. The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.
Keywords: water stress response, root growth

overall_design:
	 Three pair-wise comparisons were made of transcripts from water-stressed and well-watered tissues in the different root tip regions. In the first comparison (C1), transcripts from region 1 of water-stressed seedlings were compared with those from region 1 of well-watered seedlings. The second comparison (C2) was made between transcripts from region 2 of the two treatments. We expected a larger number of genes to be differentially expressed in region 2 because its elongation rate decreased greatly under water-stressed compared with well-watered conditions. To prioritize the differentially expressed genes revealed in this comparison, a distinction was made between those genes that are associated with growth inhibition in region 2 specifically as a response to water stress, and those genes that are involved in root cell maturation whether under stress or control conditions. A hypothetical example of the former might be genes involved in auxin response since water stress can increase maize root auxin content [8] and application of exogenous auxin can shorten the root growth zone [9]. An example of the latter might involve genes for secondary wall synthesis, e.g., [10]. To experimentally make this distinction a third pair-wise comparison (C2/3) was included to compare expression of genes between water-stressed region 2 and well-watered region 3 as these are both regions of cell maturation. Genes differentially expressed in both C2 and C2/3 are more likely to cause growth inhibition at low water potential and are not likely to be part of the maturation program itself, whereas genes differentially expressed only in C2 are more likely related to maturation.
Four biological replicates were included each with dye-swap. The maize oligonucleotide array comes in two slides, A and B. Thus for each of the three comparisons made there were 16 slides (4 biological reps, 2 for dye-swap, 2 parts to an array).

middle: G

first: Wenjing

last: Tao

first: Babu

last: Valliyodan

first: Kegui

last: Chen

first: Lindsey

last: Hejlek

first: Jong-Joo

last: Kim

first: Mary

last: LeNoble

first: Jinming

last: Zhu

first: Hans

last: Bohnert

first: David

last: Henderson

first: Daniel

last: Schachtman

first: Georgia

last: Davis

first: Gordon

middle: K

last: Springer

first: Robert

last: Sharp

first: Henry

middle: T

last: Nguyen


title: Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells

status: Public on Mar 13 2008

city: Bethesda

first: Thomas

last: Wadlmann

state: MD

address: 10 Center Drive

department: Metabolism Branch

institute: NCI/NIH

summary:
The mechanism whereby IL-9 stimulated monocytes, promote proliferation of co-cultured ATL cells remains undefined. To obtain preliminary clues concerning this contribution, transcription profiles were obtained between monocytes derived from ATL patients and those derived from healthy donors as assessed by cDNA microarray.
Keywords: disease state design

overall_design: The experiment included 3 biological replicate ATL samples and 3 biological replicate normal samples. The Stratagene Universal Human RNA Reference sample was used as a control.


title: Gene expression-based, HOXC6 WT versus KO mouse prostates

city: Atlanta

first: Colleen

middle: D

last: McCabe

address: 615 Michael St

institute: Emory University

summary:
This study was used to identify biologically relevant targets of HOXC6 in normal prostate.
Keywords: gene expression profiling

overall_design: Three HOXC6 knockout and three HOXC6 WT mouse prostates were collected at 32 weeks of age and analyzed for gene expression on Illumina mouse-v6 platform

first: Carlos

last: Moreno


title: Effect of a naturally eQTN on the yeast transcriptome

city: Cambridge

first: Christian

last: Landry

state: MA

address: 16 Divinity avenue

department: OEB

institute: Harvard University

summary:
We identified a mutation that is a frameshift mutation in a mononucleotide run of eight consecutive T's in the coding region of the gene SSY1, which encodes a key component of a plasma-membrane sensor of extracellular amino acids.We introduced it into the S288c background and examined the effect on gene expression.
Keywords: Total gene expression analysis

overall_design: S288C wt, S288C ssy1-t9 and S288C ssy1-ko were compared

first: Kyle

last: Brown


title: Effects of nitric oxide on Salmonella adapted at pH 4.4

city: Aurora

first: Travis

last: Bourret

state: CO

institute: University of Colorado Health Sciences Center

summary:
Reactive nitrogen species (RNS) derived from dietary and salivary inorganic nitrates (NO3-) foment innate host defenses associated with the acidity of the stomach.  The mechanisms by which these reactive species exert antibiotic activity in the gastric lumen are, however, poorly understood.  To identify targets of RNS, the genetically tractable acid tolerance response (ATR) that enables enteropathogens to survive the harsh acidity of the stomach was screened for signaling pathways responsive to RNS. The nitric oxide (NO) donor spermine NONOate derepressed the Fur regulon that controls secondary lines of resistance against organic acids.  Despite inducing a Fur-mediated adaptive response, acidified RNS largely boosted gastric host defenses as demonstrated by the fact that Salmonella bacteria exposed to spermine NONOate during mildly acidic conditions were not only shed in low amounts in feces, but also exhibited ameliorated oral virulence.  NO prevented Salmonella from mounting a de novo ATR, but was unable to suppress an already functional protective response, indicating that RNS target regulatory cascades but not the effectors that defend against the rigors of gastric acidity.  Transcriptional and translational analyses revealed that the PhoPQ signaling cascade is a critical ATR target of NO in rapidly growing Salmonella.  Inhibition of PhoPQ signaling appears to contribute to most of the NO-mediated abrogation of the ATR in log phase bacteria, because the augmented acid sensitivity of phoQ-deficient Salmonella was not further enhanced after RNS treatment. Since PhoPQ-regulated acid resistance is widespread in enteric pathogens, the RNS-mediated inhibition of the Salmonella ATR described herein may represent a common component of the innate host defenses of the gastric lumen.
Keywords: acid tolerance response, nitric oxide

