title: Wild type yeast and H3del(1-28) and H4del(2-26) yeast grown in complete synthetic media

status: Public on Feb 10 2006

city: Albany

first: Randall

middle: Heywood

last: Morse

institute: Wadsworth Center

summary:
Yeast lacking the H3 or H4 amino termini, and corresponding wild type strains, were grown in synthetic media.  These conditions induce Gcn4-activated transcription.
Keywords: Genetic modification

overall_design: Three replicates of the H4del(2-26) and corresponding wild type strains, and four replicates of the H3del(1-28) and corresponding wild type strains, were performed.  Note the strains are congenic, but differ in whether the histones were present on TRP1 marked (H4) or LEU2 marked (H3) plasmids.  Samples were analysed using Affymetrix S98 microarrays.

first: Cailin

last: Yu

middle: H


title: Carbon-limited anaerobic/aerobic growth of S.cerevisiae-New set

status: Public on May 23 2006

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary:
Addition of 3 new arrays made from carbon limited chemostat of CENPK113-7D and 3 new arrays made from aerobic carbon limited chemostat of CENPK113-7D Complmentary data to the data of the serie GSE1723.
Keywords: Chemostat-based transcriptome response comparison

overall_design:
GSM108368, GSM 108369 and GSM108370 are biological replicates
GSM108392, 108393, 108394 are biological replicates

Complmentary data to the data of the serie GSE1723.

first: Marinka

last: Almering

first: Pascale

middle: A

last: Daran-Lapujade

first: Jack

middle: T

last: Pronk

first: SiewLeng

last: Tai


title: LD/DD time course of cn bw Drosophila

status: Public on Feb 03 2006

city: Southampton

first: Herman

last: Wijnen

state: Hampshire

address: Life Sciences Building 85 - Highfield Campus

department: Centre for Biological Sciences

country: United Kingdom

institute: University of Southampton

summary:
Mechanisms composing Drosophila's clock are conserved within the animal kingdom. To learn how such clocks influence behavioral and physiological rhythms, we determined the complement of circadian transcripts in adult Drosophila heads. High-density oligonucleotide arrays were used to collect data in the form of three 12-point time course experiments spanning a total of 6 days. Analyses of 24 hr Fourier components of the expression patterns revealed significant oscillations for 400 transcripts. Based on secondary filters and experimental verifications, a subset of 158 genes showed particularly robust cycling and many oscillatory phases. Circadian expression was associated with genes involved in diverse biological processes, including learning and memory/synapse function, vision, olfaction, locomotion, detoxification, and areas of metabolism. Data collected from three different clock mutants (per0, tim01, and ClkJrk), are consistent with both known and novel regulatory mechanisms controlling circadian transcription (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71).
For more information see also http://biorhythm.rockefeller.edu
Keywords: Time course

overall_design:
cn bw flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lights on
during the LD cycle and Circadian time 0 (CT0) as the time corresponding to
subjective lights-on during freerun in DD, time courses were collected in a ZT4-
ZT8-ZT12-ZT16-ZT20-ZT24-CT4-CT8-CT12-CT16-CT20-CT24
 schedule. Heads
were isolated by breaking up frozen flies and passing them through a set of
sieves. RNA was prepared using Rnazol (Tel-test) or Trizol (Life Technologies) extraction. Additional purification of the RNA samples was
achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA
probe was generated from 25 μg of purified RNA and hybridized as described
previously (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71).
For more information see also http://biorhythm.rockefeller.edu

first: Adam

last: Claridge-Chang

first: Catharine

last: Boothroyd

first: Michael

middle: W

last: Young


title: LD/DD time course of y w Drosophila #2

overall_design:
y w flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lights on
during the LD cycle and Circadian time 0 (CT0) as the time corresponding to
subjective lights-on during freerun in DD, time courses were collected in a ZT4-
ZT8-ZT12-ZT16-ZT20-ZT24-CT4-CT8-CT12-CT16-CT20-CT24 schedule. Heads
were isolated by breaking up frozen flies and passing them through a set of
sieves. RNA was prepared using Rnazol (Tel-test) or Trizol (Life Technologies) extraction. Additional purification of the RNA samples was
achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA
probe was generated from 25 μg of purified RNA and hybridized as described
previously (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71).
For more information see also http://biorhythm.rockefeller.edu


title: LD/DD time course of y w Drosophila #1

overall_design:
y w flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lightson
during the LD cycle and Circadian time 0 (CT0) as the time corresponding to
subjective lights-on during freerun in DD, time courses were collected in a ZT2-
ZT6-ZT10-ZT14-ZT18-ZT22-CT2-CT6-CT10-CT14-CT18-CT22 schedule. Heads
were isolated by breaking up frozen flies and passing them through a set of
sieves. RNA was prepared using Rnazol (Tel-test) or Trizol (Life Technologies) extraction. Additional purification of the RNA samples was
achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA
probe was generated from 25 μg of purified RNA and hybridized as described
previously (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71).
For more information see also http://biorhythm.rockefeller.edu


title: X linked dystonia parkinsonism

city: Tokushima

first: Gen

last: Tamiya

state: Tokushima

address: Kuramoto

department: Department of Neurology, Graduate School of Medicine

country: Japan

institute: Tokushima University

summary:
Investigation of expression profile in XDP brains.
Keywords: an XDP patient and neurologically normal control

overall_design: Comparison between XDP and control tissues.


title: Microarray-assisted Cloning of Mutants: Expression Profiling of tom-1 and unc-43

status: Public on Jan 02 2006

city: Boston

last: Dybbs

state: MA

department: Molecular Biology

country: USA

institute: Mass General Hopital

summary:
Analysis of gene expression data in two C.elegans mutant strains: KP3293 tom-1(nu468) and KP3365 unc-43(n1186); hif-1(nu469).  These results support the utility of microarray hybridizations to facilitate positional cloning.
Keywords: other

first: Joshua

last: Kaplan

first: John

last: Ngai


title: Expression profile of erythrocytes

status: Public on Feb 01 2006

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

country: Germany

institute: BMFZ

summary:
Human erythrocytes lack a nucleus and are considered to be incapable of protein synthesis. Nevertheless these anucleated cells regulate a number of gene expressions as well as posttranscriptional and postranslational modifications of proteins. We evaluated which genes are transcribed in mature erythrocytes.
Keywords: expression profile

overall_design: Seven independent samples from healthy human donors were analyzed. Genes that had a detection call "present" in all seven array experiments were selected for further analysis.

first: Svetlana

last: Kabanova

first: Petra

last: Kleinbongard

first: Sonja

last: Balke

first: T.

last: Jax

first: M.

last: Kelm


title: Pac1+/+ versus Pac1-/- TG-macrophages_LPS 6h

status: Public on Jan 10 2006

city: Darlinghurst

first: Charles

middle: Reay

last: Mackay

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute for Medical Research

summary:
LPS-stimulated macrophages from Pac1+/+ and Pac1-/- mice were compared to assess gene expression changes in the absence of PAC-1 (also known as Dual specificity phosphatase 2).
Keywords: Comparison of Pac1+/+ with Pac1-/- activated macrophages

overall_design: Age matched Pac1+/+ and Pac1-/- littermates were used to obtain equal numbers of thiolycollate-elicited macrophages. Pure populations of macrophages were stimulated with 100 ng/ml of LPS for 6 hours. 6 hours was chosen to assess mainly inflammatory gene expression.

first: Kate

middle: L

last: Jeffrey

middle: R


title: Twist Heat Shock in C. elegans

status: Public on Jan 01 2006

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Three biological replicates of each treatment were generated and the expression profiles were determined using Affymetrix C. elegans arrays.  Comparisons between the sample groups allow the identification of genes expression patterns.
Keywords: repeat

overall_design: Two genotype of C. elegans with 3 biological replicates that were treated with or with no heat shock

first: Ann

last: Corsi

last: Krause


title: WT Vs TIM-MJD

status: Public on Nov 21 2005

city: Jerusalem

first: Sebastian

last: Kadener

address: Alexander Silberman Inst. of Life Sciences, Edmund Safra Givat Ram Campus

department: Biological Chemistry

country: Israel

institute: Hebrew University

summary:
WT flies or flies of the strain Tim-gal4; UAS-MJD78Q. All samples were collected at ZT16 after 3 days of training in LD conditions.
Keywords: ordered

last: Rosbash

first: Elzbieta

last: Kula

first: Juan

last: Botas

first: Jeffrey

last: Hall

last: Pyza

first: Adriana

last: Villella


status: Public on Dec 04 2005

city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

institute: National Institute of Biomedical Innovation

summary:
Analysis of ZM behavioral differentiation. 3-5 days nonvirgin female fly heads.
Keywords: other

first: Mickael

last: Kohn

first: Anthony

last: Greenberg

first: Joshua

last: Shapiro

first: Chung-I

last: Wu


title: Mouse Tumor Dataset

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

summary:
previously published mouse data
Pubmed IDS: 12754511, 12839964
Keywords: disease state analysis

overall_design: see Black, EP, et.al., Cancer Res. 2003 Jul 1;63(13):3716-23 and Huang, E., et.al. Nat Genet. 2003 Jun;34(2):226-30.


