title: Identification of SRF binding sites in Three Human Cell types

first: Sara

last: Cooper

department: Genetics

institute: Stanford University

summary:
We used chromatin immunoprecipitation (ChIP) in combination with human promoter microarrays to identify 216 putative SRF binding sites in the human genome.  We performed independent quantitative PCR validation at over half of these sites that resulted in 146 sites we assert to be true binding sites at over 90% confidence.  Nearly half of the sites are bound by SRF in only one of the three cell types we tested, providing strong evidence for the diverse roles for SRF in different cell types.
Keywords: ChIP-chip

overall_design: SRF binding was tested in three different cell lines.  It was validated by qPCR.  Using the proximal promoter arrays, we are assaying binding in approximately 19,000 human promoters.


title: Microarray identification of functional modules involving Haptoglobin and/or Hemopexin

status: Public on Nov 01 2006

city: Trieste

first: Diego

last: Vozzi

address: Via dell'Istria

department: Dipartimento di Scienze della Riproduzione

country: Italy

institute: Ospedale Burlo-Garofalo

summary:
Haptoglobin and Hemopexin are plasma acute phase proteins that bind with high affinity hemoglobin and heme, respectively. Several studies have demonstrated that they have a key role in the protection against oxidative stress and inflammation. However, little is known about the functional modules in which they are involved. To gain insights into this issue, we integrated bioinformatic and experimental approaches to identify genes coexpressed with Haptoglobin or Hemopexin and modulated in Haptoglobin and/or Hemopexin knock-out mice. These genes have a high probability to be functionally related to Haptoglobin and/or Hemopexin.
Keywords: haptoglobin, hemopexin, microarray, bioinformatics

overall_design:
We performed a gene expression analysis of the livers of Hp- and/or Hx-null mice compared to wild-type controls. The mice used in the following experiments, i.e. wild-type (Hp+/Hx+/), Hp-null (Hp-/-Hx+/), Hx-null (Hp+/Hx-/-), and HpHx-null (Hp-/-Hx-/-), were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.
We have three experimental points: Hx-null mice, Hp-null mice and HpHx-null mice.
At least 5 adult mice per genotype were perfused via aorta with PBS, sacrificed  and their liver pooled. Thirty microgram of total RNA were subjected to direct labeling reaction by incorporation of cyanin 3 (Cy3) or cyanin 5 (Cy5) fluorescent dyes into the cDNA by priming with oligo(dT). Four replicates were set up for each experimental point. In order to exclude artifacts resulting from different dye usage, we employed the dye-swap approach.

first: Sharmila

last: Fagoonee

first: Ferdinando

last: Di Cunto

first: Stefano

last: Volinia

first: Maurizio

last: Pellegrino

first: Paolo

last: Gasparini

first: Lorenzo

last: Silengo

first: Fiorella

last: Altruda

first: Emanuela

last: Tolosano


title: benzo(a)pyrene_MCF7_HepG2

status: Public on Oct 24 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

summary:
MCF-7 and HepG2 cells were exposed to a range of concentrations of benzo(a)pyrene or benzo(e)pyrene (0-5 uM) for up to 48 h and gene expression analysis performed.
Keywords: dose response

overall_design: 96 samples  - cells exposed to benzo(a)pyrene or benzo(e)pyrene dissolved in DMSO were compared to cells exposed to DMSO alone

first: Sarah

middle: L

last: Hockley

first: Volker

middle: M

last: Arlt

first: Daniel

last: Brewer

first: David

middle: H

last: Phillips


title: Poplar flowering and maturation GeneXp arrays

status: Public on Oct 11 2006

city: Corvallis

first: Jingyi

last: Li

state: OR

country: USA

institute: Oregon State University

summary:
To identify candidate genes involved in maturation and flowering, we conducted microarray expression studies using two poplar genotypes (Populus trichocarpa x P. deltoides hybrids) represented in continuous age gradients of one to six years. We designed 70-mers for 228 poplar genes and microarray studies were carried out using the microplate-based 96-well BioGridArray platform (GeneXP Biosciences).   Floral buds, vegetative buds and shoot tips were collected at different seasonal time points from juvenile and adult trees and from both basal and upper branches of mature trees.
Keywords: Maturation and Flowering

sample_organism:
Populus trichocarpa
Populus deltoides

overall_design: The experiment was carried out using the microplate-based 96-well BioGridArray platform (GeneXP Biosciences).  Each of 228 oligonucletides were duplicated in each well. Two human genes, beta-actin and gapdh , were also printed on all arrays as negative controls.  plus ten arabidopsis oligonucleotides selected by GeneXP and used to measure quality of hybridization. For each of 16 samples, two seperate RNA isolations were performed and were considered as biological replicates. Each biological replicate was labeled with Cy5, and hybridized to duplicated wells.

first: Olga

last: Shevchenko

first: Ove

last: Nilsson

first: Steve

last: Strauss

first: Amy

last: Brunner


title: Tissue specificity of gene expression profiling from mussels in normal conditions.

status: Public on Oct 10 2006

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary:
We examined tissue specificity of gene expression in control mussels. Total RNA was isolated from gills (G), digestive gland (DG), tissues involved in contraction/motility (FML: foot/adductor muscles/ligaments) and reproduction (GM: gonads and mantle) producing four tissue-specific samples. Total RNA was reverse-transcribed and labeled using a Cy3-dCTP and Cy5-dCTP direct incorporation.
Each sample was hybridized in competition with the total pool (equal RNA amounts from G, DG, GM and FML) and the relative abundance of each gene was measured by directly comparing fluorescent signals for each probe. We reversed labeling of pool tissues (reference) and single tissue sample in each experiment, thus carrying out two separate hybridizations for each tissue.

Keywords = mussels
Keywords = tissue specificity
Keywords = normal conditions
Keywords = gene expression profiling
Keywords: ordered

first: Paola

last: Venier

first: Cristiano

last: De Pittà

first: Francesco

last: Marsano

first: Alberto

last: Pallavicini

first: Laura

last: Varotto

first: Chiara

last: Romualdi

first: Aldo

last: Viarengo


title: Gene expression profiling of mussels treated with two chemical mixtures

summary:
We examined gene expression profiling of mussels treated with two chemical mixtures composed by heavy metals or organic compounds, both including genotoxic agents (cadmium, benzo[a]pyrene, 1-nitro/amino-pyrene) and other contaminants (cupper, mercury, fluoranthene, TCDD). For  digestive gland one RNA sample from control mussels and one from each treatment group (7 mussels) were competitively hybridized on the MytArray 1.0. Total RNA was reverse-transcribed and labeled using a Cy3-dCTP and Cy5-dCTP direct incorporation. We carried out two separate hybridizations for each treatment conditions.
Keywords = mussels
Keywords = heavy metals
Keywords = organic compaunds
Keywords = gene expression profiling
Keywords: ordered

last: Rolualdi


title: GATA-3 maintains luminal cell differentiation in the mammary gland and in breast cancer

city: Indianapolis

first: Hosein

last: Kouros-Mehr

state: IN

address: 533 Merrill St.

department: Oncology

institute: Eli Lilly

summary:
We have identified GATA-3 as a critical regulator of luminal cell differentiation in the mammary gland.  Acute loss of GATA-3 in the adult mammary gland leads to an expansion of an undifferentiated luminal epithelium and the formation of a multi-layered epithelium.  Here we report microarray analysis of mammary glands that have undergone acute loss of GATA-3
Keywords: genetic modification

overall_design: Adult GATA-3flox/flox; WAP-rtTA-Cre and GATA-flox/+; WAP-rtTA-Cre mice were administered doxyxcline for 5 days and their mammary glands harvested.  Total RNA was extracted by the Trizol method.  Het mammary gland total RNA was labeled with Cy5 while Null mammary gland total RNA was labeled with Cy3.  Microarray hybridization was performed on spotted oligonucleotide microarrays with 38,000 features.  Lowess print-tip normalization and analysis was performed on the Acuity software package (V 4.0)

first: Zena

last: Werb


title: Double-tiled DNA microarrays -- proof of principle

status: Public on Oct 23 2006

city: Baltimore

first: Sarah

last: Wheelan

state: MD

address: 550 N. Broadway

institute: Johns Hopkins University School of Medicine

type: Expression profiling by genome tiling array

summary:
We have developed a double-tiling method that effectively doubles the number of sequences on a microarray, and with these arrays we confirm that our design can be utilized quickly and easily.
Keywords: testing novel microarray design

overall_design: GPL4107 is a double-tiled array, and GPL4111 is a conventional array. Both contain the entire yeast genome at approximately 150 and 280 bp resolution, respectively. Our proof-of-principle experiments were done with plasmids; we subsequently performed a more complex experiment (comparing galactose vs glucose-grown yeast) on both the double-tiled arrays and on the conventional array (for use as a standard).