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Microarray analyses were conducted comparing transcript levels of log-phase Salmonella cultured in minimal E salts + 0.4% glucose, pH 4.4 in the presence or absence of 250 µM spermine NONOate for 1 hour.  Microarrays were performed in triplicate under identical conditions (3 biological replicates).

first: Steffen

last: Porwollik

first: Michael

last: McClelland

first: Rui

last: Zhao

first: Todd

last: Greco

first: Harry

last: Ischiropoulos

first: Andres

last: Vazquez-Torres


title: Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HOXC6-HA/YFP

summary:
The transcription factor HOXC6 is upregulated in human prostate cancer. SiRNA knockdown of HOXC6 induces apoptosis in LNCaP cells while upregulation rescued LNCaP cells from siRNA-induced apoptosis.
We used chromatin immunoprecipitaiton followed by microarray to identify the gene promoters that are bound by HOXC6 in LNCaP cells.
Keywords: Stable expression and chromatin immunoprecipitation

overall_design: LNCaP cells were stabely infected with a lentivirus containing HOXC6-HA-IRES-YFP or IRES-YFP alone.  Cells were sorted for YFP expression and expanded in tissue culture.

first: Moreno

last: Carlos


title: Gene expression in Maize root region 2 at low water potential

first: William

last: Spollen

overall_design:
	Three pair-wise comparisons were made of transcripts from water-stressed and well-watered tissues in the different root tip regions. In the first comparison (C1), transcripts from region 1 of water-stressed seedlings were compared with those from region 1 of well-watered seedlings. The second comparison (C2) was made between transcripts from region 2 of the two treatments. We expected a larger number of genes to be differentially expressed in region 2 because its elongation rate decreased greatly under water-stressed compared with well-watered conditions. To prioritize the differentially expressed genes revealed in this comparison, a distinction was made between those genes that are associated with growth inhibition in region 2 specifically as a response to water stress, and those genes that are involved in root cell maturation whether under stress or control conditions. A hypothetical example of the former might be genes involved in auxin response since water stress can increase maize root auxin content [8] and application of exogenous auxin can shorten the root growth zone [9]. An example of the latter might involve genes for secondary wall synthesis, e.g., [10]. To experimentally make this distinction a third pair-wise comparison (C2/3) was included to compare expression of genes between water-stressed region 2 and well-watered region 3 as these are both regions of cell maturation. Genes differentially expressed in both C2 and C2/3 are more likely to cause growth inhibition at low water potential and are not likely to be part of the maturation program itself, whereas genes differentially expressed only in C2 are more likely related to maturation.
Four biological replicates were included each with dye-swap. The maize oligonucleotide array comes in two slides, A and B. Thus for each of the three comparisons made there were 16 slides (4 biological reps, 2 for dye-swap, 2 parts to an array).

first: Wenjing

last: Tao

first: Babu

last: Valliyodan

first: Kegui

last: Chen

first: Lindsey

last: Hejlek

first: Jong-Joo

last: Kim

first: Mary

last: LeNoble

first: Jinming

last: Zhu

first: Hans

last: Bohnert

first: David

last: Henderson

first: Daniel

last: Schachtman

first: Georgia

last: Davis


title: Global Transcriptional Analysis of Mycoplasma hyopneumoniae Following Exposure to Norepinephrine

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary:
The goal of this study is to gain a better understanding of the transcriptional responses of M. hyopneumoniae under norepinephrine stress. Six independent RNA samples from norepinephrine-exposed cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other three arrays to overcome dye bias.
Keywords: stress response

first: Michael

last: Oneal

first: Erin

middle: R

last: Schafer

first: Melissa

last: Madsen


title: Human skeletal muscle differentiation time course

status: Public on Mar 02 2008

city: Boston

first: Jason

middle: Blair

last: Warner

address: 12 Carriage DrHarvard Medical School New Research Building, Room 466D

institute: Brigham & Women's Hospital / Harvard Medical School

summary:
We have developed an algorithm (“Lever”) that systematically maps metazoan DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our “PhylCRM” algorithm, in the noncoding sequences surrounding genes in a collection of gene sets. When these gene sets correspond to Gene Ontology (GO) categories, the results of Lever analysis allow the unbiased assignment of functional annotations to the regulatory motifs and also to the candidate CRMs that comprise the genomic motif occurrences. We demonstrate these methods using human myogenic differentiation as a model system, for which we statistically assessed greater than 25,000 pairings of gene sets and motifs / motif combinations. These results allowed us to assign functional annotations to candidate regulatory motifs predicted previously, and to identify gene sets that are likely to be co-regulated via shared regulatory motifs. Lever allows moving beyond the identification of putative regulatory motifs in mammalian genomes, towards understanding their biological roles. This approach is general and can be applied readily to any cell type, gene expression pattern, or organism of interest.
Keywords: expression profiling, time course

overall_design: Primary human skeletal muscle cells were grown in proliferating medium (DMEM + 10% FCS) for 48 hours until about 80% confluence. Cells were then switched to differentiation medium (DMEM/F12 + 2% horse serum) for 48 hours. Total RNA was extracted from cells at -48, -24, 0, +12, +24, and +48 hours relative to induction of differentiation, and labeled with either Cy5 or Cy3. Universal total RNA was also labeled  with either Cy3 or Cy5 and was hybridized to the array with the experimental sample. Dye-swaps were performed in addition to duplicate hybridizations for a total of 4 hybridizations per timepoint.