title: Global effects of spt10 mutations on gene expression in budding yeast.

status: Public on Dec 22 2005

first: David

middle: Johannes

last: Clark

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

summary:
Using yeast strains based on the protease-deficient strain BJ5459 (= wild type), the effects of the spt10-null and spt10-C388S mutations on global gene expression were assessed and compared.  BJ5459 (wild type) and BJ-SPT10(C388S)-HA cells were grown in synthetic complete medium to A600 = 0.6. RNA was prepared using an RNeasy kit (Qiagen).  Biotinylated cRNA was prepared from three independently prepared sample pairs and hybridised to Affymetrix S98 arrays and detected using fluorescently labelled streptavidin.  The wild type and the spt10-C388S average signals each represent the average of the signals from three arrays. The P-value is an indicator of the statistical significance of the difference between the average signals for wild type and the C388S mutant. The lower the value, the greater the significance. The gene descriptor is provided by Affymetrix.
Keywords: mutant yeast strain comparison

overall_design: Three RNA samples from wild type, spt10-null and spt10-C388S cells were prepared independently on three occasions. These nine RNA samples were used to make cRNA and hybridised separately to Affymetrix S98 arrays at the same time.

first: Geetu

last: Mendiratta

first: Peter

last: Eriksson

first: Chang-Hui

last: Shen

middle: J


title: Short term perturbation

status: Public on Dec 16 2005

first: Jean-Marc

last: Daran

summary:
Study of the short term (within the first 330 seconds)  transcriptional response of S.cerevisiae  upon a sudden addition of glucose.
Keywords: glucose pulse, chemostat culture, glucose catabolite repression

overall_design:
Chemostat cultivation – Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30˚C, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase.
Glucose pulse experiment - At the age of 7 dilution times, the steady state chemostat culture was perturbed by the addition of 20 ml of glucose solution (200 g/l) to the fermentor so that the residual glucose concentration was suddenly increased to about 1 g/l (5.56 mM). The glucose solution was rapidly injected by a pneumatic system (< 1 s). Samples were taken prior to the glucose pulse (steady state samples) and within 360 s transient after the perturbation.

Verduyn,C., Postma,E., Scheffers,W.A., and van Dijken,J.P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.

middle: P

last: Kresnowati

first: W.

last: van Winden

last: Almering

middle: S

last: Daran-Lapujade

first: J.

last: Heijnen

last: Pronk

first: JM


title: Expression data from early Drosophila embryo

city: Marseille cedex 9

first: Fanny

last: PILOT

address: Campus de Luminy case 907

department: Institut de Biologie du Développement de Marseille (IBDM)

country: France

institute: UMR6545 CNRS-Université de la Méditerrannée

summary:
Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium.
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: time course

overall_design: Drosophila embryos were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at five time-points: before pole cell formation, i.e. before zygotic transcription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisation and at the beginning (T3) and the end (T4) of gastrulation.

first: Thomas

last: LECUIT

first: Christelle

last: THIBAULT

last: PHILIPPE

first: Celine

last: LEMMERS

first: Jean-Paul

last: CHAUVIN


title: Logic of the yeast metabolic cycle

status: Public on Oct 27 2005

city: Dallas

first: Benjamin

last: Tu

state: TX

address: 5323 Harry Hines Blvd.

department: Biochemistry

institute: UT Southwestern Medical Center

summary:
affymetrix gene expression data over three successive metabolic cycles
Keywords: yeast, time course, metabolic cycle

overall_design: 12 time intervals per cycle, ~25 min per time interval

first: Andrzej

last: Kudlicki

first: Maga

last: Rowicka

first: Steven

last: McKnight


title: 4Y vs 1-11 combined CD4 sort

status: Public on Nov 05 2005

city: Stanford

first: Lawrence

last: Steinman

state: CA

address: 279 Campus Drive, Rm B002

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

summary:
Local catabolism of the amino acid tryptophan (Trp) by indoleamine-2,3-dioxygenase (IDO) is considered an important mechanism of regulating T cell immunity. We show that IDO transcription was increased upon stimulation of myelin-specific T cells with tolerogenic altered self-peptides. Catabolites of Trp suppressed proliferation of myelin-specific T cells and inhibited production of proinflammatory TH1 cytokines. N-(3,4,-dimethoxycinnamoyl) anthranilic acid (3,4-DAA), an orally active synthetic derivative of the Trp metabolite anthranilic acid, reversed paralysis in mice with experimental  autoimmune encephalomyelitis, a model of multiple sclerosis (MS). Trp catabolites and their derivatives offer a new strategy for treating TH1-mediated autoimmune diseases, such as MS.

4Y vd 1-11 comparison files are available as supplementary files.
Keywords: 48hr activation, MBPAc1-11 Cd4+ T cell, murine Mu11ksubA and Mu11subB combined anaylsis

overall_design: Double stranded cDNA was generated from total RNA extracted from MBP Ac 11-11 activated purified CD4+ T cells.  Biotinylated cRNA was manufactured by in vitro transcription and hybridized to the Affymetrix genechip murine Mu11k set according to the manufacturer's protocols.  Results were calculated as the ratio of mean average differences for each gene in 4Y versus Ac1-11 stimulated samples.

first: Michael

last: Platten

first: Peggy

last: Ho

first: Hideki

last: Garren


title: Mapping Determinants of Human Gene Expression by Regional and Whole Genome Association

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Baseline expression levels of genes in CEPH individuals from the International HapMap Project were measured using the Affymetrix Human Genome Focus Arrays.  Arrays were analyzed using MAS 5.0 software (Affymetrix).
Keywords = Gene Expression, lymphoblastoid cells, human
Keywords: other

first: Richard

last: Spielman

first: Joshua

last: Burdick

first: Teresa

middle: M

last: Weber

first: Vivian

middle: G

last: Cheung

first: Cliona

last: Molony

first: James

last: Devlin

first: Kathryn

last: Ewens


title: Adenovirus infected murine embryonic fibroblasts

status: Public on Oct 20 2005

first: Zachary

middle: Conrad

last: Hartman

address: Research Drive MSRB rm 414

department: Surgery

summary:
The innate immune response to 1st generation adenoviral vectors was ascertained through high level infection of primary cells from a inbred mouse strain, replete with an intact and functioning TLR system.
Keywords: Immune Response

overall_design: Quiescent murine C57/Bl6 fibroblasts were Ad (E1-E3-LacZ at MOI=300) or Mock infected.  Sixteen hrs post-infection, RNA was harvested, transcribe to cDNA and bitotin-labeled, and hybridized to Mu11k A and B arrays.

middle: C

first: Andy

last: Amalfitano

first: Joesph

last: Nevins

first: Esther

last: Black


title: Temporal pattern of gene expression in the late third instar larvae and prepupae of Drosophila melanogaster

status: Public on Oct 04 2005

city: Athens

first: Robert

middle: B

last: Beckstead

state: GA

address: 119 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

summary:
This study identifies genes that alter their expression in synchrony with the late third instar and prepupal pulses of 20E.
Keywords: time course

overall_design: RNA was isolated from w1118 whole animals staged at -18, -4, 0, 2, 4, 6, 8, 10, and 12 hours relative to pupariation, labeled, and hybridized to Affymetrix Drosophila Genome Arrays.