middle: J

first: Francisco

last: Martinez-Murillo

first: Rafael

middle: A

last: Irizarry

first: Jef

middle: D

last: Boeke


title: Identification of MglA-regulated genes reveals novel virulence factors in F. tularensis

status: Public on Oct 20 2006

city: Stanford

first: Anna

last: Brotcke

state: CA

department: Microbiology and Immunology

summary:
The facultative intracellular bacterium Francisella tularensis causes the zoonotic disease tularemia.  F. tularensis resides within host macrophages in vivo and this ability is essential for pathogenesis.  The transcription factor MglA is required for expression of several Francisella genes that are necessary for replication in macrophages and for virulence in mice.  We hypothesized that identification of MglA-regulated genes in the Francisella genome by transcriptional profiling of wild-type and mglA mutant bacteria would lead to the discovery of new virulence factors utilized by F. tularensis.  One hundred and two MglA-regulated genes were identified, the majority of which were positively regulated, including all of the Francisella Pathogenicity Island (FPI) genes.  We mutated novel MglA-regulated genes and tested the mutants for their ability to replicate and to induce cytotoxicity in macrophages, and to grow in mice.  Mutants in MglA-regulated genes within the FPI (pdpB and cds2), as well as outside the FPI (FTT0989, oppB, and FTT1209c), were either attenuated or hypervirulent in macrophages as compared to the wild-type strain.  All of these mutants exhibited decreased fitness in vivo in competition experiments with wild-type bacteria.  We have identified 5 new Francisella virulence genes and our results suggest that characterization of additional MglA-regulated genes will yield further insights into the pathogenesis of this bacterium.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Computed


title: Global transcription pattern of virulent S. pneumoniae strain D39 (NCTC) compared to that of strains R6 and D39 (Lilly)

status: Public on Oct 09 2006

city: Bloomington

first: Krystyna

last: Kazmierczak

address: 1001 E. Third St.

department: Biology

institute: Indiana University

summary:
Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenicity. To date, the complete genome sequences have been reported for only two S. pneumoniae strains; TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report herein the genome sequences of two different isolates of strain D39 and the corrected sequence and updated annotation of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only 5 relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single base pair changes, 6 deletions, 4 insertions, and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed.
Keywords: bacterial strain comparison, bacterial isolate comparison

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.  Data were also normalized with background subtraction (not shown); expression ratios did not differ significantly with or without background subtraction.
Tables of average fold changes are included as supplementary material for the accompanying manuscript (Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison With That of Unencapsulated Laboratory Strain R6, Lanie J.A. et al, J. Bact, accepted).

first: Joel

last: Lanie

first: Wai-Leung

last: Ng

first: Tiffany

last: Andrzejewski

first: Tanja

last: Davidsen

first: Kyle

last: Wayne

first: Herve

last: Tettelin

first: John

middle: I

last: Glass

first: Malcolm

middle: E

last: Winkler


title: Androgen receptor coregulators baseline comparisons

status: Public on Oct 12 2006

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary:
LNCaP cells are an established androgen receptor expressing prostate carcinoma cell line. Human foreskin fibroblasts also expressing the androgen receptor were obtained from phenotypic normal male individuals. Cells were cultured either at confluency leading to G0 cell cycle state or while they were proliferating. Cells were either untreated, or treated with dihydrotestosterone (DHT) or ethanol (ETOH) which also served as the solvent for the DHT. All experimental RNA samples derived from the untreated or treated cell lines were hybridized on cDNA arrays against a common reference. This reference was composed out of common reference CRG (50%) and out of fibroblast RNA (50%). This reference is also called "mixed reference" in the description of the 26 individual experiments.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Compound Based Treatment: dihydrotestosterone (DHT) or ethanol (ETOH = solvent)
Cell Line: genital fibroblast cell line or prostate carcinoma cell line (LNCaP)
Culture Synchrony: Go or proliferation
Keywords: strain_or_line_design


title: Carboxyltransferase Subunit of the Acyl-CoA Carboxylase in Mycobacterium tuberculosis.

status: Public on Oct 07 2006

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

summary:
The Mycobacterium tuberculosis acyl-CoA carboxylases provide the building blocks for de novo fatty acid biosynthesis by fatty acid synthase (FAS) I and for the elongation of FAS I end-products by the FAS II complex to produce meromycolic acids. M. tuberculosis genome contains three biotin carboxylase subunits (AccA1-3) and 6 carboxyltransferase subunits (AccD1-6) of which AccD6 is located in a genetic locus that contains members of the FAS II complex. We found by microarray and quantitative real-time RT-PCR analysis that the transcripts of AccA3, AccD4, AccD5 and AccD6 are expressed at high levels during exponential growth phases of M. tuberculosis in vitro.
Keywords: Time course, developmental stages

overall_design: The microarray hybridization was performed to compare general gene expression changes along with Acyl-CoA carboxylase subunits between an exponential growth phase and late-log phase. Wild-type Mtb cells were inoculated in the complete liquid medium, and grown until OD~0.5, which is chosen as a reference exponential growth stage. Samples were prepared after further growth until the OD values doubles in the same medium as was in the reference culture.

first: Jaiyanth

last: Daniel

first: Tae-Jin

last: Oh

first: Pappachan

last: Kolattukudy


title: Modulation of gene expression in a human cell line caused by poliovirus, vacciniavirus and interferon

status: Public on Oct 16 2006

city: Oslo

first: Bjorn

last: Grinde

state: Oslo

address: Geitmyrsveien 75

department: Infectious Disease Control

country: Norway

institute: Norwegian Institute of Public Health

summary:
A human embryonic fibroblast cell line was synchronously infected with poliovirus in the absence or presence of interferon-α, or with vacciniavirus, a virus that is not inhibited by interferon. The titers were sufficient to yield productive infection in a majority of the cells. The cells were harvested in triplicate at various time-points, and the transcriptosome compared with mock infected cells using oligo-based 35 k microarrays. The project had two purposes: to characterize the cellular response and to look for candidate genes involved in viral defense. The changes in gene expression due to vaccinia virus did not correspond to those caused by poliovirus. More surprisingly, neither did the changes when comparing 8 h and 16 h of poliovirus infection. However, a large proportion of the genes up-regulated by interferon-α were also up-regulated by poliovirus, both at 8 h and 16 h. Interferon-α inhibited poliovirus replication, thus the observations suggest that the cells do launch an antiviral response to poliovirus. Moreover, as interferon genes were not induced, the data indicate that several of the relevant genes can be activated in an interferon independent manner. Further analyses of the data led to a list of candidate antiviral genes. Functional information was limited, or absent, for most of these genes.
Keywords: Poliovirus; Vacciniavirus; Interferon; Microarray; Gene expression; Defense genes

overall_design: A human cell culture was used to investigate the response to viral infections. The cells were incubated for 1 h with either poliovirus or vacciniavirus, washed and incubated for another 4 to 16 h. Total RNA from three parallel cell cultures were used for each time point and compared with mock infected cells. Interferon-alpha, at a concentration sufficient to inhibit poliovirus replication, was used to help single out genes that might be involved in viral defence.

first: Bjørn

first: Marc

last: Gayorfar

first: Gunnar

last: Hoddevik


title: Expression data from BY4743 and dbr1 yeast

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary:
Introns in pre-mRNAs must be spliced out prior to their translation.  During splicing, introns are removed in the form of a lariat, in which the 5' end is linked to the 2' hydroxyl of an internal adenosine.  Lariat degradation is initiated by an 2'-5' phosphodiester-specific RNA endonuclease which debranches these lariat RNAs to linear form.  Deletion of the debranching enzyme is yeast results in the accumulation of lariat introns.  We used this accumulation to identify spliced lariat introns on a genome-wide scale in S. cerevisiae using tiling microarrays.
Keywords: two sample comparison, 3 biological replicates

overall_design: Total RNA from BY4743 and dbr1 yeast was harvested, labeled as double-stranded probes and hybridized to Affymetrix tiling microarrays.  Signals enriched in the dbr1 strain were mapped to genomic coordinates to assess correspondence with known intron regions and identify novel spliced sequences.

first: S

last: Fields

first: J

first: Z

last: Zhang


title: Temporal Biofilm Expression of E. coli K-12 after 4, 7, 15, and 24 hr

city: College Station

first: Thomas

middle: K.

last: Wood

state: TX

address: 220 Jack E. Brown Building

department: Artie McFerrin Department of Chemical Engineering

institute: Texas A & M University

summary:
Temporal expression of biofilm and suspenion samples from E. coli wild type cultured on glass wool in LB medium. Samples removed after 4, 7, 15, and 24 hr of culturing
Keywords: time course (temporal exression)

overall_design:
LB medium cultured with glass wool
biofilm and suspenion cell samples
time points of 4, 7, 15, and 24 hr

first: Joanna

last: Domka

first: Jintae

middle: K


title: pH and Anaerobiosis Coregulate Metabolism, Multidrug Transporters, and Envelope Composition in Escherichia coli K-12

status: Public on Oct 01 2006

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

summary:
In Escherichia coli, pH-dependent gene expression varies with oxygen level.  Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005).  E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5.  Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays.
pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration.  Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration.   Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp).  The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR).  Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis.  Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH.  A core group of 236 genes showed similar pH response with or without aeration.  Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the “constitutive” Na+/H+ antiporter (nhaB), and over thirty unidentified proteins.    Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL).
Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm.
Keywords: Steady State

overall_design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration.  The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5.  Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. For each of the three pH conditions, RNA was isolated from five independent cultures. Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures. To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1. ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001). For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).

first: Everett

middle: T

last: Hayes

first: Jessica

middle: C

last: Wilks

first: Elizabeth

last: Yohannes

first: Daniel

middle: P

last: Tate

first: Michael

last: Radmacher

first: Sandra

middle: S

last: BonDurant


title: hES cell FGF2 re-stimulation experiments

status: Public on Oct 03 2006

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
This series includes hES cell samples starved and re-stimulated with FGF2. Controls were FGF2-starved but not re-stimulated. Two independent experiments were carried out (one sample plus control each).
Keywords: Growth factor stimulation experiment

overall_design: hES cells were grown in conditioned medium for 2 days, starved in unconditioned medium (UM) without FGF2 and with 30uM of SU5402 (Calbiochem), for 24h, and, after extensive washing, re-treated with 40 ng/ml of FGF2 in UM for 4h. Controls were FGF2-starved but not re-stimulated. After the FGF2 starvation period the cells did not show any obvious signs of spontaneous differentiation.