first: Anthony

last: Philippakis

first: Savina

last: Jaeger

first: Fangxue

middle: S

last: He

first: Jolinta

last: Lin

first: Martha

last: Bulyk


title: Diamond Back Moth treatment

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

summary:
Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown at 20˚C constant temperature, 8 hr/16 hr Light/Dark photoperiod at 50-60% ambient humidity, for 8 to 9 weeks.  Short day conditions prevented the onset of flowering and the plants were thus maintained in growth stage 1 (leaf production) with 13 to 15 rosette leaves larger than 1mm (stage 1.13 to 1.14). Diamondback moth (DBM, Plutella xylostella) larvae were maintained on cabbage (Brassica oleracea) plants in a climate-controlled room at 25ºC, 12 hr photoperiod with 50%-60% relative humidity.
Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod).  For insect treatment, seven Diamondback moth (DBM, Plutella xylostella) larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately.  All rosette leaves were harvested at 1h, 4h, 12h, and 24h after onset of continuous herbivory and flash frozen in liquid nitrogen. Control plants were maintained under the same conditions and harvested in parallel.
Keywords: time course, stress response, herbivory response

overall_design:
For each time point (1h, 4h, 12h, and 24h) two biological replicates (DBM treatment) were performed. Control plants were harvested in parallel. Total RNA from each sample was used for two labelling reactions using dye-flips (Cy5 or Cy3) and labelled cDNA from treatment and control plants were co-hybridized. Thus, for each time-point four replicates were analyzed each comparing treatment with the corresponding control (rep1 and rep2 are dye-flips of biological replicate 1, and rep3 and rep4 are dye-flips of biological replicate 2).
For background correction, we defined the mean of the lowest 10% of spot intensities from a particular subgrid as the background for that subgrid. This mean was subtracted from each spot in the subgrid. Signal intensities that did not exceed the background plus 3 standard deviations thereof were defined as not detectable and were excluded from further analyses. We normalized using loess curves thus generating log2 transformed expression ratios comparing DBM treatment with control. These ratios are given in the VALUE columns of each array.

first: Sunita

last: Chowrira

first: Nathalie

last: Mattheus

first: Dana

last: Aeschliman

first: Gen-Ichiru

last: Arimura

first: Joerg

last: Bohlmann


title: Gene expression in Maize root region 1 at low water potential

first: William

last: Spollen

summary:
Previous work showed that the maize primary root adapts to low water potential (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low water potential.  To identify mechanisms that determine these responses to low water potential, transcript expression was profiled in these regions of water-stressed and well-watered roots.  In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation.  Responses of gene expression to water stress in regions 1 and 2 were largely distinct.  The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2.  Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit.  A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit.  The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.
Keywords: water stress response, root growth

overall_design:
Three pair-wise comparisons were made of transcripts from water-stressed and well-watered tissues in the different root tip regions.  In the first comparison (C1), transcripts from region 1 of water-stressed seedlings were compared with those from region 1 of well-watered seedlings.  The second comparison (C2) was made between transcripts from region 2 of the two treatments.  We expected a larger number of genes to be differentially expressed in region 2 because its elongation rate decreased greatly under water-stressed compared with well-watered conditions.  To prioritize the differentially expressed genes revealed in this comparison, a distinction was made between those genes that are associated with growth inhibition in region 2 specifically as a response to water stress, and those genes that are involved in root cell maturation whether under stress or control conditions.  A hypothetical example of the former might be genes involved in auxin response since water stress can increase maize root auxin content [8] and application of exogenous auxin can shorten the root growth zone [9].  An example of the latter might involve genes for secondary wall synthesis, e.g., [10].  To experimentally make this distinction a third pair-wise comparison (C2/3) was included to compare expression of genes between water-stressed region 2 and well-watered region 3 as these are both regions of cell maturation.  Genes differentially expressed in both C2 and C2/3 are more likely to cause growth inhibition at low water potential and are not likely to be part of the maturation program itself, whereas genes differentially expressed only in C2 are more likely related to maturation.
Four biological replicates were included each with dye-swap. The maize oligonucleotide array comes in two slides, A and B.  Thus for each of the three comparisons made there were 16 slides (4 biological reps, 2 for dye-swap, 2 parts to an array).