first: Geanette

last: Lam

first: Carl

last: Thummel


title: Identification of genes dependent on the Ecdysone receptor (EcR) at the onset of metamorphosis in Drosophila

summary:
This study identifies those genes that are dependent on EcR for their proper regulation at the onset of metamorphosis in Drosophila melanogaster.
Keywords: Nuclear receptor gene regulation

overall_design: hs-EcRi-11 third instar larvae were heat-treated twice at 37°C, each time for 1 hour, at 24 hours and 18 hours prior to pupariation, as described [29]. RNA was harvested for microarray analysis at -4, 0, and 4 hours relative to pupariation from three independent collections of animals for each time point. Data obtained from these arrays was compared to array data from control animals at the same stages of development to identify EcR-dependent genes.


title: Identification of 20E-regulated genes in Drosophila cultured larval organs

summary:
To identify 20E-regulated genes, wandering third instar larvae were dissected and their organs were cultured in the presence of either no hormone, 20E alone, cycloheximide alone, or 20E plus cycloheximide for six hours.
Keywords: Hormone response

overall_design: Eight partial blue gut third instar larvae were dissected in each well of a 9 well glass dish (Corning) and cultured in ~100 µl oxygenated Schneiders Drosophila Medium (Gibco) at 25°C. Cultures were incubated in an a styrofoam box under a constant flow of oxygen. Following an initial incubation of 1 hour, the medium was removed and replaced with either fresh Schneiders Drosophila Medium (no hormone), medium plus 8.5x10-5 M cycloheximide (Sigma), medium plus 5x10-6 M 20-hydroxyecdysone (Sigma), or medium plus cycloheximide and 20E, each for 6 hrs at 25°C. Organs were collected and RNA extracted from these samples was analyzed on Affymetrix Drosophila Genome Arrays.


title: The search for enzymes responsible for metabolism of nucleoside analogs

status: Public on Oct 30 2005

city: Ann Arbor

first: Philip

middle: Larson

last: Lorenzi

state: MI

institute: University of Michigan

summary:
Affymetrix U95Av2 expression data from human intestinal cells (Caco-2) and tissues from all intestinal segments (duodenum, jejunum, ileum, colon).  Entries contain the search terms "glycosylase, phosphorylase, cytochrome or nucleoside," which were relevant to our search for enzymes capable of cleaving the N-glycosidic bond of nucleoside analog drugs.
Keywords = glycosylase
Keywords = phosphorylase
Keywords = nucleoside
Keywords: parallel sample

first: Christopher

last: Landowski

first: Gordon

last: Amidon


title: Gene expression in alveolar macrophages from phenotypically normal smokers compared to non-smokers

status: Public on Sep 26 2005

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Cigarette smoking is the leading cause of the respiratory diseases collectively known as chronic obstructive pulmonary disease (COPD). While the pathogenesis of COPD is complex, there is abundant evidence that alveolar macrophages (AM) play an important role. Based on the concept that COPD is a slow-progressing disorder likely involving multiple mediators released by AM activated by cigarette smoke, the present study focuses on the identification of previously unrecognized genes that may be linked to early events in the molecular pathogenesis of COPD, as opposed to factors associated with the presence of disease. To accomplish this, microarray analysis using Affymetrix microarrays was used to carry out an unbiased survey of the differences in gene expression profiles in the AM of phenotypically normal, ~20 pack-yr smokers compared to healthy non-smokers. Although smoking did not alter the global gene expression pattern of AM, 75 genes were modulated by smoking, with 40 genes up-regulated and 35 down-regulated in the AM of smokers compared to non-smokers. Most of these genes belong to the functional categories of immune/inflammatory response, cell adhesion and extracellular matrix, proteolysis and antiproteolysis, lysosomal function, antioxidant-related, signal transduction and regulation of transcription. Of these 75 genes, 69 have not been previously recognized to be up- or down-regulated in alveolar macrophages in association with smoking or COPD, including genes coding for proteins belonging to all of the above categories, and others belonging to various functional categories or of unknown function. These observations suggest that gene expression responses of alveolar macrophages associated with the stress of cigarette smoking are more complex than previously thought, and offer a variety of new insights into the complex pathogenesis of smoking-induced lung diseases.
Keywords: Comparison of gene expression profile in smokers vs non-smokers

overall_design:
5 non smokers and 5 smokers
Alveolar macrophages were obtained from bronchoalveolar lavage

first: Adriana

last: Heguy

first: Timothy

last: O' Connor

first: Stefan

last: Worgall

first: Ben-Gary

last: Harvey

first: Neil

last: Hackett

first: Ronald

last: Crystal


title: Post-Transcriptional Role for the Yeast Paf1-RNA Polymerase II Complex is Revealed by Identification of Primary Targets

status: Public on Aug 26 2005

city: Denver

first: Judith

middle: A.

last: Jaehning

state: CO

address: 4200 E. 9th Avenue Campus Box B-121

department: Biochemistry and Molecular Genetics

institute: UCHSC

summary:
To identify the direct targets of the Paf1/RNA polymerase II complex we compared expression profiles of isogenic wild type and paf1 and ctr9 mutant strains. We also created a Tet-regulated form of Paf1 and monitored expression patterns after shut off of Paf1. Samples were isolated at one hour intervals from 1 to 8 hours after shut off.
Keywords: single channel nucleotide

overall_design: Transcripts were compared on Affymetrix microarrays using standard protocols.

first: Kristi

last: Penheiter

first: Taylor

last: Washburn

first: Stephanie

middle: E

last: Porter

first: Matthew

last: Hoffman

middle: A


title: A Distinct QscR Regulon in the Pseudomonas aeruginosa Quorum Sensing Circuit

status: Public on Jan 18 2006

city: Seattle

first: Yannick

last: Lequette

state: WA

address: 1959 NE PACiFiC

department: Microbiology HSB -I420 BOX 357242

institute: University of Washington

summary:
To better understand the role of QscR in P. aeruginosa gene regulation and to better understand the relationship between QscR, LasR and RhlR control of gene expression we used transcription profiling to identify a QscR-dependent regulon. Our analysis revealed that QscR activates some genes and represses others. Some of the repressed genes are not regulated by the LasR-I or RhlR-I systems while others are. The LasI-generated 3-oxododecanoyl-homoserine lactone serves as a signal molecule for QscR. Thus QscR appears to be an integral component of the P. aeruginosa quorum sensing circuitry. QscR uses the LasI-generated acyl-homoserine lactone signal and controls a specific regulon that overlaps with the already overlapping LasR and RhlR-dependent regulons.
Keywords: Quorum sensing regulon, Direct activation

overall_design:
First comparisaon
We first compared transcriptomes of the qscR mutant P. aeruginosa PAO-R3 and the parental strain PAO1 at several points during growth (OD600nm 0.5, 0.8, 1.4, 2.0 and 3.5). To identify those genes with expression significantly different between PAO1 and PAO-R3 at different culture densities we used CYBER-T. The Bayesian prior estimate was 10 and the sliding window size was 101. The p-value threshold was 0.001, the posterior probability of differential expression >0.95, and fold change was >2.5.

Second comparison
We selected genes that were at least 3-fold differentially expressed in the strain containing the L-arabinose promoter-driven qscR allele vs the strain containing L-arabinose promoter-driven qscR-Ddbd allele, and were also at least 3-fold differentially expressed in the parent strain PAO1 as compared to the strain containing the qscR null mutation. RNA were extracted from cultures at OD 0.5, 0.8, 1.4, 2.0 and 3.5

first: Joon-Hee

last: Lee

first: Fouzia

last: Ledgham

first: Andree

last: Lazdunski

first: Peter

last: Greenberg


title: PA2384 and iron starvation in P. aeruginosa

status: Public on Sep 07 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The gene PA2384 in Pseudomonas aeruginosa PAO1, annotated originally as unknown function, has been previously shown to be dramatically responsive to iron limitation. In the present study, PA2384 is shown by bioinformatics analysis to have a weak similarity to the N-termini DNA binding domain of fur, a well-known ferric uptake regulator. To experimentally investigate the function of PA2384 P. aeruginosa PAO1 recombinant (pUCP20::PA2384) overexpressing PA2384 and PA2384 knock-out mutant PAO1-23844 are constructed and studied. Physiological characterization in a carefully controlled cultivation system shows that the knockout strain needed a longer lag phase to grow and exhibited a significantly reduced production speed of siderophore (pyoverdine and pyochelin) in the stationary phase. Genome-scale transcriptional profiles at different growth stages are compared between the wild type and ∆PA2384 mutant grown under iron-limiting conditions. The expression of more than 350 genes is affected. Among them, seventy-one genes involved in iron uptake are significantly induced by PA2384. 102 quorum sensing (QS) dependent genes exhibited differential transcription. They include genes related to the biosynthesis of some important virulence factors such as pyocyanin, rhamnolipids and hydrogen cyanide. Transcription of genes responsible for the synthesis of Pseudomonas Quinolone Signal (PQS) is greatly advanced by the knockout of PA2384. We postulate that PA2384 affects QS via PQS. Furthermore, the knockout of PA2384 also results in altered expression of genes involved in electron transfer, central metabolism, phosphorus starvation and translation. It implies that PA2384 may affect more basic physiology than only respond to iron uptake and is a versatile global regulator in P. aeruginosa under iron starvation.
Keywords: iron starvation, quorum sensing, time course