first: Hans

last: Lehrach

first: James

last: Adjaye


title: Synthetic lethality/slow growth with acs2-Ts8

first: Hidekazu

last: Takahashi

state: Maryland

address: 339 Broadway Research Building, 733 North Broadway

department: High Throughput Biology Center

summary:
Obtain synthetic lethality/slow growth gene interactors of acs2-Ts8
Keywords: gene mutation

overall_design: The DNAs from one control single YKO population and one experimental double YKO acs2-Ts8 were labeled with Cy5 and Cy3. These labeled DNAs were hybridized to obtain the signal ratio Cy5/Cy3 (C/E).

first: Jef

last: Boeke


title: NGM versus CeMM growth

status: Public on Oct 18 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
These three arrays are replicate extractions and hybridizations. Each array hybridizes labeled RNA from NGM plate grown, mixed stage, animals (Channel 1) against labled RNA from liquid CeMM grown, mixed stage, animals (Channel 2).
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Media: Channel 1 is NGM grown mixed stage animals, Channel 2 is CeMM grown mixed stage animals
Keywords: replicate_design

first: Catharine

last: Conley


title: MES-4, an autosome-associated HMT that participates in silencing the X chromosomes in the C. elegans germ line

status: Public on Sep 30 2006

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

summary:
Microarray-based expression profiling of dissected gonads from mes-4 mutants reveals that MES-4 is required to repress expression of a set of X-linked genes.
Keywords: Mutant analysis of mes-4 in dissected C. elegans gonads

overall_design: We isolated dissected gonads from mes-4(bn85) mutant adults and compared to dissected gonads from wild type (N2 animals.  RNA was linearly amplified prior to labeling for all genotypes.  Comparison was done in quadruplicate on independently grown and isolated animals.


title: Translational control of cell viability downstreams of eIF4E, using polyribosome RNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary:
Aberrant activation of the translation initiation machinery is a common property of malignant cells, and is essential for breast carcinoma cells to manifest a malignant phenotype. How does sustained activation of the rate limiting step in protein synthesis so fundamentally alter a cell? In this report, we test the post transcriptional operon theory as a possible mechanism, employing a model system in which apoptosis resistance is conferred on NIH 3T3 cells by ectopic expression of eIF4E. We show (i) there is a set of 255 transcripts that manifest an increase in translational efficiency during eIF4E-mediated escape from apoptosis; (ii) there is a novel prototype 55 nt RNA consensus hairpin structure that is overrepresented in the 5'-untranslated region of translationally activated transcripts; (iii) the identified consensus hairpin structure is sufficient to target a reporter mRNA for translational activation under pro-apoptotic stress, but only when eIF4E is deregulated; and (iv) that osteopontin, one of the translationally activated transcripts harboring the identified consensus hairpin structure functions as one mediator of the apoptosis resistance seen in our model. Our findings offer genome-wide insights into the mechanism of eIF4E-mediated apoptosis resistance and provide a paradigm for the systematic study of posttranscriptional control in normal biology and disease.
Keywords: common reference, various polyribosome fractions

overall_design: To globally address the issue of which transcripts mediate the anti-apoptotic functions of eIF4E, we used a model in which NIH 3T3 cells ectopically overexpress translation initiation factor 4E (eIF4E) resulting in an apoptosis-resistant and tumorigenic phenotype. We performed a comprehensive study of apoptosis resistance in the NIH 3T3/4E model using an array containing 15k cDNAs and ESTs (NIH 15k collection printed at The Ontario Cancer Institute). To facilitate data analysis in the two-color competitive hybridization microarray approach employed, we used a universal standard mRNA [non-stratified poly(A) selected RNA derived from NIH 3T3 cells cultured in full growth medium]. We compared signals generated from this standard to both the light (fractions 4–6, <1 ribosome/transcript) and the heavy (fractions 7–10, >1 ribosomes/transcript) polyribosome fractions of RNA from NIH 3T3 and NIH 3T3/4E cells cultured either in complete growth medium or after 16 h of serum starvation, a time point before any evidence of cytochrome c release from the mitochondria, a signature step at the apex of the cell death program. We selected the 16 h time point in order to identify genes that might govern the decision to enter the apoptotic pathway, and exclude those involved in the actual process of cell execution.


title: Gene expression profiling of native mussels from Venice lagoon area

first: Gerolamo

last: Lanfranchi

summary:
We examined gene expression profiling of native mussels that were sampled in early summer 2003 from sites of the Venice lagoon area known to be differently affected by chemical pollution: Sites 1 and 2 close to the industrial district of Marghera and Site 3 close to the Lido lagoon outlet. Site 4, a current mussel farm located offshore, has been chosen as source of reference targets for microarray hybridizations. We have limited the preliminary assessment to the digestive gland.
Digestive gland total RNA of each Site was hybridized in competition with the offshore mussels (Site 4 - Reference) and the relative abundance of each gene was measured by directly comparing fluorescent signals for each probe. We carried out two separate hybridizations for each site of the Venice lagoon area..

Keywords = digestive gland
Keywords = Venice lagoon
Keywords = chemical pollution
Keywords = native mussels
Keywords = transcriptional profiling
Keywords: ordered

first: Paola

last: Venier

first: Cristiano

last: De Pittà

first: Francesco

last: Marsano

first: Alberto

last: Pallavicini

first: Laura

last: Varotto

first: Chiara

last: Romualdi

first: Aldo

last: Viarengo


title: Bacteriophage BFK 20 gene expression study

status: Public on Oct 13 2006

city: Bratislava 45

first: Tomas

last: Majtan

address: Dubravska cesta 21

department: Department of Molecular Genomics

country: Slovakia

institute: Institute of Molecular Biology SAS

summary:
This microarray serie represents the complete gene expression study of bacteriophage BFK 20 during the infection of its host Brevibacterium flavum CCM 251.
Keywords: time course

overall_design: Gene expression was measured at fourteen time intervals (0, 1, 3, 5, 7, 10, 15, 20, 30, 40, 50, 60, 80 and 120 min) during phage infection according to proposed loop. Each sample was directly compared to the previous and to the next sample (point of total RNA isolation).

first: Jozef

last: Timko

first: Gabriela

last: Bukovska


title: Cotton spotted oligonucleotide microarrays for gene expression analysis

status: Public on Sep 22 2006

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

summary:
Microarrays offer a powerful tool for diverse applications plant biology and crop improvement.  Recently, a global assembly of cotton ESTs was constructed based on three Gossypium.  Using that assembly as a template, we now describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species.  Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of more than 150,000 cotton ESTs derived from 30 different cDNA libraries representing many different tissue types and tissue treatments.  A total of 13,158 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome but also including previously studied cotton genes, duplicated gene pairs derived from a paleoduplication event, transcription factors, and homology to protein coding genes in Arabidopsis.  About 10% of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery.  Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the array has direct application for analysis of the fiber transcriptome.  To illustrate the utility of the array, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results.  The cotton microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.
Keywords: self vs. self; platform testing

platform_organism:
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Three replications of leaf and bud RNA were collected from the 4-5 plants grown in green houses at Iowa State University.  RNA was separately extracted and pooled into a single 'leaf' and 'bud' sample.  These pooled RNA samples were then amplified (TargetAmp, Epicentre) and labelled with Cy3 and Cy5.  The bud samples were split into two so as to minimize any error that might arise from something besides the microarray.  Replication bud vs. bud' and leaf vs. bud experiments were carried out.  Data were analyzed in R and the results are present to the research community documenting the availability of a cotton oligonucleotide microarray.

first: Joshua

last: Udall

first: Jordan

last: Swanson

first: Lex

last: Flagel

first: Ran

last: Hovav

first: Ryan

last: Rapp

first: Dan

last: Nettleton

first: Jeffrey

middle: Z

last: Chen

first: Jonathan

middle: F

last: Wendel


title: Gene expression profiling of primary breast carcinomas from patients at high risk for local recurrence

status: Public on Sep 24 2006

city: Amsterdam

first: Bas

last: Kreike

address: Plesmanlaan 121

department: Radiotherapy

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Purpose: Several risk factors for local recurrence of breast cancer after breast conserving therapy (BCT) have been identified. The identification of additional risk factors would be very useful in guiding optimal therapy and also improve understanding of the mechanisms underlying local recurrence. We used cDNA microarray analysis to identify gene expression profiles associated with local recurrence.
Experimental Design: Using 18K cDNA microarrays, gene expression profiles were obtained from 50 patients who underwent BCT. Of these 50 patients 19 developed a local recurrence; the remaining 31 patients were selected as controls as they were free of local recurrence at least 11 years after treatment. For 9/19 patients also the local recurrence was available for gene expression profiling. Unsupervised and supervised methods of classification were used to separate patients in groups corresponding to disease outcome and to study the overall gene expression pattern of primary tumors and their recurrences.
Results: Hierarchical clustering of patients did not show any grouping reflecting local recurrence status. Supervised analysis revealed no significant set of genes that was able to distinguish recurring tumors from non-recurring tumors. Paired-data analysis of primary tumors and local recurrences showed a remarkable similarity in gene expression profile between primary tumors and their recurrences.
Conclusions: No significant differences in gene expression between primary breast cancer tumors in patients with or without local recurrence after breast conserving therapy were identified. Furthermore, analyses of primary tumors and local recurrences show a preservation of the overall gene expression pattern in the local recurrence, even after radiotherapy.
Keywords: gene expression profiling