first: Wenjing

last: Tao

first: Babu

last: Valliyodan

first: Kegui

last: Chen

first: Lindsey

last: Hejlek

first: Jong-Joo

last: Kim

first: Mary

middle: E

last: LeNoble

first: Jinming

last: Zhu

first: Hans

last: Bohnert

first: David

last: Henderson

first: Daniel

last: Schachtman

first: Georgia

last: Davis

first: Gordon

last: Springer

first: Robert

last: Sharp

first: Henry

last: Nguyen


title: Bacillus subtilis tagD mutant

city: Martinsried

first: Christoph

last: Schaab

address: Fraunhoferstrasse 20

institute: GPC Biotech AG

summary:
The bacterial cell wall has been a celebrated target for antibiotics and holds real promise as a target for the discovery of new chemical matter to surmount pervasive multi-drug resistance among pathogenic bacteria.  While the walls of Gram-negative bacteria are composed primarily of peptidoglycan, those of Gram-positives are more substantial and contain, in addition, large amounts of the polymer teichoic acid, covalently attached to peptidoglycan.  Wall teichoic acids are a diverse group of phosphate-rich, extracellular polysaccharides that have been largely regarded as ancillary cell surface components.  Recently, wall teichoic acid was shown to be essential to the proper rod-shaped cell morphology of the prototype Gram-positive bacterium Bacillus subtilis and an important virulence factor for the human pathogen Staphylococcus aureus.  Thus wall teichoic acid synthesis is an intriguing target for the development of new cell wall-active antibiotics.  Nevertheless, recent studies have shown that the dispensability of genes encoding teichoic acid biosynthetic enzymes in both B. subtilis and S. aureus is paradoxical and complex.  Here, we report here on the discovery of a promoter (PywaC), which is sensitive to lesions in teichoic acid synthesis.  Using this promoter we developed a luminescent, cell-based, reporter system to take a chemical-genetic approach to understanding the complexity of wall teichoic acid biogenesis using a large collection of antibiotics of well characterized biological activity.  Our results reveal surprising interactions among undecaprenol, peptidoglycan and teichoic acid biosynthesis that help explain the complexity of teichoic acid gene dispensability.  Furthermore, the new reporter assay represents an exciting avenue for the discovery of novel antibacterial molecules that impinge broadly on Gram-positive bacterial cell wall biogenesis.
Keywords: comparison between depleted and repleted tagD mutant

overall_design:
A conditional xylose-inducible tagD mutant of B. subtilis was generated. Cells were grown in the presence and absence of xylose. Cells grown in the absence of xylose stopped growing after tagD depletion.
Two time points were analysed. Time point 1: early depletion. Time point 2: late depletion, i.e. close to death.

first: Kathryn

last: Miller

first: Amit

last: Bhavsar

first: Bernd

last: Hutter

first: Eric

last: Brown


title: Gene expression oocyte quality in the hen

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. The study was performed using two complementary approaches: a descriptive study of standard laying hens and then a differential study performed with hens from experimental lines expressing broad variations of achieved fertility (approximately 20 per cent). A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance.
Keywords: oocyte competence, fertility

overall_design:
All the samples were bissected from the F1 oocyte stage , and DPF+ and DPF- samples were compared in order to find differentially expressed genes that could explain the difference in fertility occuring between the two divergently selected lines. HG+ and HG- samples were compared in order to find differentially expressed genes that could explain the difference in fertility occuring between a single line. Indeed we hypothesize that mechanisms and genes related to fertility between 2 lines or in a single one might be different.
This study had 8 samples (a biological replicate of each sample) :
DPF+ F1 1 and DPF+ F1 2
DPF- F1 1 and DPF- F1 2
HG+ F1 1 and HG+ F1 2
HG- F1 1 and HG F1 2

first: Sandrine

last: Balzergue

first: Florence

last: Batellier

first: Marie-Laure

last: Martin-Magniette

first: Sebastien

last: Elis


title: Ribosomal protein S3: a functional component of NF-kB p65 binding complexes

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary:
To explore the effects on the NF-kB transcriptome after knockdown of RPS3 in stimulated T cells, we performed microarray assays comparing RPS3-silenced versus NS-treated samples on the same chip. p65-silenced versus NS-treated samples were used as a control.
Keywords: time series design

overall_design: Jurkat cells transfected with control siRNA versus RPS3 or p65-siRNA were stimuated with TCR for 1, 3, or 6 hours for a total of 6 arrays.


title: Identification of c-myc target genes by siRNA

summary:
To identify c-myc target genes by siRNA transfection in a lymphoma cell line.
Keywords: time series design

overall_design: OCI-Ly10 cells were transfected with c-myc siRNA pool versus control siRNA or buffer for a total of 4 microarrays.


title: Gene expression analysis of TNF-alpha stimulated CaCo-2 cells

status: Public on Feb 29 2008

city: Rostock

first: Hermann

last: Schulze

address: Ernst-Heydemann-Str. 6

institute: Universitätsklinik Rostock

summary:
The series was designed to obtain gene expression patterns of TNF-alpha stimulated CaCo-2 cells.
Keywords: TNF-alpha stimulation

overall_design: This series represents a group of 18 samples in 2 groups: 10 samples derived from not stimulated CaCo-2 cells, 8 samples from CaCo-2 cells stimulated with TNF-alpha in final concentration of 5 ng/ml for 60 min.

last: Häsler

first: Nancy

last: Mah

first: Tim

last: Lu

first: Susanna

last: Nikolaus

first: Christine

last: Costello

first: Stefan

last: Schreiber


title: Defining the molecular basis of dendritic cell mediated tolerance

status: Public on Feb 28 2008

city: Oxford

first: Kathleen

last: Nolan

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: Oxford University

summary:
 Using a TCR transgenic transplantation model a series of differently modulated bmDC (IL10, TGFb and VD3 treated, +/-LPS) were established that could mediate tolerance following adaptive transfer.  These modified cells, in contrast to untreated 'immature' bmDC retained their capacity to tolerise following exposure to LPS.  The unmodified, non-tolerogenic, LPS-treated cells provided a comparator population to facilitate investigation into molecular expression patterns that correlate with functional phenotype.
Keywords: pattern searching, immune tolerance, dendritic cell

overall_design: To investigate transcriptional-based explainations for the shared tolerancing-inducing phenotype of bmDC cultured under different growth contexts, pattern searching was performed across 29 SAGE libraries, using bmDC+LPS (one long and one short SAGE library) as a non-tolerant comparator (GSM580, GSM767, GSM1681-2, GSM3677-79, GSM3681-6, GSM3824-29, GSM3832-7, GSM132450 and GSM160043, two independant LPS+ comparator libraries were included while all the other libraries were single biological/technical replicates) . Pattern searching of the SAGE data was combined with equivalent analysis of single channel micro-array data (E-MEXP-845) to select genes to be included on Taqman low density microfluidic card. QPCR was used to verify expression patterns using three biological replicates of the complete cohort of tolerogenic and the non-tolerogenic comparator DC populations.