overall_design: mutant and wilde type biological replicates were analyzed at 3 timepoints

first: Ping

last: Zheng

first: Jibin

last: Sun

first: Jan

last: Buer

first: An-Ping


title: Gene expression profiles of adult peripheral and cord blood mononuclear cells altered by lipopolysaccharide

status: Public on Aug 21 2005

city: Heidelberg

first: Lutz

last: Koch

address: Im Neuenheimer Feld 153

department: Department of Paediatrics

institute: University of Heidelberg

summary:
Neonatal gram-negative sepsis is often characterized by a fulminat clinical course compared to adults resulting in higher morbidity and mortality. Genome-wide gene expression analysis can provide insights into the molecular alterations in sepsis. To evaluate in vitro activation of the neonatal and adult immune system, gene expression patterns were compared in mononuclear cells from cord (CBMNC) and adult peripheral blood (APBMNC). To better understand the influence of early molecular signals on the effects of sepsis, Affymetrix gene profiling (8475 genes) was done on RNA isolated from CBMNC and APBMNC without and after incubation with 100 ng/ml lipopolysaccharide (LPS). We demonstrated significant alterations in the expression of 108 CBMNC and APBMNC genes compared with basal levels, 188 significant changes in CBMNC, and 97 in APBMNC, including cytokines, chemokines, and immunoregulatory genes. Furthermore, we found five genes showing a significant interaction effect between cell-type and LPS-stimulation, including tumor necrosis factor receptor superfamily, member 6 (FAS), absent in melanoma 2 (AIM2), malic enzyme 1 (ME1), hemoglobin epsilon 1 (HBE1), and trans-prenyltransferase (TPRT). These results provide further support for a marked difference in the pathogenesis of neonatal and adult sepsis and may stimulate additional studies to investigate some of the altered genes as potential new targets for diagnostic tools and therapeutic strategies.
Keywords: LPS response

overall_design: The statistical analysis was carried out using the software package R, version 1.9.1, together with libraries gcrma and limma of the Bioconductor Project, version 1.4. The data preprocessing steps, background-adjustment, normalization and computation of GCRMA gene expression measures, were performed according to Wu et al. For the statistical analysis empirical Bayes inference for linear models with factors treatment (basal and LPS stimulated) and cell type (CBMNC and APBMNC) and their interaction was used. From there moderated t-statistics based on shrinkage of the estimated sample variance towards a pooled estimate and corresponding p-values were calculated for comparisons LPS stimulated vs. basal expression for adult and neonatal MNC, and neonatal vs. adult MNC with and without LPS-treatment, respectively, as well as for the interaction effect of the factors treatment and cell type. P-values for each comparison were adjusted according to Benjamini and Hochberg to control the false discovery rate. We used a threshold of 0.01 for the adjusted p-values and selected only those probe sets which showed a fold change => 2

first: Otwin

last: Linderkamp

first: Carina

last: Ittrich

first: Axel

last: Benner

first: Johannes

last: Poeschl


title: STS107 T-cell activation at 1g vs. vg

status: Public on Aug 25 2005

first: Jim

last: Boonyaratanakornkit

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

summary:
Peripheral blood leukocytes of three human donors (Donors 2, 4, and 5) were isolated from blood bank buffy-coat preparations by Ficoll-Hypaque density gradient centrifugation, and T-cells were purified with high affinity negative selection human CD3+ T-cell enrichment columns.  The cells were resuspended in RPMI-1640 with 10% FCS with approximately 3-8 millions cells/mL at room temperature overnight.  T-cells were then either unactivated (1g 0 hr), activated (1g 4 hr) with a final concentration of 5 mg/mL Con A + 4 mg/mL anti-CD28 antibody and incubated for 4 hours at 37°C, or loaded onto a RPM rotating at 60°/s (vg).  T-cells loaded on the RPM were cultured for 2 hours prior to collection or activation to allow equilibration of cells to the new environment.  After incubation, 1 mL of 4 M guanidinium isothiocyanate in 750 mM sodium citrate buffer, pH 7, with N-lauroylsarcosine and beta-mercaptoethanol was added to lyse cells and stabilize RNA.
Keywords: ordered


title: Microarray Analysis of Pseudomonas aeruginosa Reveals Induction of Pyocin Genes in Response to Hydrogen Peroxide

status: Public on Aug 15 2005

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary:
Background: Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection.  P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans.  Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure.
Results: Herein, we performed a genome-wide transcriptome analysis of the cellular responses to hydrogen peroxide in order to determine a more complete picture of how oxidative stress-induced genes are related and regulated.
Our data reinforce the previous conclusion that DNA repair proteins and catalases may be among the most vital antioxidant defense systems of P. aeruginosa.  Our results also suggest that sublethal oxidative damage reduces active and/or facilitated transport and that intracellular iron might be a key factor for a relationship between oxidative stress and iron regulation.  Perhaps most intriguingly, we revealed that the transcription of all F-, R-, and S-type pyocins was upregulated by oxidative stress and at the same time, a cell immunity protein (pyocin S2 immunity protein) was downregulated, possibly leading to self-killing activity.
Conclusions: This finding proposes that pyocin production might be another novel defensive scheme against oxidative attack by host cells.
Keywords: Transcriptome study, oxidative stress response

overall_design: We conducted four and five independent microarray experiments with biological replicates in the absence (control) and the presence (experimental) of hydrogen peroxide, respectively.

first: Wook

first: David

last: Small

first: Freshteh

last: Toghrol

first: William

last: Bentley


title: Role of yeast Spt10p in gene expression

status: Public on Sep 23 2005

last: Clark

summary:
Comparison of gene expression patterns for wild type yeast (BJ5459) and spt10-null::URA3 cells. Triplicate samples.
Keywords = yeast SPT10
Keywords: repeat sample

first: Peter

middle: R

last: Eriksson

first: Geetu

last: Mendiratta

first: Neil

last: McLaughlin

first: Tyra

last: Wolfsberg

first: Leonardo

last: Marino-Ramirez

first: Tiffany

last: Pompa

first: Mohendra

last: Jainerin

last: Landsman

first: Chang-Hui

last: Shen


title: YDRseries3, Yeast desiccation / rehydration time course

status: Public on Aug 01 2005

city: Blacksburg

first: Richard

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

institute: Virginia Polytechnic Institute and State University

summary:
This series represents Experiment 3 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.
Keywords = BY4743
Keywords = desiccation
Keywords = glucose-limited
Keywords = rehydration
Keywords = yeast
Keywords: time-course

first: Jatinder

last: Singh

first: Deept

last: Kumar

first: Naren

last: Ramakrishnan

first: Vibha

last: Singhal

first: Jody

last: Jervis

first: James

middle: F

last: Garst

first: Stephen

last: Slaughter

first: Andrea

last: DeSantis

first: Malcolm

last: Potts


title: YDRseries2, Yeast desiccation / rehydration time course

summary:
This series represents Experiment 2 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.
Keywords = BY4743
Keywords = desiccation
Keywords = glucose-limited
Keywords = rehydration
Keywords = yeast
Keywords: time-course


title: YDRseries1, Yeast desiccation / rehydration time course

summary:
This series represents Experiment 1 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.
Keywords = BY4743
Keywords = desiccation
Keywords = glucose-limited
Keywords = rehydration
Keywords = yeast
Keywords: time-course


title: Kidney development time course

status: Public on Jul 20 2005

city: St Lucia

first: Darrin

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
Series_overall_design: To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.
Keywords: time-course