first: Hans

last: Halfwerk

first: Marc

last: Van de Vijver


title: Transcriptional profile of Candida glabrata ingested by murine macrophage-like cells (J774A.1) for 2 and 6 hours

status: Public on Oct 19 2006

first: Brendan

last: Cormack

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

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

summary:
A set of 5,908 69-70 mers oligonucleotides that correspond to all C. glabrata putative open reading frames and some non-coding sequences was designed and synthesized at Pasteur Institute, France. Each oilgonucleotide was dissolved into 50% DMSO and spotted on UltraGAPsTM glass slides (Corning Incorporated, Acton, MA) in duplicate to generate whole genome microarray for C. glabrata. The microarray was printed at Biotechnology Research Institute/National Research Council of Canada in Montreal. The sequence information of the oligonucleotides and the micorarray setup can be found at platform GPL3922. Using the microarray, the transcriptional profiles of C. glabrata cells that were coincubated with J774A.1 murine Macrophage-like cells for 2 and 6 hrs were examined. At each time point, three biological repeats were done. 20 ug of total RNA from either macrophage-ingested C. glabrata cells (experimental sample) or the medium-alone controls (control sample) was used to synthesize Cy5- or Cy3-labeled cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5- or Cy3-dCTP (PerkinElmer). For each pair of experimental and control samples, dye-swap was performed, that is, two probe mixtures, the Cy5-experimental plus the Cy3-control probes, and conversely, the Cy3-experimental plus the Cy5-control probes were individually hybridized with a single C. glabrata microarray slide. The hybridization and subsequent washing conditions follows the instruction on the manual for UltraGAPsTM glass slides. The hybridized microarrays were scanned with Axon 4000B scanner, and Data were extracted using Axon GenePix program. Log2 (experimental/control) for each spot on the microarray was calculated. From each dye-swap experiment, the Log2 (experimental / control) for each spot were averaged. Finally, 6 Log2 (experimental/control) values (3 repeats × duplicate spots on each slide) were imported into SAM (significance analysis of microarrays) software for statistical analysis. For genes that are considered significantly induced or repressed, the median of false discovery rate (FDR) equals to 0, while the 90% FDR is less than 0.001.
Keywords: transcriptional profiling by microarray

overall_design:
GSM140373 and GSM140374 are dye-swap experiment #1 for hour 2 time point; GSM140375 and GSM140621 are dye-swap experiment #2 for hour 2 time point; GSM140625 and GSM140626 are dye-swap experiment #3 for hour 2 time point.
GSM140627 and GSM140631 are dye-swap experiment #1 for hour 6 time point; GSM140632 and GSM140633 are dye-swap experiment #2 for hour 6 time point; GSM140634 and GSM140635 are dye-swap experiment #3 for hour 6 time point.

first: Kaur

last: Rupinder

first: Biao

last: Ma


title: Regulation of sexual development of Plasmodium by translational repression.

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary:
Translational repression of messenger RNAs (mRNAs) plays an important role in sexual differentiation and gametogenesis in multicellular eukaryotes. Translational repression and mRNA turnover were shown to influence stage-specific gene expression in the protozoan Plasmodium. The DDX6-class RNA helicase, DOZI (development of zygote inhibited), is found in a complex with mRNA species in cytoplasmic bodies of female, blood-stage gametocytes. These translationally repressed complexes are normally stored for translation after fertilization. Genetic disruption of pbdozi inhibits the formation of the ribonucleoprotein complexes, and instead, at least 370 transcripts are diverted to a degradation pathway.
Keywords: P. berghei, gene expression

overall_design: mRNA abundance was compared between dozy mutana nd wt parasite strains.

first: Gunnar

last: Mair

first: Joanna

last: Braks

first: Lindsey

last: Garver

first: Joop

last: Wiegant

first: Neil

last: Hall

first: Roeland

middle: W

last: Dirks

first: Shahid

middle: M

last: Khan

first: Chris

last: Janse

first: Andrew

last: Waters


title: Regulation of hypothalamic gene expression by glucocorticoid: implications for energy homeostasis

city: Hershey

first: Yuichiro

last: Nishida

state: PA

address: 500 University Drive

department: Department of Anatomy and Physiology

institute: Penn State College of Medicine

summary:
The current study has investigated the hypothalamic gene expressions regulated by glucocorticoid (GC), key hormones in energy homeostasis. Using serial analysis of gene expression (SAGE) method, we have studied the effects of adrenalectomy (ADX) and GC on the transcriptomes of mouse hypothalamus. Approximately, 180 000 SAGE tags, which correspond to 50 000 tag species, were isolated from each group of intact or adrenalectomized mice, as well as 1, 3 and 24 hours after GC injection. ADX has upregulated diazepam binding inhibitor gene expression, while downregulating vomeronasal 1 receptor D4, genes involved in mitochondrial phosphorylation (cytochrome c oxidase 1 and NADH dehydrogenase 3), 3b-hydroxysteroid dehydrogenase-1, and prostaglandin D2 synthase. GC has increased the gene expression levels of dehydrogenase/reductase member 3, prostaglandin D2 synthase, solute carrier family 4 member 4, and five cytoskeletal proteins including myosin light chain phosphorylatable fast and troponin C2 fast. On the other hand, GC has reduced the mRNA levels of calmodilin 1 and expressed sequence tag similar to (EST) calmodilin 2, ATP synthase F0 subunit 6, and solute carrier family 4 member 3. Moreover, seven uncharacterized and 43 novel transcripts were modulated by ADX and GC. The current study has identified genes that may regulate hypothalamic systems governing energy balance in response to ADX and GC.
Keywords: Hormone effect analysis

overall_design: Male C57BL6 mice were obtained from Charles River Laboratories (St. Constant, QC, Canada), at 12-14 weeks of age. Mice were housed in an air-conditioned room (19-25 degree) with controlled lighting from 07:15 to 19:15 h and were given free access to food (Lab Rodent Diet No. 5002) and water. One week prior to sampling of hypothalamus, adrenalectomy was performed in mice of all experimental groups (n = 12 per group). ADX mice received sodium chloride (0.9g/dl) in their drinking water after the surgery. GC (corticosterone, 0.1 mg per mouse) was subcutaneously injected to ADX mice and the hypothalamus was harvested at 1 hour (ADX + GC 1 h), 3 hours (ADX + GC 3 h) and 24 hours (ADX + GC 24 h) after the GC injection. ADX received an injection of vehicle solution (5% ethanol with 0.4% methocel A15LV premium) at 24 hours prior to sacrifice. All mice were killed between 08:30 and 12:30 by decapitation under isoflurane anesthesia. Brain was removed from the skull and the hypothalamus was immediately dissected, frozen in liquid nitrogen, pooled together for each group, and stored at -80 degree until RNA extraction.

first: Mayumi

last: Yoshioka

first: Jonny

last: St-Amand


title: Tissue profiling of phosphodiesterases

city: Berkeley

first: Jonathan

middle: L

last: Bingham

address: 733 Allston Way

institute: Jivan Biologics, Inc

summary:
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Keywords: tissue profiling

overall_design: 24 human tissues plus one control pool were selected to investigate tissue-specific transcription and RNA splicing of the human phosphodiesterases

first: Subha

last: Srinivasan


title: Livers of mice fed an atherogenic diet for 6 or 24 weeks

status: Public on Sep 19 2006

city: Kanazawa

first: Naoto

last: Matsuzawa-Nagata

state: Ishikawa

address: 13-1 Takara-machi

department: Medicinal Infomation

country: Japan

institute: Kanazawa University Graduate School of Medical Science

summary:
To address the molecular basis for atherogenic diet-induced liver injury, we performed microarray analysis using livers at early (6 weeks) and pre-cirrhosis stages (24 weeks) in the development of steatohepatitis.

The Atherogenic diet up-regulated the gene expression for fatty acid synthesis, inflammatory cytokines, oxidative stress, and fibrosis, and with down-regulation of fatty acid beta-oxidation. The addition of a high-fat component to the Atherogenic diet up-regulated the gene expression for fatty acid synthesis and transport pathways and down-regulated some of the antioxidant genes.
Keywords: time-course

overall_design: For oligo-microarrays (AceGene Mouse Oligo Chip 30K; DNA Chip Research, Yokohama, Japan). Each microarray hybridization sample and the reference amino allyl aRNA were labeled with mono-reactive NHS esters of Cy5 and Cy3, respectively. Microarray hybridization and washing were performed according to the manufacturer’s instructions, and then scanned using an Agilent G2505B microarray scanner (Agilent Technologies, Palo Alto, CA, USA), followed by image analysis using GenePix Pro 4.1 software (Axon Instruments, Union City, CA, USA). Microarray data were normalized (LOWESS method) using GeneSpring v7.2 software (Agilent Technologies), and exported into tab-deliminated files for further analysis.