middle: F

first: Alison

last: Paterson

first: Claire

last: Farquhar

first: Hugo

last: Garcia Rueda

first: Stephen

last: Yates

first: Nigel

middle: J

last: Saunders

first: Paul

last: Fairchild

last: Cobbold

first: Herman

last: Waldmann


title: Salt regulated gene expression in Helicobacter pylori

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

institute: Vanderbilt University

summary:
In this study, we tested the hypothesis that high salt concentrations might alter gene expression in H. pylori.  Analysis here provides into the role that salt may play in H. pylori pathogenesis. .
Keywords: comparison of salt reponsive gene expression, dose response

overall_design: H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%)  The bacterial cells were then grown for 10 h, in fresh brucella broth at either 0.25% or 1.5% salt, harvested by centrifugation, and frozen at -80oC. RNA isolated was reverse transcribed and used to probe H. pylori Panorama arrays

last: Cover

first: Victor

last: Torres


title: CD14: A co-receptor for damage-associated molecular pattern

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

country: South Korea

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

summary:
The gene expression profiles were compared between C57BL/6 WT and CD14 knockout mice using microarray analysis after stimulating peritoneal cells with necrotic fibroblasts.
Keywords: stimulus or stress design

overall_design: Two samples were from peritoneal macrophages isolated from C57BL/6 WT mice, one stimulated with necrotic fibroblasts and one untreated control. Two samples were from peritoneal macrophages isolated from C57BL/6 CD14 knockout mice, one stimulated with necrotic fibroblasts and one untreated control. Technical replicates were performed.


title: Gene expression analysis of TNF-alpha stimulated THP-1 cells

first: Hermann

last: Schulze

summary:
The series was designed to obtain gene expression patterns of TNF-alpha stimulated THP-1 cells.
Keywords: TNF-alpha stimulation

overall_design: This series represents a group of 15 samples in two groups: 7 samples derived from not stimulated THP-1 cells, 8 from THP-1 cells stimulated with TNF-alpha in a final concentration of 5 ng/ml for 60 min.

first: Robert

last: Häsler

last: Mah

last: Lu


title: RNA from 3 d and 2 d old embryos of mibta52b, mibm132 and mibtfi91, and RNA from 3 d, 2d and 1 d old embryos of mibta52b

city: Singapore

first: Govindarajan

last: Kunde Ramamoorthy

address: 60, Biopolis Street, Genome

department: Research Computing Group

country: Singapore

institute: Genome Institute of Singapore

summary:
The Notch signaling is an evolutionarily conserved signal transduction cascade that plays essential roles in a variety of developmental processes. In this study, we examined the mib mutants for defects in pancreas development using in situ hybridization and GFP expression analysis of pancreas-specific GFP lines, and carried out the global gene expression profile analysis of three different mib mutantalleles. Global expression profile analysis showed that there is a significant difference in gene expression profile of wild type and three mib mutant alleles. There are 91 differentially expressed genes that are common to all three mib alleles. Through detailed analysis of microarray data we have identified several previously characterized genes and some putative Notch-responsive genes involved in pancreas development, and validated theirexpression profile using real-time PCR and in situ hybridization. We propose that this study provides a useful resource of global gene expressionprofile in mib mutants, which will be helpful in identifying the function of novel genes involved in Notch signaling and Notch-responsive genesinvolved in a variety of developmental processes.
Keywords: comparison of global gene expression in mib mutant and wild type embryos

overall_design: All samples were analysed on Zebrafish microarray chips generated at the Genome Institute of Singapore

first: Ashok

last: Hegde

first: Kenny

middle: Q

last: Tay

first: Nick-Chuanxin

last: Qiu

first: Kunde

last: Govindarajan

first: Joshy

last: George

first: Steven

middle: H

last: Ho

first: Zhiyuan

last: Gong

first: Sinnakaruppan

last: Mathavan

first: Yun-Jin

last: Jiang


title: Identification of genes involved in the proliferative response to estrogen (E2)

first: Caleb

last: Kallen

address: 1639 Pierce Drive, WMB 4211

department: Gynecology and Obstetrics

institute: Emory University School of Medicine

summary:
The Human Genome Project promised to promote large-scale functional analyses necessary for the diagnosis and treatment of complex diseases. Here we demonstrate an integrated approach to the study of a transcriptional regulatory cascade involved in the progression of breast cancer and we identify a protein associated with disease progression. Using chromatin immunoprecipitation and genome tiling arrays, whole genome mapping of transcription factor binding sites was combined with gene expression profiling to identify genes involved in the proliferative response to estrogen (E2). Using RNA interference, selected ERa and c-Myc gene targets were knocked down to identify mediators of E2-stimulated cell proliferation. Tissue microarray screening revealed that high expression of an epigenetic factor, the estrogen-inducible histone variant H2A.Z, is significantly associated with lymph node metastasis and decreased breast cancer survival. Detection of H2A.Z levels independently increased the prognostic power of biomarkers currently in clinical use. This integrated approach has accelerated the identification of a molecule linked to breast cancer progression, has implications for diagnostic and therapeutic interventions, and can be applied to a wide range of cancers.
Keywords: treated vs. untreated

overall_design: MCF7 cells treated with E2 (10nM) or Ctrl (vehicle) for 4, 12 or 24 hours. Each hormone treatment time was performed at least three times and hybridizations included dye swaps.