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Sean

last: Grimmond

first: Xiaolin

last: Cui

first: Jianhua

last: Zhang

first: Penglin

last: Ma

first: Daniela

last: Myers

first: Ilana

last: Goldberg

first: Kelly

middle: J

last: Sittler

first: Jennifer

last: Barb

first: Peter

last: Munson

first: Ana

middle: del

last: Pilar Cintron

first: Shuibang

last: Wang

first: J.

middle: Philip

last: McCoy

first: Robert

middle: L

last: Danner


title: The Jak-STAT signaling pathway is required but not sufficient for the antiviral response of drosophila

status: Public on Aug 08 2005

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

institute: CNRS

summary:
The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection.
Keywords: JAK/STAT virus drosophila immunity

overall_design: For each experimental challenge (Tris or DCV, 24 or 48 hours after infection), three biologically independent samples composed of 45 male Oregon R flies were used. Infection has been performed by injecting viral stocks prepared in Tris solution. Injection of the same volume of Tris has been used as control. Infected flies were then incubated for 24 or 48 hours.

first: Catherine

last: Dostert

first: Emmanuelle

last: Jouanguy

first: Phil

last: Irving

first: Laurent

last: Troxler

first: Delphine

last: Galiana-Arnoux

first: Charles

last: Hetru

first: Jules

last: Hoffmann


title: YDRseries4, Comparison commercial dry active yeast to BY4743

first: Richard

last: Helm

summary:
This series represents the analysis of a commercial dry active yeast (purchased locally).  The genetics of this sample is unknown.
Keywords = commercial
Keywords = dry active yeast
Keywords: other

first: Jatinder

last: Singh

first: Deept

last: Kumar

first: Naren

last: Ramakrishnan

first: Vibha

last: Singhal

first: Jody

last: Jervis

first: James

last: Garst

first: Stephen

middle: M

last: Slaughter

first: Andrea

last: DeSantis

first: Malcolm

last: Potts


title: Non Small Cell Lung Cancer

city: Tel Aviv

first: Elinor

last: Dehan

institute: Tel Aviv University

summary:
This series contain 36 samples obtained from human lung tissue and includes the following:
7 Adenocarcinoma samples.
16 Squamous cell carcinoma samples.
1 AdenoSquamous sample.
2 Renal Metastasis.
1 Colon metastasis.
7 normal lung tissue adjacent to the tumors.
2 commercial normal lung RNA.
Keywords = Lung
Keywords = Non Small Cell Lung Cancer
Keywords = Adenocarcinoma
Keywords = Squamous Cell Carcinoma
Keywords = Normal Lung.
Keywords: other

first: Naftali

last: Kaminski


city: Dublin

first: Edward

last: Fox

country: Ireland

institute: Conway Institute

summary:
Melanoma progression model:DAC-mediated gene expression
Keywords: other

first: Orla

last: Bergin

first: William

last: Gallagher

first: Zoe

last: Kelly

first: Mairin

last: Rafferty

first: Linda

last: McArdle

first: Ilse-Maria

last: Nolan

first: Caroline

last: Currid

first: Fiona

last: O'Mahoney

first: Aileen

last: Byrne

first: Alison

last: Murphy

first: Raymond

last: Stallings

first: Jane

last: Plumb

first: Robert

last: Brown

first: Peter

last: Dervan

first: David

last: Easty


title: Melanoma progression model: Differential Gene Expression

summary:
Melanoma progression model
Keywords: other


title: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.

status: Public on Jul 18 2005

city: Madison

first: Alan

middle: D

last: Attie

state: WI

address: 433 Babcock Drive

institute: University of Wisconsin-Madison

summary:
The expression of adipogenic genes is decreased in obesity and diabetes mellitus
Samuel T. Nadler*, Jonathan P. Stoehr*, Kathryn L. Schueler*, Gene Tanimoto, Brian S. Yandell, and Alan D. Attie*,§
Departments of * Biochemistry, and  Statistics and Horticulture, University of Wisconsin, Madison, WI, 53706; and  Affymetrix, Inc., Santa Clara, CA 95051

Communicated by Neal L. First, University of Wisconsin, Madison, WI, July 13, 2000 (received for review April 3, 2000)

Obesity is strongly correlated with type 2 diabetes mellitus, a common disorder of glucose and lipid metabolism. Although adipocytes are critical in obesity, their role in diabetes has only recently been appreciated. We conducted studies by using DNA microarrays to identify differences in gene expression in adipose tissue from lean, obese, and obese-diabetic mice. The expression level of over 11,000 transcripts was analyzed, and 214 transcripts showed significant differences between lean and obese mice. Surprisingly, the expression of genes normally associated with adipocyte differentiation were down-regulated in obesity. Not all obese individuals will become diabetic; many remain normoglycemic despite profound obesity. Understanding the transition to obesity with concomitant diabetes will provide important clues to the pathogenesis of type 2 diabetes. Therefore, we examined the levels of gene expression in adipose tissue from five groups of obese mice with varying degrees of hyperglycemia, and we identified 88 genes whose expression strongly correlated with diabetes severity. This group included many genes that are known to be involved in signal transduction and energy metabolism as well as genes not previously examined in the context of diabetes. Our data show that a decrease in expression of genes normally involved in adipogenesis is associated with obesity, and we further identify genes important for subsequent development of type 2 diabetes mellitus.
Keywords: Genetic modifications and strain difference

overall_design:
For obesity study, lean samples include C57BL/6J  lean, (C57BL/6J X BTBR) F1 and BTBR lean, obese sampples incluse C57BL/6J-ob/ob, (C57BL/6J X BTBR) F2-ob/ob and BTBR-ob/ob. All samples are subjected to Mu11K A and B arrays.
For diabetes study, B6-ob/ob, (C57BL/6J X BTBR) F2-ob/ob low glucose, (C57BL/6J X BTBR) F2-ob/ob medium glucose, (C57BL/6J X BTBR) F2-ob/ob high glucose, and BTBR-ob/ob samples were analyzed for genes whose expression levels changes correlated with the plasma glucose levels in these mice. All samples are subjected to Mu11K A and B arrays.

first: Samuel

middle: T

last: Nadler

first: Jonathan

middle: P

last: Stoehr

first: Kathryn

last: Schueler

first: Gene

last: Tanimoto

first: Brian

middle: S

last: Yandell


title: Gene Expression Profiles of Scd1 knockout mice vs wild type mice on chow diet: Liver.

status: Public on Jul 14 2005

summary:
Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity.

Ntambi JM, Miyazaki M, Stoehr JP, Lan H, Kendziorski CM, Yandell BS, Song Y, Cohen P, Friedman JM, Attie AD.

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA. ntambi@biochem.wisc.edu

Stearoyl-CoA desaturase (SCD) is a central lipogenic enzyme catalyzing the synthesis of monounsaturated fatty acids, mainly oleate (C18:1) and palmitoleate (C16:1), which are components of membrane phospholipids, triglycerides, wax esters, and cholesterol esters. Several SCD isoforms (SCD1-3) exist in the mouse. Here we show that mice with a targeted disruption of the SCD1 isoform have reduced body adiposity, increased insulin sensitivity, and are resistant to diet-induced weight gain. The protection from obesity involves increased energy expenditure and increased oxygen consumption. Compared with the wild-type mice the SCD1-/- mice have increased levels of plasma ketone bodies but reduced levels of plasma insulin and leptin. In the SCD1-/- mice, the expression of several genes of lipid oxidation are up-regulated, whereas lipid synthesis genes are down-regulated. These observations suggest that a consequence of SCD1 deficiency is an activation of lipid oxidation in addition to reduced triglyceride synthesis and storage.
Keywords: Genetic modifications

overall_design: RNA was isolated from livers of 10 individual 6-week-old female mice by using a standard method. Mouse genome U74A arrays were used to monitor the expression level of approximately 10,000 genes and expressed sequence tags (Affymetrix). Genes differentially expressed were identified by comparing expression levels in SCD1–/– and wild-type mice.

first: Hong

last: Lan

first: Nadler

last: Samuel

first: Mark

last: Gray-Keller

first: James

last: Ntambi


title: GSC differentiation-reversion test

status: Public on Jun 15 2005

city: Baltimore

first: Allan

middle: C

last: Spradling

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution/HHMI

summary:
gene expression is tested for an association with GSCs by comparing expression levels in ovary tips of c587-GAL4; hs-bam  UAS-dpp females at 0 hr, 20 hr and 50 hr after heat shock ;  results of two independent experiments are given as expt 1 and expt 2
Keywords: time course, heat shock, bam overexpression

overall_design:
0 hr  ovary tips contain many GSCs
20 hr  hs-bam has induced differentiation of all GSCs
50 hr  Bam has turned over and cystocytes have reverted to become GSCs again
see Kai et al. (2005) Dev. Biol.