title: Androgen receptor-coregulators hormone responsiveness LNCaP / GSF

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein

summary:
The text description is: LNCaP are androgen receptor expressing prostate carcinoma cells. Genital skin fibroblasts also express the androgen receptor. Cells were either proliferating or they were G0-arrested. Treatment of cells was performed with either the androgen DHT (dihydrotestosterone), the androgen analogue R1881 (methyltrienolone), or the solvent ethanol. Some hybridizations were performed in the type 1 design. In these cases, the hormone treated sample was hybridized against the ethanol treated sample on the same microarray. Hormone mediated induction or repression of gene transcription can directly be deduced from R/G normalized ratios on arrays. For other experiments, the ethanol treated control and the hormone treated experiment were hybridized on separate microarrays against a common reference of RNA. This reference was composed out of common reference batch CRG (50%) and a fibroblast RNA (50%). This reference was called mixed reference. For all experiments, the same batch of mixed reference was used.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Compound Based Treatment: Ethanol, R1881 (methyltrienolone), or DHT (dihydrotestosterone)
Cell Line: LNCaP (prostate cancer) or foreskin fibroblasts
Culture Synchrony: proliferation / Go-arrest
Keywords: compound_treatment_design

overall_design: Computed

first: Samuel

last: DePrimo


title: Basal Cell Carcinoma Tumor-derived Fibroblasts

status: Public on Oct 05 2006

city: Stanford

first: Julie

middle: B.

last: Sneddon

address: Beckman Center, Room 400

department: Stanford Biochemistry

institute: Stanford

summary:
Dataset contains samples that are all fibroblast cells that have been cultured from fresh human tissue.  Fibroblasts were derived either from tumor (basal cell carcinoma) or non-tumor (control) tissue.  Samples were maintained in DMEM, 10% FBS, glutamine, pen/strep and passaged for 4 passages before RNA harvest was performed using Invitrogen FastTrack.  Reference channel RNA is the same for each array in the dataset and is Stratagene Universal Reference RNA.  Hybridizations were performed for 14-18 hours at 65 C.  Scanning was performed using AxonScanner and data were analyzed using GenePix 3.0.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Disease State: Tumor-derived
Keywords: Logical Set


title: Sluggish Fermentation

status: Public on Sep 15 2006

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast.
Keywords: Time course

overall_design: Three replicates of five time points taken at 24, 48, 80, 96 and 144 hours after yeast inoculation

last: Garcia-Martinez


title: Normal Fermentation

summary:
Gene expression analysis of a time course experiment of a synthetic must (nitrogen-rich) fermentation by a natural wine yeast.
Keywords: Time course

overall_design: Three replicates of three time points taken at 24, 48 and 96 hours after yeast inoculation

middle: E


title: Gene expression of 4hr serum stimulated mouse ES cells after 72hr serum starvation

city: Fukuoka

first: Yoshinori

middle: N

last: Ohnishi

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
Among fos family genes modulating the cell fates such as cell proliferation, differentiation and cell death, only the fosB gene produces two forms of mature mRNA for FosB and deltaFosB proteins by alternative splicing of an exonic intron in the exon 4. FosB dramatically enhances the transcription regulation of AP-1 dependent promoters by Jun, while deltaFosB, a truncated form of FosB lacking its C-terminal transactivation domain, suppresses the function of Jun. We and other have shown that FosB and deltaFosB have a distinct function to control the cell fate as well as neuronal functions based on their exogenous expression. To elucidate the authentic function of each protein, it is essential to control each expression separately. We established a mutant mouse embryonic stem (ES) cell line carrying homozygous fosBd/d alleles which encode exclusively deltaFosB, and compared its gene expression profile and phenotypes with fosB-null and wild-type ES cell lines. Both mutant ES cells are devoid of FosB, therefore the common phenotypes between the two mutant ES cells in comparison to wild type depict the effects of FosB deficiency. Opposite phenotypes between the two are considered to be determined by deltaFosB itself. We analyzed the gene expression and cellular function among these two mutant and wild-type ES cells.
Keywords: mouse ES cells (wild type and fosB gene mutant types)

overall_design: Total RNA was purified from ES cells grown in the absence of feeder cells using the Isogen kit (Nippon Gene), according to the manufacturer’s instructions. For DNA microarray experiments, Total RNA (10 microg) were labeled using the Agilent Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. One microgram of each Cy3-labeled wild-type and Cy5-labeled mutant cDNA or each Cy3-labeled mutant and Cy5-labeled wild-type cDNA, respectively, were mixed, then hybridized to Agilent Mouse cDNA Microarrays (G4104A, design file number: 000522R000679, Agilent Technologies) with 8500 unique clones from Incyte’s mouse UniGene 1 clone set, according to the manufacturer's hybridization protocol. After the washing step, the microarray slides were analyzed with an Agilent G2565AA microarray scanner system. These experiments were carried out in duplicate using exchanged dye-labeled cDNA probes (i.e., Cy3 and Cy5 dye-swapping experiments).

first: Yoko

middle: H

first: Katsuhisa

last: Yamazaki

first: Yohei

last: Tominaga

first: Kunihiko

last: Sakumi

first: Yusaku

last: Nakabeppu


title: Recovered Fermentation

summary:
Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen
Keywords: Time course

overall_design: Three replicates of five time points taken at 24, 48, 80, 96 and 144 hours after yeast inoculation. Time points 24 and 48 hours are common to Sluggish fermentation. Time points at 80, 96 and 144 hours are exclusive of this experiment.


title: Microarray gene expression analysis in atrophying rainbow trout muscle: An unique non-mammalian muscle degradation model

status: Public on Oct 04 2006

city: Morgantown

first: Mohamed

last: Salem

state: WV

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

institute: West Virginia University

summary:
Muscle atrophy is a physiological response to diverse physiological and pathological conditions that trigger muscle deterioration through distinct cellular stimuli. Despite different physiological signals, the resulting biochemical changes in atrophying muscle share many common cascades. Muscle deterioration as a physiological response to the energetic demands of fish spawning represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophying  fast-switch muscles from gravid rainbow trout in comparison to sterile fish. A total of 202 unique transcripts were reproducibly identified as 82 up- and 120 down-regulated genes in atrophying muscles. Transcripts having gene ontology biological process identifiers were grouped according to their functions. Muscle deterioration was associated with elevated expression of genes involved in the catheptic and collagenase proteolytic pathways, the aerobic ATP production, buffering, utilization and growth arrest. Whereas, atrophying muscle showed down-regulation of genes encoding serpin (a serine proteinase inhibitor), enzymes of anaerobic respiration, muscle proteins as well as genes required for RNA and protein biosynthesis/processing. Therefore, gene transcription of atrophying trout muscle changed in a manner similar to mammalian muscle atrophy. These changes result in an arrest of normal cell growth, net protein loss, and a decreased dependence on glycolytic cellular respiration characteristic of fast-switch muscle to aerobic respiratory mechanisms. Other changes/mechanisms unique to the fish model were discussed including genes associated with muscle atrophy reported for the first time.
Keywords: muscle atrophy

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design:
Mature female, fertile (diploid) and sterile (triploid) rainbow trout  were collected from Flowing Springs Trout Farm (Delray, WV) during the fall spawning season in early October. Fish from each group were cultured in identical raceways receiving water from a common spring at temperature of 13±3 oC.  Fish were fed ad libitum  using demand-feeders.  As confirmed by dissection, fertile fish were gravid with a gonado-somatic index (GSI) of 15.8 ± SD 0.3 (n=5).  The GSI of sterile fish was 0.3± SD 0.2 (n=5).  White muscle samples from five fish of each group were collected from the dorsal musculature and flash frozen in liquid nitrogen and stored at -80 oC until RNA extraction.
Total RNA was isolated using the Trizol reagent (Invitrogen) according to manufacturer’s instruction. Poly(A)+ RNA was purified using Oligotex mRNA Mini Kit (Qiagen) according to manufacturer’s instruction. A salmonid microarray containing cDNAs representing 16,006 genes selected from atlantic salmon and rainbow trout expressed sequence tag databases  was used to profile changes of gene expression in spawning-induced atrophying muscles.

first: Brett

last: Kenney

first: Caird

last: Rexroad

first: Jianbo

last: Yao


title: MCT-1 enhances translation

city: Baltimore

first: Ronald

middle: B

last: Gartenhaus

address: 655 W Baltimore st

department: Greenbaum Cancer Center

institute: University of Maryland

summary:
MCT-1 is an oncogene initially identified in a human T-cell lymphoma. Subsequently, MCT-1 protein levels were found to be elevated in a subset of diffuse large B-cell lymphoma. Forced expression of MCT-1 has recently been shown to induce cell proliferation as well as activate survival-related pathways protecting lymphoid cells from apoptosis. We document here that MCT-1 interacts with the density-regulated protein (DENR/DRP), containing the SUI1 translation initiation domain, found in many translation initiation factors. MCT-1 contains the PUA domain, a recently described RNA binding domain that is found in several tRNA and rRNA modification enzymes. Our findings established that MCT-1 protein is interacting with the cap complex through its PUA domain and enhances translation. Furtheremore, our data support a putative role for the MCT-1 oncogene in translation and suggests a mechanism for its role in lymphomagenesis.
Keywords: Gene upregulation by MCT-1

overall_design: The aim is to determine which genes are being actively translated when MCT-1 protein is overexpressed. In order to achieve that, we used the polysome associated mRNAs from 293HEK cells expressing MCT-1 or empty vector as control. These mRNAs were then analyzed on a Human apoptosis and cell cycle gene array.