title: Gene expression in normal tissues detected by newly developed chicken 44K microarray

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary:
Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7.  Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10).
Keywords: characteristics of newly developed microarray using different normal tissue

overall_design: Loop design was carried on for all of tissue samples from the six chickens. Samples of four tissues from a chicken were used in each loop. The order of the tissues in each loop was changed so that all pairs of tissues were combined on an array with an equal number of times. Dye swap was used so that each tissue was measured an equal number of times with each dye. Data from 12 measurements for each tissue were collected, in total, 48 measurements from 24 arrays.

first: Xianyao

last: Li

first: Hsini

last: Chiang

first: James

last: Zhu


city: East Lansing

first: Mark

last: Wong

state: MI

address: 3 Natural Resources

department: Crops and Soil Sciences

summary:
Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family.
Keywords: control study: target detection and specificity

sample_organism:
Human adenovirus 41
Human adenovirus 40

overall_design: 2 lab strains of adenovirus (type 40 and 41) were extracted directly from ATCC samples. Viral DNA was was extracted and labeled with Cy3 and Cy5 dyes for Adenovirus type 40 and 41 respectively.

first: Joan

middle: B

last: Rose


title: Salmon Macrophage early response to Aeromonas salmonicida

status: Public on Feb 27 2008

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

institute: National Research Council

summary:
Aeromonas salmonicida is a fish pathogen that causes furunculosis. Virulent strains of this bacterium are able to infect salmonid macrophages and survive within them, although mechanisms favouring intracellular survival are not completely understood. It is known that A. salmonicida cultured in vivo in the peritoneal cavity of the host undergoes changes in gene expression and surface architecture compared with cultures grown in vitro in broth. Therefore, in this study, the macrophage responses to A. salmonicida grown in vivo and in vitro were compared. Enriched macrophages isolated from head kidney of Atlantic salmon (Salmo salar) were infected in vitro in 96-well microtitre dishes and changes in gene expression during the infection process were monitored using a custom Atlantic salmon cDNA microarray. A. salmonicida cultures grown in tryptic soy broth and in peritoneal implants were used to infect the macrophages. The macrophages were harvested at 0.5, 1.0 and 2.0 h after addition of the bacteria to the medium. Significant changes in gene expression were evident by microarray analysis at 2.0 h post-infection in macrophages infected with broth-grown and implant-grown bacteria; however, qPCR analysis revealed earlier up-regulation of JunB and TNF-alpha in macrophages exposed to the implant-grown bacteria. Up-regulation of those genes and others is consistent with the effects of extracellular products of aeromonad bacteria on macrophages and also suggests initiation of the innate immune response.
Keywords: time course

overall_design: Enriched macrophages from 24 responder fish that showed positive respiratory burst in response to phorbol myristate acetate were plated in individual wells of 96-well flat-bottom polystyrene tissue culture plates. A. salmonicida were added to the macrophages, and incubated for 0.5, 1.0 or 2.0 h. Control wells received 10 ul of HBSS. Three replicate infections were performed for each type of bacteria. Hybridizations were carried out in duplicate, reversing the fluors for each sample on the second chip.

first: Katherine

middle: V

last: Ewart

first: Jeffrey

middle: W

last: Gallant

first: Krista

last: Melville

first: Susan

last: Douglas


title: CmeR functions as global regulator in Campylobacter jejuni

first: Qijing

last: Zhang

address: 1116 Veterinary Medicine Complex

department: Veterinary Microbiology and Preventive Medicine

summary:
In Campylobacter jejuni CmeR functions as a transcriptional repressor modulating the expression of the multidrug efflux pump CmeABC, which plays an important role in the resistance to antimicrobial agents and bile compounds.  Using DNA microarray, we identified multiple genes that are either activated or repressed by CmeR in C. jejuni. The DNA microarray data was independently confirmed by quantitative real-time RT-PCR. The CmeR-regulated genes encode products of diverse functions including membrane proteins, drug efflux transporters, the C4-dicarboxylate transport/utilization system, and enzymes involved in the biosynthesis of capsular polysaccharide (CPS). Immunoblotting and Alcian blue staining further showed that CPS production is reduced in the cmeR mutant, confirming the regulation of CPS production by CmeR. Electrophoretic mobility shift assay revealed that recombinant CmeR bound specifically to several intergenic regions in the CPS gene cluster, suggesting that CmeR directly regulates this gene cluster. In the chicken host, the mutant carrying a null mutation in cmeR was severely outcompeted by the isogenic wild-type strain. Together these data indicate that CmeR functions as a global regulator in C. jejuni, modulates the expression of genes encoding diverse functions, and is important for the fitness of Campylobacter in the intestinal tract.
Keywords: cell type comparison

overall_design: To compare the transcriptomes of the CmeR mutant and NCTC11168, equal volumes of Cy3- or Cy5-labeled cDNAs from the wild-type or cmeR mutant strain were combined and then hybridized to the microarray slides. A second microarray slide was hybridized with the dyes reversed to the two samples to normalize for dye bias. The hybridization experiment was repeated three times by using total RNA isolated from three independent experiments. Thus, six technical replicates from three biologically independent experiments were used for data analysis.