first: Toshie

last: Kai

first: Dianne

last: Williams


title: YeastGLUGAL experiment

status: Public on Jul 04 2005

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

summary:
Global Gene expression analysis of Saccharomyces cerevisiae grown in micro-scale sirred bioreactors equipped with real-time measurements of growth kinetics and humidity control
Keywords: other

first: Paolo

last: Boccazzi

first: Zhiya

last: Zhang

first: Kazuhiko

last: Kurosawa

first: Nicolas

last: Szita

first: Klavs

last: Jensen

first: Anthony

last: Sinskey


title: GSC vs Kc

summary:
This series compares gene expression between germ line stem cells (GSCs) purified either from bam mutant or Dpp-overexpressing ovaries, with gene expression in Kc cells
Keywords: bam mutant, Dpp overexpression

overall_design:
3 replicates of GSCs from bam mutant ovaries
3 replicates of GSCs from Dpp overexpressing ovaries
3 replicates of Kc tissue culture cells


title: Yeast Histone H4 K91A versus wild type

status: Public on May 24 2005

city: Columbus

last: Parthun

state: OH

address: 1645 Neil Ave.

department: Molecular and Cellular Biochemistry

institute: Ohio State University

summary:
Yeast strain containing either a histone H4 wild type or K91A allele was grown in YPD to mid-log phase and harvested.  Three replicates of each allele were performed
Keywords: repeat sample

first: Jianxin

last: Ye

first: Xi

last: Ai

first: Ericka

last: Eugeni

first: Liwen

first: Laura

last: Carpenter

first: Mary

last: Jelinek

first: Michael

last: Freitas


title: TFIIH mutants treated with methyl methanesulfonate

status: Public on Apr 20 2005

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Purpose of profiling experiment was to examine effects of a mutation of a subunit of TFIIH, ssl1p, which has ubiquitin ligase activity.
The whole complex has previously been shown to have both kinase and helicase activities.  We wanted to see if 1) there were
general transcriptional defects with these mutations, as there are with other mutations to kinase activity, and 2) if there
were transcriptional effects on DNA repair machinery when the mutants were treated with MMS, which is an alkylating agent.
Keywords: other

first: Claudio

last: Masuda

last: Joazeiro

first: Yuichiro

last: Takagi

first: Wei-Hau

last: Chang

first: Hirofumi

last: Komori

first: Dong

last: Wang

first: Tony

last: Hunter

first: Roger

last: Kornberg


title: rrp6 delta and 	rrp6 delta, trf4 delta vs WT

status: Public on Apr 28 2005

city: Paris

first: Alain

last: Jacquier

institute: Institut Pasteur

summary:
BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30°C to OD 0.6 in YPD.

BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30°C to OD<0.6 in YPD.
Keywords: other


title: Genome_Wide_Oscillations_in_Yeast

status: Public on Apr 29 2005

city: Duarte

first: Robert

last: Klevecz

address: 1450 E. Duarte Rd.

department: Biology

institute: Beckman Research Institute of the City of Hope

summary:
In order to test the idea that the cell is an attractor and to examine in detail the connectivity relationships among genes, it was essential to have a very reproducible and precise biological system.  Oscillations in respiratory activity in budding yeast and other organisms have been known for many years. This benchmark oscillation is now shown to be a global manifestation of a genome wide oscillation in transcription. Using Affymetrix S98 chips, the patterns of gene expression were followed by sampling at 4-minute intervals through three cycles of the DO oscillation. Phase assignments were made based on the dissolved oxygen cycle. Two different cultures were sampled and a total of 68 RNA samples were prepared.  Choices of samples for microarray analysis were based on RNA quality, consistent with having a complete set of 32 samples chosen to represent three cycles of the DO oscillation.  Ten were chosen from the first experiment and 22 from the second experiment.  Analysis using singular value decomposition recognizes a small difference in cycle time between the two experiments. Strictly speaking, there are no replicates.  The time of maximum gene expression in the cycle was determined by phase grouping and averaging gene expression in the three replicates, assigning the phase of maximum expression to each transcript then examining how well this assignment is reproduced through the three cycles.  We found that 5329 expressed genes were present in at least one sample and used them in our analysis.
The correct order is GSM48136, GSM48137, GSM48138, GSM48139, GSM48140, GSM48131, GSM48132, GSM48133, GSM48134, GSM48135, GSM48149, GSM48150, GSM48141, GSM48151, GSM48142, GSM48143, GSM48144, GSM48145, GSM48146, GSM48147, GSM48148, GSM48160, GSM48161, GSM48162, GSM48157, GSM48158, GSM48152, GSM48159, GSM48153, GSM48154, GSM48155, GSM48156
Keywords: time-course

first: James

last: Bolen

first: Gerald

last: Forrest

first: Douglas

middle: B

last: Murray


title: HIV-1 infection in human PBMCs in vivo

status: Public on Jan 22 2005

city: Rockville

first: Maryanne

last: Vahey

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

summary:
We used Affymetix HG Focus GeneChip to measure the expression levels of HIV seronegative and seropositive individuals in human PBMCs in vivo. GSM39104 -GSM39115 are HIV seronegative samples; GSM39116-GSM39137 are HIV seropositive but drug naive samples; GSM39138-GSM39147 are HIV seropositive samples used to test serostatus biomarker; GSM39148-GSM39170 are HIV seropositive individuals whose CD4 cells decrease over time; GSM39171-GSM39187 are HIV seropositive individuals whose CD4 cells increase over time; GSM39188-GSM39190 are HIV seropositive samples used to test CD4 cell increase/decrease over time.
Keywords: other

first: Christian

last: Ockenhouse

first: Wendy

last: Bernstein

first: Zhining


title: Sorted wing disc proneural cluster cells

status: Public on Mar 05 2005

city: La Jolla

first: Nick

last: Reeves

address: 9500 Gilman Dr.

department: Section of Cellular and Developmental Biology

institute: University of California, San Diego

summary:
Fluorescence-activated cell sorting of M4-GFP wing imaginal disc cells was used to recover a purified population of the cells that comprise the “proneural clusters” from which sensory organ precursors of the peripheral nervous system (PNS) arise.  Whole-genome microarray analysis and in situ hybridization was then used to identify and verify a set of genes that are preferentially expressed in proneural cluster cells.  Genes in this set encode proteins with a diverse array of implied functions, and loss-of-function analysis of two candidate genes shows that they are indeed required for normal PNS development.
Keywords = Proneural
Keywords = PNS
Keywords = PNC
Keywords = SOP
Keywords: parallel sample

middle: W

last: Posakony


title: Global gene expression analysis of gastric cancer by oligonucleotide microarrays

status: Public on May 22 2005

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

institute: The University of Tokyo

summary:
To gain molecular understanding of carcinogenesis, progression, and diversity of gastric cancer, 22 primary human advanced gastric cancer tissues and 8 noncancerous gastric tissues were analyzed by high-density oligonucleotide microarray in this study. Based on expression analysis of approximately 6800 genes, a two-way clustering algorithm successfully distinguished cancer tissues from noncancerous tissues. Subsequently, genes that were differentially expressed in cancer and noncancerous tissues were identified; 162 and 129 genes were highly expressed (P < 0.05) >2.5-fold in cancer tissues and noncancerous tissues, respectively. In cancer tissues, genes related to cell cycle, growth factor, cell motility, cell adhesion, and matrix remodeling were highly expressed. In noncancerous tissues, genes related to gastrointestinal-specific function and immune response were highly expressed. Furthermore, we identified several genes associated with lymph node metastasis including Oct-2 or histological types including Liver-Intestine Cadherin. These results provide not only a new molecular basis for understanding biological properties of gastric cancer, but also useful resources for future development of therapeutic targets and diagnostic markers for gastric cancer.
Keywords: other

first: Yoshitaka

last: Hippo

first: Hirokazu

last: Taniguchi

first: Shuichi

last: Tsutsumi

first: Naoko

last: Machida

first: Ja-Mun

last: Chong

first: Masashi

last: Fukayama

first: Tatsuhiko

last: Kodama

first: Hiroyuki

last: Aburatani


title: Cyclosporine A timecourse 0, 12, 48 hours

status: Public on Dec 20 2004

first: Craig

last: Slattery

summary:
Effect of 4.2 micromolar Cyclosporine A on human renal proximal tubular cell line HK-2 over 48 hours
Keywords: time-course

first: Tara

last: McMorrow

first: Michael

last: Ryan


title: Affy data from WT, FHL1 deleted and FHL1,IFH1 double deleted strains.

status: Public on Dec 22 2004

city: Bronx

first: Jonathan

middle: R.

last: Warner

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

summary:
Affymetrix experiment performed on RNA isolated from Wild type, FHL1 deleted and FHL1,IFH1 double deleted strains. Data aquired in duplicate.