first: Line

last: Reinert


title: Differential gene expression between juvenile and adult dura mater

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

summary:
BACKGROUND: Although reossification of large calvarial defects is possible in children, adults lack this tissue engineering capacity. In this study, the authors compared the differences in gene expression between juvenile and adult dura mater using a mouse cDNA microarray with 42,000 unique elements. METHODS: Non-suture-associated parietal bone was harvested from 6-day-old and 60-day-old mice. The dura mater was carefully dissected from the calvarial disk and snap-frozen. RNA was extracted from pooled dura mater for microarray analysis. The 25 most differentially expressed genes were listed, as were selected bone-related genes. In addition, quantitative real-time reverse-transcriptase polymerase chain reaction confirmation of selected genes-BMP-2, BMP-4, and BMP-7; and osteopontin (OP), osteocalcin (OC), and FGFR-1-was performed. : Juvenile dura mater expressed significantly greater amounts of BMP-2 and OP. Minimal difference in OC expression was observed between juvenile and adult dura mater. Extracellular matrix proteins (Col3a1, 5a1, 6a1, and fibronectin 1), osteoblast differentiation markers (Runx2/Cbfa1, Itm2a, and FGFR-1), and the growth factor Ptn were among other genes with greater expression in juvenile dura mater. Markers of osteoclasts (Acp5, MMP9, Ctsk) and the multiple candidate gene Ntrk2 were also expressed at higher levels in the juvenile dura mater. CONCLUSIONS: These findings suggest a more differentiated osteoprogenitor population to exist along with a greater presence of osteoclasts in the juvenile dura mater relative to adults. In addition to establishing a baseline difference in gene expression between juvenile and adult dura mater, new genes potentially critical to the regenerative potential of juvenile calvaria were identified.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Oliver

last: Aalami


title: Comparative transcriptome analysis of four cell lines

first: Boris

last: Greber

address: Röntgenstraße 20

institute: Max Planck Institute for Molecular Biomedicine

summary:
Hybridisations were carried out to define a fibroblast-like cell type derived from H9 human embryonic stem cells.
Keywords: cell type comparison

overall_design: The four cell lines were grown as detailed in the individual data sheets.

first: Hans

last: Lehrach

first: James

last: Adjaye


title: FGF2 stimulation experiment with CF1 mouse embryonic fibroblasts

summary:
Mouse embryonic fibroblasts stimulated with varying doses of FGF2 in conventional hES cell medium were analysed on whole-genome expression chips to reveal altered expression of genes encoding secreted proteins.
Keywords: Growth factor stimulation experiment

overall_design: as detailed for the individual samples


title: Transcriptional profiling of a Staphylococcus aureus clinical isolate UAMS1 and its isogenic agr and sarA mutants

city: Pearl River

first: Ellen

last: Murphy

state: NY

address: 401 N. Middletown Road

department: Vaccines

institute: Wyeth Research

summary:
The purpose of this study was to compare the global, growth phase-dependent transcriptional profiles of two isolates of Staphylococcus aureus. One isolate is a prototypic laboratory strain named RN6390, and has been used frequently as a model organism for study of staphylococcal physiology and virulence. However, recent studies indicate that RN6390 is not, in general, genotypically or phenotypically representative of clinical isolates of Staphyloccos aureus. Therefore, there is no current comprehensive picture of gene expression patterns in a virulent, clinical isolate of Staphyloccous aureus. For these reasons, we compare the transcriptional profile of RN6390 to that of a virulent clinical isolate, UAMS-1. Also included in this study is profiling of two UAMS-1 regulatory mutants, UAMS-155, and UAMS-929. These strains possess mutations in the accessory gene regulator (agr) and staphylococcal accessory regulator (sarA) genes, respectively. These two genes are well described global regulatory molecules that are reported to play important roles in controlling virulence factor production and biofilm formation in Staphylococcus aureus. However, most study of these two molecules has been limited to laboratory strains such as RN6390. For these reasons, this study also includes transcriptional profiling of UAMS agr and sarA mutants.
Keywords: Comparative, growth phase-dependent transcriptional profiling of bacterial strains and isogenic regulatory mutants

overall_design: For the experiments comparing UAMS-1 to RN6390, two replicate hybridizations were performed using two independently isolated RNA samples were performed for each growth phase and each strain. Likewise, for both the agr and sarA profiling experiments, two replicate hybridizations were performed using two independently-isolated RNA samples were performed for each growth phase and each mutant.

last: Cassat

first: Paul

last: Dunman

first: Katherine

last: Palm

first: Steven

last: Projan

first: Mark

last: Smeltzer

first: Karen

last: Beenken

first: Kenneth

last: Bayles


title: Genome-Wide Mapping of Growth Regulated Genes in Burkholderia pseudomallei

city: Singapore

first: Fiona

last: Rodrigues

address: 60 Biopolis Street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

summary:
Many microbial pathogens express specific virulence traits at distinct growth phases. To investigate the molecular pathways linking bacterial growth to pathogenicity, we characterized the genome-wide growth transcriptome of the tropical pathogen Burkholderia pseudomallei (Bp), the causative agent of melioidosis. Using fine-scale sampling, approximately 17% of all Bp genes were found to display regulated expression during growth, manifested primarily as discrete waves of gene expression tightly associated with distinct growth phases and transition points. A functional curation of these clusters provided evidence of a global ‘just-in-time’ production strategy to ensure the synthesis of molecular constituents only when needed.  We observed regulation of multiple virulence factors at all growth phases, and by analyzing the early-phase transcriptome data, we identified and experimentally validated serC as a novel virulence factor in mice. Immunization of mice with serC-disrupted Bp also conferred protection against subsequent challenges with different wild-type Bp strains, demonstrating the potential utility of the serC mutant as an attenuated vaccine. We found a significant bias in early phase genes on Chromosome 1, supporting its proposed role as the ancestral Burkholderia chromosome, and utilized a chromosomally ordered co-expression metric to define ~100 putative operons throughout the Bp genome. These results extend our knowledge of virulence pathways in Bp, and suggest that molecular events at all growth phases, including early phase, are likely to play important roles in microbial pathogenicity."
Keywords: Time Series Comparison Bp (K96243)

overall_design: All time series sample were assessed on Bp_array_v2

first: F

first: M

last: Sarkar-Tyson

first: SV

last: Harding

first: SH

last: Sim

first: HH

last: Chua

first: CH

last: Lin

first: H

last: Xu

middle: K

last: Krishna

first: K

last: Sung

last: Yu

first: W

last: Chen

first: TP

last: Atkins

first: RW

last: Titball

first: P

last: Tan


title: Leu3 ChIP-chip

status: Public on Sep 08 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by genome tiling array

summary:
Detect Leu3 targets in S. cerevisiae.
Keywords: ChIP-chip

overall_design:
7 replicates of CHIP-chip of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP tagged
anti-MBP(Abcam65)

first: Xiao

last: Liu

first: Cheol-Koo

last: Lee

first: Neil

last: Clarke


title: furB knockout

city: Padova

first: Elisa

last: Dainese

state: Veneto

address: Via Gabelli 63

department: Microbiology and virology

institute: Univerity of Padua

summary:
We used DNA microarrays to define the M. tuberculosis FurB regulon.
For this porpouse we constructed a M. tuberculosis strain where furB was disrupted and its transcriptional profile was compared on DNA microarray with the transcriptional profile of its parental strain (H37Rv). A total of 32 genes included in 16 putative transcription units were shown to be up-regulated in the mutant relative to H37Rv. No repressed genes were identified. Seven representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was clearly higher in the furB mutant strain relative to H37Rv
Keywords: comparative genomic hybridization

overall_design: Hybridizations were performed using RNA extracted from three different biological samples. Each sample was hybridized twice through reverse labelling of the respective cDNAs.

first: Riccardo

last: Manganelli


title: Response to low dose ionizing radiation in male mouse

city: Augusta

first: Yutao

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

summary:
Male mice 10-14 weeks of age were exposed in vivo to 10 rad X-ray.  The objective is to extract information on gene networks from the microarray data.
Keywords: Ionizing radiation

overall_design: Control mice were sham-exposed.  Spleen was harvested 3.5 hrs post-irradiation.  Each hybridization consists of one control mouse and one exposed mouse randomly paired to form a biological replicate.  Each biological replicate was hybridized in duplicate, incorporating a dye swap to control for dye-specific effects.

first: Brynn

last: Voy


title: Estrogen Receptor binding site mapping by ChIP-on-chip

status: Public on Sep 05 2006

first: Vinsensius

last: Vega

address: 60 Biopolis Street

summary:
MCF-7 breast cancer cells were treated with estradiol and then chromatin immunoprecipitation assays were performed to isolate estrogen receptor and associated genomic DNA binding sites.
Keywords: ChIP-on-chip samples

overall_design: ChIP DNA fragments were end-labeled with biotinylated nucleotides and then labeled with Cy3-avidin and hybridized to human promoter arrays to detect estrogen receptor binding sites.