first: Ying

last: Wang

first: Feng

last: Shi

first: Yiwen

last: Barton

first: B

last: Guo

first: Sonia

last: Pereira

first: Paul

last: Plummer

first: Dan

last: Netlleton

first: Jun

last: Lin


title: High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and polIV mutants

status: Public on Feb 25 2008

city: Norwich

first: Frank

last: Schwach

address: University of East Anglia

department: School of Computing Sciences

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary:
Comparison of the endogenous small RNA content of Arabidopsis flower bud tissue: wild type vs. mutants in polIV pathways
Keywords: High throughput 454 small RNA sequencing.

overall_design: Size fractionated small RNA from total RNA extracts was ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to 454 high throughput pyrosequencing. Please see www.454.com for details of the sequencing technology.

first: Rebecca

middle: A

last: Mosher

first: David

last: Studholme

middle: C

last: Baulcombe


title: Gene expression profile of a murin neuroblastoma cell line infected with the prion strain 22L

status: Public on Feb 22 2008

city: München

first: Christian

last: Bach

address: Trogerstr. 30

institute: TU München

summary:
The underlying pathogenic mechanisms of prion infection are not well characterized. To study the effect of prion infection on gene expression in neuronal cell cultures, a neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Large scale expression analysis was performed using a cDNA microarray chip comprising about 21,000 spotted ESTs. Over hundred genes were identified that are differentially expressed in 22L-infected cells when compared to uninfected cells. Several of the identified changes in gene expression have also been reported for other neurodegenerative diseases such as Alzheimer`s disease.
Keywords: cDNA arrays, prion, N2a, neuroblastoma cell line, murine

overall_design: A neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Eight replicates including four dye swap experiments have been performed for the comparison of prion infected cells versus control cells.

first: Hermann

last: Schätzl

first: Christine

last: Leib-Mösch

first: Ina

last: Vorberg

first: Marion

last: Horsch

first: Johannes

last: Beckers


title: A. burtoni male social phenotypes "loop 1"

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary:
the goal of this experiment is to identify the molecular modules that underlie social phenotypes in A. burtoni
Keywords: loop design comparison of dominant (T) subordinate (NT) and brooding female (F) phenotypes 6 individuals of each phenotype under normal mixed population conditions

overall_design: n of 6 for each phenotype. each labeld 2 times (once each color) and compared directly to two individuals of each other phenotype. 36 hybes = complete design plus 4 extra

first: Renn

last: Suzy

first: Hofmann

last: Hans

first: Aubin-Horth

last: Nadia


title: FLT3 gene-expression signature in normal karyotype AML

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Acute myeloid leukemia with normal karyotype (NK-AML) represents a cytogenetic grouping with intermediate prognosis but substantial molecular and clinical heterogeneity.  Within this subgroup, presence of FLT3 (FMS-like tyrosine kinase 3) internal tandem duplication (ITD) mutation predicts less favorable outcome.  The goal of our study was to discover gene-expression patterns correlated with FLT3-ITD mutation, and to evaluate the utility of a FLT3 signature for prognostication.
The dataset comprises gene-expression profiles of 137 normal karyotype acute myeloid leukemia (NK-AML) specimens carried out using Stanford cDNA microarrays, to accompany the study of L Bullinger et al.  For each array, Channel 2 represents Cy5-labeled NK-AML RNA, and Channel 1 Cy3-labeled universal reference RNA.
Keywords: Logical Set

overall_design: DNA microarrays were used to profile gene expression in a training set of 65 NK-AML cases.  Supervised analysis was applied to build a gene expression-based predictor of FLT3-ITD mutation status.  The predictor was then evaluated by classifying expression profiles from an independent test set of 72 NK-AML cases.

first: Lars

last: Bullinger


title: Examination of protein expression patterns of closely related Salmonella serovars using 2D GE and MS/MS

city: London

first: Vesela

last: Encheva

state: Greater London

address: 61 Colindale Avenue

department: Centre for Infections

institute: Health Protection Agency

summary:
The objective of the present investigation was to consider the level of variation in the protein expression patterns of closely related Salmonella serovars, in order to search for protein factors with levels of expression or posttranslational modifications characteristic for each serovar. For the comparative expression analysis we have utilised classic 2D GE approach which revealed several proteins with serovar specific expression as well as proteins which do not alter their expression levels between serovars and strains. The proteins of interest were identified using LC/MS/MS.
Keywords: 2D GE, MS/MS

sample_organism: Salmonella enterica subsp. enterica serovar Pullorum

sample_organism: Salmonella enterica subsp. enterica serovar Dublin

sample_organism: Salmonella enterica subsp. enterica serovar Choleraesuis

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Analysis of 12 strains of S. enterica representing five different serovars.