In S. cerevisiae the mRNAs from the 138 ribosomal protein (RP) genes are amongst the most abundant in the cell, and their transcription is regulated tightly so that they are the most prominent cluster in most transcriptome experiments.  It has recently been observed that the proteins Fhl1p and Ifh1p are found almost exclusively at RP genes (Lee et al., Science, 298, 799-804, 2002;Jorgensen et al., Genes Dev, 18, 2491-2505 2004; Schawalder et al Nature in press; Rudra et al , EMBO J. submitted), and data suggests they are the true transcription factors.
This experiment utilizes Affymetrix arrays to measure the level of all mRNAs in cells with a deletion of FHL1 or of both FHL1 and IFH1, compared to the wild type strain, W303.  Such mutant cells are viable but grow very slowly (Hermann-Le Denmat S. et al., Mol Cell Biol, 14, 2905-2913, 1994; Cherel and Thuriaux, Yeast, 11, 261-270, 1995).  Total RNA was made from log phase cells, amplified according to conventional methods, and hybridized to the array.  (Since the total RNA/cell of the mutants is only a fifth of the wt, each mutant required five times the number of cells to provide the same amount of RNA.)  The experiment was carried out in duplicate and the six tables provide the raw data from the wt, W303,  delFHL1, and delFHL1, delIFH1 strains.
Although we expected that the RP genes would be substantially reduced in these mutant cells, they are only slightly less abundant than normal in comparison to all other mRNAs!  The interesting result is that the cells respond to a severe deficiency of ribosomes by reducing the level of nearly all mRNAs to match the capacity of the translational apparatus.
Keywords = Ribosome
Keywords = FHL1
Keywords = IFH1.
Keywords: parallel sample

first: Dipayan

last: Rudra

first: Yu

last: Zhao


title: Experimental condition

city: Groton

first: Gregory

last: Warnes

state: CT

address: Eastern Point Road

institute: Pfizer Inc., Groton, CT - USA

summary:
BY4730 cultures were exposed to medium containing dilutions of test agent (Cisplatin (Cis), 600mg/mL; Methylmethane sulfonate (MMS), 0.12% v/v; Bleomycin (Bleo), 0.15U/mL; NaCl, 10mg/mL; ethanol, 15% v/v) for 120 min. Control cultures were either mock-treated with the solvent, DMSO (for comparison to Cis, MMS, Bleo) or maintained in media (for comparison to ethanol and NaCl) for 120 mins. Sample preparation and processing procedures were performed according the Affymetrix Genechipâ Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). Briefly, total RNA was isolated from thawed cell pellets using a hot phenol protocol described by Schmitt et. al. (1990). Total RNA was converted to poly(A)+ mRNA and isolated using Oligotex mRNA kit. Double stranded cDNA was generated by using T7-(dT) 24 oligo primer (Genset Corp., San Diego, CA) and Superscript Double Stranded cDNA Synthesis Kit (Gibco BRL, Carlsbad, CA). The cDNA was used for in vitro transcription (IVT) with Enzo BioArray RNA Transcript Labeling Kit to incorporate biotinylated ribonucleotides. Biotinylated cRNA (15 mg) was fragmented in 40 mM tris-acetate, pH 8.1; 30 mM MgOAc; 100 mM KOAc. Samples were then hybridized with Affymetrix probe array Yeast Genome S98 at 45°C for 16 hours with constant rotation. Hybridized probe arrays were washed and stained using an Affymetrix GeneChipâ Fluidics Station 400 and protocol EukGE-WS2. The chips were scanned using the Affymetrix GeneArray Scanner.
Keywords: repeat sample

first: Ebru

last: Caba

first: Donna

middle: A

last: Dickinson

first: Jiri

last: Aubrecht


title: leu3p dependent transcription

status: Public on Dec 17 2004

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary:
Transcriptional regulation of branched-chain amino acid metabolism in Saccharomyces cerevisiae involves two key regulator proteins, Leu3p and Gcn4p. Leu3p is a pathway-specific regulator, known to regulate six genes involved in branched-chain amino acid metabolism and one gene in nitrogen assimilation. Gcn4p is a global regulator, involved in the general response to amino acid and purine starvation. To investigate the contribution of Leu3p in regulation of gene expression, a leu3D strain was compared to an isogenic reference strain using DNA-microarray analysis. This comparison was performed for both glucose-grown, ammonium-limited and ethanol-limited, ammonium-excess chemostat cultures. In ethanol-limited cultures, absence of Leu3p led to reduced transcript levels of six of the seven established Leu3p target genes, but did not affect key physiological parameters. In ammonium-limited cultures, absence of Leu3p caused a drastic decrease in storage carbohydrate content. mRNA levels of genes involved in storage carbohydrate metabolism were also found reduced. Under N-limited conditions, the leu3D genotype elicited an amino-acid starvation response, leading to increased transcript levels of many amino acid biosynthesis genes. By combining the transcriptome data with data from earlier studies that measured DNA binding of Leu3p both in vitro and in vivo, BAT1, GAT1 and OAC1 were identified as additional Leu3p-regulated genes. This study demonstrates that unravelling of transcriptional regulation networks should preferably include several cultivation conditions and requires a combination of experimental approaches.
Keywords: ordered

first: Viktor

last: Boer

first: Marinka

middle: H

last: Almering

first: Johannes

last: de Winde

first: Jack

last: Pronk


title: DNA damage response (NCS treatment) in several siRNA-manipulated cellular systems

status: Public on Mar 23 2005

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

summary:
Response to treatment with the radiomimetic drug NCS in cells knocked-down for ATM, p53, and the Rel_A subunit of NFkB; and in control un-infected cells and cells infected with siRNA against LacZ
Keywords = DNA damage
Keywords = ATM
Keywords = p53
Keywords = RelA
Keywords: other

first: Sharon

last: Rashi-Elkeles

first: Yaniv

last: Lerenthal

first: Chaim

last: Linhart

first: Tamar

last: Tenne

first: Ninette

last: Amariglio

first: Gideon

last: Rechavi

first: Ron

last: Shamir

first: Yosef

last: Shiloh


title: Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression

status: Public on Nov 16 2004

city: Seattle

first: James

last: Ronald

institute: University of Washington

summary:
By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains.  We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM.  A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments.  The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003).  We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium.  We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays.  In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed.

Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821).

The results are part of Ronald et al. (2005) describing a novel use of oligonucleotide expression arrays to perform genotyping.   This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.

first: J

last: Akey

last: Whittle

first: E

middle: N

last: Smith

first: G

last: Yvert

first: L

last: Kruglyak


status: Public on Apr 06 2005

city: Rochester

first: David

middle: George

last: Monroe

state: MN

address: 100 2nd St SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary:
U2OS-ERa, U2OS-ERb, and U2OS-ERab cells treated with 4HT or E2
Keywords: other

middle: G


title: Genes regulated by mating, sperm or Acps

status: Public on Dec 09 2004

city: Ithaca

first: Lisa

middle: A.

last: McGraw

address: 421 Biotechnology Bldg.

department: Molecular Biology and Genetics

institute: Cornell University

summary:
Comparison of gene expression between females that were either virgin, mated to normal males, mated to spermless males (sons of tudor) or mated to sperm-less/Acp-less males (DTA-E).
Keywords: other

first: Greg

last: Gibson

first: Andrew

last: Clark

first: Mariana

middle: F

last: Wolfner


title: CEBPE WT vs. KO peritoneal lavage cells

status: Public on May 31 2005

city: Los Angeles

first: Adrian

middle: Friedrich

last: Gombart

institute: Cedars-Sinai Medical Center

summary:
Experimental Design
Prior studies of C/EBPe-deficient myeloid cells from both humans and mice, demonstrated an essential role for C/EBPe in the normal development and function of both neutrophils and macrophages. There are striking parallels between human neutrophil specific granule disease (SGD) due to mutations in the CEBPE gene and the murine C/EBPe-deficient condition.  This indicates that the C/EBPe-deficient murine model will serve as an extremely powerful tool in further characterizing this rare human disease.  In this study, we sought to define further the role that C/EBPe plays in mediating host immune function by identifying possible target genes of C/EBPe in both neutrophils and macrophages.  This study was designed to elucidate the effects of the CEBPE gene knockout in murine myeloid cells.