first: Chin-Yo

first: Say-Li

last: Kong


title: E. coli K-12 mutant ycfR biofilm vs wild type 15 hr LB glu biofilm cells

status: Public on Sep 26 2006

city: College Station

first: Rodolfo

middle: Garcia

last: Contreras

email: Rodolfo.Garcia@chemail.tamu.edu, Xuesong.Zhang@chemail.tamu.edu, Thomas.Wood@chemail. tamu.edu

address: Room 502 Jack E. Brown building 3122 TAMU

department: Chemical Engineering

institute: Texas A and M University

summary:
E. coli K-12 BW25113 mutant strain ycfR expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. All samples cultured in LB glu with glass wool
Keywords: Cell type comparison

overall_design:
Strains: E. coli K-12 BW25113 wild type and mutant ycfR
Medium: LB glu
Biofilm grown on glass wool
Time: 15 hr
Cell type: biofilm

first: Xue-Song

last: Zhang

last: Garcia Contreras

first: Thomas

last: Wood


title: M cell, FAE and VAE expresssion profiles

status: Public on Sep 27 2006

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

country: Ireland

institute: UCC

summary:
M cells are specialized epithelial cells occurring in the follicle-associated epithelium (FAE) overlying the Peyer’s patch. M cells transcytose macromolecules and microorganisms from the gut lumen to the underlying organized mucosal lymphoid follicles. Thus, M cells are a portal to the mucosal immune system and are crucial for the study of pathogenesis and mucosal vaccine design. Although characterization has been primarily performed to date using immunohistochemistry and in vitro cell culture techniques, little is known about the genetic factors in vivo distinguishing M cells from other intestinal epithelial cells. Our aim was to develop a method to isolate viable murine M cells for the purpose of generating an expression profile of murine M cells compared to FAE enterocytes and villus associated enterocytes (VAE).
Peyer’s patches were microdissected from murine small intestine and the FAE isolated by enzymatic digestion. M cells were isolated using magnetic bead cell sorting of FITC-UEAI lectin stained FAE. Analysis of M cell, FAE and VAE gene expression was performed using cDNA arrays and Real-time RT-PCR.
Altered expression of several genes involved with cell structure, differentiation and cell-interaction was observed. In murine M cells; E-cadherin, Ccl20, Ccl25 and Lamr1 were increased in expression, compared to the neighboring FAE enterocytes. Cxcr4 and PIN were found increased, with Il-18 and Bad decreased in expression, in both M cell and FAE enterocytes compared to VAE.This gene expression profile of in vivo murine M cells, FAE and VAE provides a portal into M cell biology previously undiscovered. This expression profile of M cells will aid in understanding pathogen-host immune interactions and contribute to the understanding of intestinal M cell biology.
Keywords: Cell type comparison

overall_design: The aim of the experiment was to identify the expression profile of M cells related to FAE , VAE and PPL.  Cells were isolated and expression profiles determined using cDNA arrays. Each normalised expression value represents a duplicate of the sample analysed .Expression changes were confirmed by RT-PCR on seperate samples isolated using the same technique

middle: A

middle: G

last: Morgan


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

status: Public on Sep 01 2006

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

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

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

first: Steven

middle: T

last: Pullan

first: Jeffrey

middle: R

last: Green


title: Time course microarray approach comparing the ectopic expression and loss-of-function of gcm to wildtype

status: Public on Sep 20 2006

city: Mainz

first: Angela

last: Becker

address: Becherweg 32

department: Institute of Genetics

institute: University of Mainz

summary:
The determination of glial fate in the developing embryonic nervous system of Drosophila is dependent on the master regulatory gene glial cells missing (gcm). gcm encodes a transcription factor and serves as a binary switch by inducing the glial fate and repressing the neuronal pathway. The ectopic expression of gcm throughout the CNS leads to excessive glia on the cost of presumptive neurons, whereas gcm loss-of-function embryos lack nearly all lateral glial cells. To date only little is known about the genetic program underlying glial differentiation.
In order to identify glial specific genes downstream of gcm we performed a whole-genome microarray approach, where we compared the gcm gain-of-function situation (GOF) and, for the first time, the gcm loss-of-function (LOF) against wildtype in a time course experiment throughout embryogenesis. Intense filtering of differentially regulated genes on behalf of statistics as well as developmental means such as profile of differential regulation enabled us to identify more than 40 novel glial genes. The confirmation of these genes by in situ hybridization revealed temporal expression profiles in all or subsets of glial cells. We give a detailed description of the expression patterns of the candidate genes and adress their regulation in the glial pathway in different glial mutant backgrounds. Additionally we started to analyze mutant phenotypes of candidate genes to clarify their functional relevance for glial differentiation.
Keywords: Drosophila,gliogenesis,time course,loss-of-function,gain-of-function

overall_design:
Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. For wt control we pooled mRNA from UAS-gcm stock B5446 and Gal4-line MZ1060 in equal amounts.
Sample collection:
Embryo samples from the MZ1060 x B5446, B5446 and MZ1060 were collected in parallel as one-hour egg lays at 25°C, which were allowed to develop to the desired stage at 29°C/18°C.
gcmN7-4 mutant flies were balanced with either Kr-GFP (for stages 10 to 13) or Ubi-GFP (for stages 14 to 16) balancer chromosomes. Eggs were collected as described above, transferred into PBS buffer supplemented with 0.3% Tween 20 and homozygous mutant embryos were automatically sorted with the CopasTM Select embryo sorter (Union Biometrica, Somerville, MA, USA) by their lack of GFP-expression.
First total RNA was isolated from all samples using the Rneasy Kit and then mRNA was isolated using the Oligotex Kit (both Qiagen,Hilden,Germany)
Microarray hybridization:
At least four independent experiments were performed for each of the 8 different stages
(embryonic stages 9 to 16) in competitive hybridizations against the pooled wildtype control of the same stage.
At least one dye swap was included in each of the repetitions.
We used the indirect labeling method, with 4,5µg random hexamer primer and 0,75µg Poly-dT primer ( both Invitrogen, Karlsruhe, Germany) added to 1µg mRNA.
For hybridization, the labeled cDNAs were taken up in SlideHyb buffer #1 (Ambion, Woodward, USA), denatured at 95°C for 5min,
and applied to the array. Hybridization was performed in appropriate chambers (TeleChem) in a waterbath at 55°C over night.
The hybridized glass slides were scanned on a ScanArray 5000 (Perkin Elmer, Wellesley, USA) using the ScanArray software (Version 3.1).
The resulting images (TIFF format, 16-bit grayscale) for each channel - Cy5 (632nm) and Cy3 (532nm) - were analyzed
further with the GenePix software (Version 5.0; Axon Instruments, Union City, USA).
As each microarray contains two replicates for each gene, we used the standard deviation (SD)
of their dye-ratio (Cy5/Cy3) to filter for reproducible hybridizations. Only if at least 30% of all genes on the array
had a SD of log(632/532) of less than 1/3 between the replicates was the microarray included for further analysis.

first: Benjamin

last: Altenhein

first: Boris

last: Beckmann

first: Christian

last: Busold

first: Jörg

last: Hoheisel

first: Gerd

last: Technau


title: Global variation of copy number in the human genome_EA

city: Santa Clara

first: Fan

last: Shen

state: CA

address: 3420 Central Expressway

institute: Affymetrix, Inc

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

summary:
Identify and categorize copy number variation in normal populations
Keywords: Copy number variation detection

overall_design: 270 Hapmap samples were hybridized to 500K EA mapping arrays (Nsp and Sty) to identifying variable copy number regions in the genome.  10 Hapmap samples were hybridized to 500K EA mapping arrays in triplicate to determine reproducibility (technical replicates).  NA15510 and NA10851 were hybridized to 500K EA mapping arrays in triplicate for parameter-tuning and validation of algorithm.


title: Molecular characterization of adult mouse subventricular zone progenitor cells during the onset of differentiation

status: Public on Sep 04 2006

city: Harlow

first: Ignacio

last: Munoz-Sanjuan

state: Essex

address: Terlings Park

department: Molecular & Cellular Neuroscience

institute: Merck Sharp & Dohme

summary:
Adult mouse subventricular zone (SVZ) neural progenitor cells (NPCs) retain the capacity to generate multiple lineages in vitro and in vivo. Thus far, the mechanisms involved in the regulation of these cells have not been well elucidated. We have carried out RNA profiling of adult SVZ cell cultures undergoing differentiation, to identify pathways that regulate progenitor cell proliferation and to define a set of transcripts that can be used as molecular tools in the drug discovery process.  We carried out a stepwise stratification of the results to identify transcripts specifically enriched in NPCs and validated some of these using comparative literature analysis, quantitative PCR and immunological techniques. The results show a set of transcription factors, secreted molecules, and plasma membrane markers which are differentially regulated during differentiation. Pathway analysis highlights alterations in IGF, Wnt and TGFbeta signalling cascades. Further characterization of these components could provide greater insight into the mechanisms involved in the regulation of neurogenesis in the adult brain.
Keywords: time-course, differentiation comparison

overall_design: Mouse subventricular zone neural stem cells cultures were prepared from C57Bl6/J mice (Johansson et al.,1999) and cultured in suspension in DFEM/F12 1:1 supplemented with PSF, B27 supplement and EGF/ FGF-2 at 20ng/ml. RNA was isolated from either expanding neurospheres in the presence of FGF2 and EGF (Reynolds and Weiss, 1992; Gritti et al., 1999), or from cultures induced to differentiate upon growth factor withdrawal or serum exposure, either after 24 hours (in suspension, to avoid changes induced by substrate attachment) or 5 days (as adherent cultures in poly-lysine and laminin-coated plates). Experiments were conducted in triplicate from independent batches of SVZ preparations. As a control for potential effects of media changes, a set of identical cultures were included where cells were grown for a further 24 hours in fresh media containing FGF2 and EGF (20 ng/ml each, normal growth media, NGM).  Fluorescently labelled aRNA from individual samples were competitively hybridised against a pool of labelled aRNA from undifferentiated reference (starting) material on custom Agilent microarrays representing ~22,500 mouse transcripts. Technical, fluor-reversed hybridisations were performed for every sample.

first: Timothy

middle: P

last: Bonnert

first: James

last: Bilsland

first: Paul

middle: C

last: Guest

last: Heavens

first: Donna

last: McLaren

first: Charlotte

last: Dale

first: Matthew

last: Thakur

first: George

last: McAllister


title: Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1.

status: Public on Sep 23 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary:
The segregation of maternal centromeres away from the paternal ones during the first division of meiosis depends on the attachment of sister kinetochores to microtubules emanating from the same spindle pole. In budding yeast monopolar attachment requires the recruitment to kinetochores of a protein complex called monopolin. The biochemical function of monopolin was unknown. Here, we have identified the casein kinase I Hrr25 as a hitherto unknown subunit of monopolin. Hrr25 differs from other monopolin components by its enzymatic activity and strong evolutionary conservation. We demonstrate that Hrr25’s kinase activity and its interaction with monopolin are both required for monopolar attachment. Accordingly, Hrr25 is associated with centromeres in meiosis I. Our results revealed a surprising new role for casein kinases and provide a hypothesis for the mechanism of monopolar attachment during meiosis I in sexually reproducing organisms: casein kinase I-dependent phosphorylation of kinetochore proteins.
Keywords: ChIP-chip, Meiosis, Cell cycle, Saccharomyces cerevisiae, Chromosome VI tiling array, Hrr25, Mam1

overall_design:
•	Experimental factors
	Distribution of the Hrr25 and Mam1 at Meiosis I. Distribution of Hrr25 in Mam1 deletion mutant (S.cerevisiae). All experiments were performed in cells with the same genetic background (Saccharomyces cerevisiae SK1).
•	Experimental design
	ChIP analysis: In all cases, hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Cerevisiae chromosome VI array was used.