title: Stress-Responsive MicroRNAs in Populus

status: Public on Feb 21 2008

city: Raleigh

first: Ying-Hsuan

last: Sun

state: NC

address: 2500 Partners II, 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

summary:
MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become a subject of intense study. They are a class of post-transcriptional, negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in tree’s responses to the stressful environments incurred over its long-term growth. Here, we reported the cloning of small RNAs from abiotic stressed tissues of P. trichocarpa and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, 9 families are novel, raising the number of the known ptc-miRNA families from 33 to 42. Total 346 targets are predicted for the cloned ptc-miRNAs using penalty scores of ≤2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six selected targets are experimentally validated. The expression of a majority of the novel miRNAs is altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known ptc-miRNAs identified 19 additional cold stress responsive ptc-miRNAs that originate from 14 miRNA gene families. Interestingly, we found that miRNAs of the same family respond differentially to the same stress. This suggests that members of a miRNA family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with development and stress response and therefore critical to plant long-term growth; and provide useful information for developing trees with a greater level of stress-resistance.
Keywords: microRNA, cold stress, time course

overall_design: MicroRNA abundance of 21 samples from 7 cold stress time point were analyzed, each cold stress time point contain three replicates. 0 hour cold stress treatment were used as control.

first: Shanfa

last: Lu

first: Vincent

last: Chiang


title: Control run hybridization

first: Mark

last: Wong

summary:
Laboratory strain poliovirus was hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-polio probes was evaluated. Specificity of the probe design was determined.
Keywords: control study: target detection and specificity

overall_design: 1 lab strain virus, poliovirus LS-C-1 was cultured on BGM cells. <24 hrs post infection, viruses were harvested and their nucleic acid was extracted. Viral RNA was labeled with Cy-3 dye and hybridized unto array.

first: Joan

last: Rose


title: Cis- and trans-Regulation of Pneumococcal spxB

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary:
Pyruvate oxidase encoded by spxB is a major virulence factor in the human respiratory pathogen Streptococcus pneumoniae. During aerobic growth, SpxB synthesizes large amounts of H2O2 and acetyl phosphate, which can serve as a phosphoryl group donor to response regulators and be converted to ATP. SpxB is the main source of the millimolar concentrations of H2O2 produced and tolerated by pneumococcus, despite its lack of a catalase. We report here the first cis- and trans-acting regulatory elements for spxB transcription. These elements were identified in a genetic screen, similar to those used previously for phase variants, for spontaneous mutations that caused colonies of virulent serotype 2 strain D39 to change from a transparent to an opaque appearance. Six of the seven opaque colonies recovered (frequency of 3 x 10-5) were impaired for SpxB function. Modeling suggested that two mutations changed amino acids in SpxB required for FAD cofactor or subunit binding. One mutation deleted a cis-acting adjacent direct repeat required for optimal spxB transcription. The other three independent mutations created the same frameshift near the start of a trans-acting regulatory gene designated as spxR. The SpxR protein contains helix-turn-helix, CBS, and HotDog domains implicated in DNA, adenosine, and CoA compound binding, respectively, consistent with the idea that SpxR positively regulates spxB transcript amount in response to energy and metabolic state rather than oxidative state. Finally, microarray analyses of a null spxB or a spxR mutant revealed the presence of a new oxidative stress response in pneumococcus and unexpectedly demonstrated that SpxR strongly positively regulates the transcript amount of the strH exoglycosidase gene, which like spxB, has been implicated in host colonization.
Keywords: genetic modification

overall_design:
Bacterial strains were grown exponentially in rich (BHI) media at 37C and an atmosphere of 5% CO2, and were processed as described in the related Sample records.  Samples were collected from three independent biological replicates and included one dye swap.
Data were normalized using the Lowess (subgrid) method without background subtraction.

first: Smirla

last: Ramos-Montanez

first: Kyle

last: Wayne

first: Jordan

middle: L

last: Morris

first: Lindsey

last: Peters

first: Malcolm

last: Winkler


title: NFkB target gene microarray during LIF-withdrawal differentiation of mouse embryonic stem cells

status: Public on Feb 20 2008

city: Cambridge

first: Josema

last: Torres-Ibanez

address: Tennis Court Road

institute: Wellcome Trust Centre for Stem Cell Research

summary:
An NFkB target gene array (Panomics, Inc., Redwood City, CA) was performed to profile the expression pattern of 107 NFkB-regulated genes in mouse embryonic stem cells. A small scale microarray was carried out using NFkB target gene array kit (Panomics, Inc., Redwood City, CA). A long sense-strand oligonucleotide for each of the 107 human genes that have been previously shown to be regulated by NFkB signaling pathway was spotted in duplicate on the nitrocellulose membrane. Biotinylated DNA was spotted along the right and bottom sides of the array membrane as control. The arrays were performed according to the manufacturer’s instructions.
Keywords: embryonic stem cell differentiation

overall_design:
CCE1.19 embryonic stem cells were plated on gelatinised plates at 2000 cells/cm2 and grown for 4 days in the presence or absence of Leukemia Inhibitory Factor (LIF). Medium was changed every other day. Then, total RNA was extracted using Tri-reagent (Helena Biosciences). 20 ug of RNA was used to prepare biotin-labeled cDNA probes through incorporation of biotin-dUTP into cDNA via reverse transcription reactions. Each biotin-labeled cDNA probe was hybridized to an array membrane at 42°C overnight in a hybridization incubator.The membrane was washed and subjected to further incubations with blocking buffer and subsequent streptavidin-conjugated HRP. The membrane was developed through chemiluminescence reactions and detected immediately by 10 seconds exposures to Kodac BioMax XAR film (Kodak, 8532665). The dots of the array were quantified through densitometric analysis using ImageJ (Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda,
Maryland, USA, http://rsb.info.nih.gov/ij). The 2 spots intensities acquired for each gene were averaged to obtain the VALUE. Empty spots signals were used as background and intensities substracted from the VALUE. The experiments include two samples, one with cells grown in the presence of LIF (control) and one of cells grown in the absence of LIF (experimental).