•	Quality control steps taken
	Confirmation using different subunits of the same complex. Confirmation of protein distribution using deletion mutant strain. Checking of the ChIP fraction by Western blotting. Mock hybridisation of samples immunoprecipitated from cells containing no tag recognized by antibody used. Swapping SUP fraction. Q-PCR.

Samples used, extract preparation and labelling:
•	The origin of each biological sample
	Saccharomyces cerevisiae (SK1).
•	Manipulation of biological samples and protocols used
	Chromatin immunoprecipitation (ChIP) and hybridization to Affimetrix high-density oligonucleotide arrays of S. cerevisiae chromosome VI were performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).
•	Technical protocols for preparing the hybridization extract
	The chromatin-immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC. DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.
•	Hybridization procedures and parameters:
	Hybridization, blocking and washing were carried out as previously described (http://everythingchromosomevi.gsc.riken.go.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
•	Measurement data and specifications:

	Arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the raw data files can be downloaded from GEO database. The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site at http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf. The analysis is available on request. For the ChrVI array, one unit for analysis (locus) was set to 300bp. Fold change value, change p-value, and detection p-value for each locus were obtained by primary analysis. For the discrimination of positive and negative signals for the binding, we used three criteria as follows. First, the reliability of the signal strength was judged by detection p-value of each locus (p-value≤0.025). Secondly, reliability of binding ratio was judged by change p-value (p-value≤0.025). Thirdly, clusters consisting of at least 900bp contiguous loci that satisfied the above two criteria were selected, because it is known that a single site of protein-DNA interaction resulted in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.

•	Array Design:

		General array design: in situ synthesized arrays by Affymetrix
		Availability of arrays: commercially available from Affymetrix
		Location and ID of each spot on arrays: available from Affymetrix on 			request
		Probe type: oligonucleotide
		The arrays used in this study can be purchased from Affymetrix:
			Chromosome VI S.cerevisiae: rikDACFC6, P/N# 510636

first: Mark

last: Petronczki

first: Joao

last: Matos

first: Saori

last: Mori

first: Juraj

last: Gregan

first: Aliona

last: Bogdanova

first: Martin

last: Schwickart

first: Karl

last: Mechtler

first: Wolfgang

last: Zachariae

first: Kim

last: Nasmyth


title: Gene expression in the duodenum of sheep genetically resistant or susceptible to nematodes

status: Public on Sep 06 2006

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

summary:
This experiment compared gene expression in the duodenum of [1] weaned genetically resistant sheep and weaned genetically susceptible sheep (84 days old) [2] genetically resistant sheep and genetically susceptible sheep that have been naturally challenged once with nematodes (175 days old) and [3] genetically resistant sheep and genetically susceptible sheep that have been naturally challenged twice with nematodes (276 days old).
Keywords: resistant v susceptible

overall_design: At each time point (T = 84, 175, 276 days) a four factorial design was used with four resistant animals and four susceptible animals. Each animal in the resistant group was compared to each animal in the susceptible group incorporating dye swaps. At T = 84 the platform GPL4072 was used. At T = 175 days the platform GPL4076 was used and at T =276 days the platform GPL4077 was used.

middle: M

first: Ken

last: Dodds

first: Allan

last: Crawford

first: John

last: McEwan


title: Embryo study

city: New Havem

first: Nyam-Osor

last: Chimgee

address: 266 Whitney Ave

department: MCDB

institute: Yale University

summary:
knock-out of Gtf2iRD1 or TFII-I in embryos
Keywords: treated vs.untreated

overall_design:
2 biological replicates of Gtf2iRD1 knockout vs wild type embryos
2 biological replicates of TFII-I knockout vs wild type embryos


title: Identification of differentially expressed genes in fetal and postnatal pig skeletal muscle

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

summary:
Fetal myogenesis and postnatal skeletal muscle hypertrophy in growing pigs are critical yet poorly understood processes.  Global gene expression analyses will increase understanding of these processes by identifying key genes and pathways controlling skeletal muscle development.  For this study, a pig 70-mer oligonucleotide microarray was used to identify differentially expressed genes in hind limb skeletal muscle of pigs at 60 days of gestation and 7 weeks of age.  This oligonucleotide microarray experiment revealed 162 genes that were differentially expressed between 60 day fetal and 7 week postnatal samples.  Relative real-time RT-PCR was used to confirm differential expression of three genes.  This experiment identified genes exhibiting different developmental patterns of gene expression in pig skeletal muscle.
Keywords: developmental study

overall_design: Oligonucleotide microarrays used for this study consisted of 13,297 70-mer oligos (Pig Array-Ready Oligo Set v. 1.0 and Pig Oligo Extension Set v. 1.0, Qiagen, Inc., Valencia, CA) each spotted once on a single slide .  Controls included 76 Arabidopsis thaliana gene spots, 17 beta tubulin spots, 17 glyceraldehyde-3-phosphate dehydrogenase spots, 85 heat shock protein gene spots, 69 ribosomal protein gene spots, 112 randomly generated negative control spots and 470 blanks.  The oligonucleotide microarray was screened with samples obtained from pigs at 60 days of gestation and 7 weeks of age postnatal (n = 3 per age).  Six oligonucleotide microarray slides were screened.  All samples were used twice, labeled once with Cy3 and once with Cy5, and each 60 day gestation sample was randomly paired with two different 7 week postnatal samples.

first: Valencia

last: Rilington

first: Nancy

last: Raney

first: Robert

middle: J

last: Tempelman

first: Matthew

last: Doumit

middle: W


title: TOS9 Regulates White-Opaque Switching in Candida albicans

city: Urrbrae

first: Anthony

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

summary:
	In Candida albicans, the a1-alpha2 complex represses white-opaque switching as well as mating.  A ChIP-chip strategy was, therefore, used to screen for genes with a1-alpha2 binding sites and expression patterns consistent with a master switch gene (MSG).  Of 51 genes identified with an a1-alpha2 binding site, one gene, TOS9, also referred to as EAP2, exhibited an expression pattern consistent with a MSG.  TOS9 is expressed in opaque, not white a/a and alpha/alpha cells and Tos9p localizes to the opaque cell nucleus.  Deletion of TOS9 blocks cells in the white phase, and misexpression in the white phase of the parent tos9+/tos9+ strain results in mass conversion to opaque.  Expression of TOS9 under control of a MET promoter rescues the TOS9 null mutant tos9-/tos9- phenotype.  Temperature-induced mass conversion of opaque to white in the parent strain results in the immediate cessation of TOS9 transcription, and loss of Tos9p prior to the point of commitment to white (the switch event), which occurs at the time of the second cell doubling.  Misexpression of TOS9, as well as inhibition of the second round of DNA replication inhibits the temperature-induced switch from opaque to white.  Based on these observations, a model is developed for the regulation and role of TOS9 in switching.
Keywords: ChIP chip

overall_design: ChIP-chip was performed on a1 and alpha2 from C. albicans. Three biological replicates were performed for each factor in each species with one replicate representing a dye swap.

first: Thyagarajan

last: Srikantha

first: Karla

last: Daniels

first: Claude

last: Pujol

first: Wei

last: Wu

first: Michael

last: Seringhaus

first: Mark

last: Gerstsin

first: Song

last: Yi

last: Snyder

first: David

last: Soll


title: Identifying transcription factor functions and targets by phenotypic activation

status: Public on Sep 14 2006

city: San Francisco

first: Esther

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

summary:
Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes and pathways induced by individual TFs that does not require knowledge of their normal activation cues. Microarray analysis of 55 yeast TFs that caused a growth phenotype when overexpressed showed that the majority caused increased transcript levels of genes in specific physiological categories, suggesting a mechanism for growth inhibition. Induced genes typically included established targets and genes with consensus promoter motifs, if known, indicating that these data are useful for identifying potential new target genes and binding sites. We identified the sequence 5'-TCACGCAA as a binding sequence for Hms1p, a TF that positively regulates pseudohyphal growth and previously had no known motif. The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology.
Keywords: phenotypic activation

overall_design: We analyzed 55 TF overexpression strains and 51 non-essential TF deletion mutants by microarray with fluor-reversal replicates. See Chua et al. (2006), PNAS PMID: 16880382 for details.

first: Gordon

last: Chua

first: Quaid

last: Morris

first: Richelle

last: Sopko

last: Robinson

first: Owen

last: Ryan

first: Brendan

last: Frey

first: Brenda

last: Andrews

first: Charles

last: Boone

first: Timothy

last: Hughes