Mice and sample preparation
The C/EBPE wild type (+/+) and –deficient (-/-) mice (129/SvEv x NIH Black Swiss) were generously provided by K.G. Xanthopoulos (Anadys Pharmaceuticals, Inc., San Diego, CA) and Julie Lekstrom-Himes (Millennium Pharmaceuticals, Inc., Cambridge, MA).  They were maintained in pathogen-free facilities on normal chow.  To prepare RNA for array hybridization, four age-matched (6-8 weeks) mice of each genotype received an intraperitoneal (IP) injection of 2 ml of 4% sterile thioglycollate broth (Sigma Chemical Co., St Louis, MO).  At 24 h post injection, all mice were sacrificed and peritoneal exudate cells were harvested by lavage with Hanks’ balanced salt solution (HBSS; Sigma Chemical Co.) and kept on ice.  Total cell numbers were counted and percentages of neutrophils and macrophages were determined by differential counting of Wright-Giemsa stained cytospins (100-200 cells per sample) using a light microscope.   The preparations were composed of approximately 30% monocytes, 60% neutrophils and 7-10% lymphocytes in both the C/EBPe+/+ (wt) and C/EBPe-/- (ko) mice.  To reduce individual variation in subsequent experiments, the cells either from all wild type or all C/EBPe-null mice were pooled prior to probe synthesis (n=1 pooled RNA for wt and n=1 pooled RNA for ko)
Total RNA and protein was isolated from cells using TRIzol reagent as described by the manufacturer (Life Technologies, Inc., Gaithersburg, MD), Dnase I treated (Promega Corporation, Madison, WI) and purified using an RNeasy spin-column (Qiagen, Valencia, CA).  The quality and balance of the RNA samples were tested by electrophoresis on a denaturing agarose gel.

Hybridization and analysis of the Affymetrix GeneChip Murine 11K Set.  The murine 11K set consists of 2 probe arrays (subarray A and B) that allow monitoring of the relative abundance of greater than 11,000 genes selected from the UniGene (8/96 and Build 4.0) and TIGR (Build 1.0 beta) databases (Affymetrix Inc, Santa Clara, CA).  Biotinylated cRNAs were prepared from the pooled RNA samples and fragmented following the manufacturer’s protocol (Affymetrix Inc.).  The murine 11K A and B arrays were prehybridized and hybridized as instructed by the manufacturer using the GeneChip Fluidics Station 400 (Affymetrix Inc.).  The probed arrays (n=1) were scanned with a Hewlett Packard Gene Array scanner.  The scanned images were analyzed to generate the quantitations based on the images using GeneChip 3.1 software (Affymetrix Inc.).  The default settings of the software were used for the analysis.
Keywords = CEBPE peritoneal macrophage neutrophil knockout
Keywords: other

first: Utz

last: Krug

last: O'Kelly

first: Eun

last: An

first: Vijaya

last: Vegesna

first: H. Phillip

last: Koeffler


title: C. elegans embryonic timecourse in wt and mutant embryos

status: Public on Apr 01 2005

city: Cambridge

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

summary:
This series of samples comprises multiple early embryonic time courses for C. elegans.  Time courses consisting of 10 time points each for 4 different genotypes are included: wild-type  (strain N2 grown on E. coli strain OP50), pie-1(zu154) (progeny of homozygous mutant mothers [Unc] of strain JJ532 grown on E. coli strain OP50), pie-1(zu154);pal-1(RNAi) (progeny of homozygous mutant mothers [Unc] of strain JJ532 grown on E. coli strain HT115 expressing pal-1 hairpin RNA), and mex-3(zu155);skn-1(RNAi) (progeny of homozygous mutant mothers [Dpy] of strain JJ518 grown on E. coli strain HT115 expressing skn-1 hairpin RNA).  Embryos were manually staged by morphology at the 4-cell stage and allowed to develop in water for defined amounts of time at 22 degrees C.  RNA was amplified as described (Baugh et al. Development, 2003; Baugh et al. Nucleic Acids Research, 2001).  This series of samples comprises all replicate data reported by Baugh et al. (Development, 2005).
Keywords: time-course

middle: Ryan

last: Baugh

first: Julia

middle: M

last: Clagget

first: Kate

last: Hill-Harfe

first: Donna

middle: K

last: Slonim

first: Eugene

middle: L

last: Brown

first: Craig

last: Hunter


title: SARS

status: Public on Jan 18 2005

city: Singapore

first: Jayapal

last: Manikandan

institute: NUS

summary:
4 controls and 10 SARS samples
Keywords: other

first: Manikandan

last: Jayapal

first: Renji

last: Regunathan

first: Alirio

middle: J

last: Melendez

first: Dessmon

last: Tai

first: Bernard

middle: P

last: Leung

last: Reghunathan

first: Li

middle: Y

last: Hsu

first: Hiok

last: Chng


title: PTSD Raw Data

status: Public on Nov 20 2004

city: Jerusalem

first: Noa

last: Shefi

department: Computer Science

institute: Hebrew University

summary:
PTSD - Posttraumatic stress disorder.
33 samples taken from PMBCs of survivors of psychological trauma, in two time points: in ER, few hours after the truma, and four months later. Some of the patients devepled chronic PTSD (17 samples) and others recovered and set to be the Control group (16 samples). This is the raw data consists of 12,600 probes from U95A chip.
Samples are labeled with 3 tags: P/C for PTSD or Control, ER/M4 - for time point of sample, D/ND for Decrement or Non-decrement symptoms over time. (e.g. sample 23C-M4-D was taken 4 months after trauma from patient 23 which belongs to the control group and showed decrease in symptoms) . Samples include the expression value, the GeneBank accession number and Affymetrix indication of valid calls.
Keywords: other

first: Ronnen

last: Segman

first: Tanya

last: Goltser

first: Nir

last: Friedman

first: Naftali

last: Kaminski

first: Arieh

last: Shalev


title: PTSD Normalized data

summary:
PTSD - Posttraumatic stress disorder.
33 samples taken from PMBCs of survivors of psychological trauma, in two time points: in ER, few hours after the truma, and four months later. Some of the patients devepled chronic PTSD (17 samples) and others recovered and set to be the Control group (16 samples). This is the normalized active genes: 4512 probes from U95A chip.
The raw data is available in series GSE845.
Samples are labeled with 3 tags: P/C for PTSD or Control, ER/M4 - for time point of sample, D/ND for Decrement or Non-decrement symptoms over time. (e.g. sample 23C-M4-D-Norm was taken 4 months after trauma from patient 23 which belongs to the control group and showed decrease in symptoms) . Samples include the expression value, the GeneBank accession number and Affymetrix indication of valid calls.
Keywords = PTSD
Keywords = Normalized
Keywords = PMBC
Keywords: other


status: Public on Nov 13 2004

city: Madison

first: Thomas

middle: William

last: Jeffries

address: One Gifford Pinchot Drive

institute: Institute for Microbial and Biochemical Technology

summary:
Response of Saccharomyces cerevisiae engineered for xylose metabolism to changes in carbon source and aeration
Keywords: ordered

first: Yong-Su

last: Jin

first: Jose

last: Laplaza

middle: W


title: Glucose dependent cell size is regulated by novel GPCR system

status: Public on Dec 08 2004

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

summary:
Experiment design
Type of experiment: Gene expression profiling analysis of S.cerevisiae W303-1a.
Experimental factor: genetic variation (WT, gpr1 and gpa2 mutant strains).
Number of hybridizations: 6. Single-colour labeling was performed for each sample.
Sample preparation:
Total RNA was prepared using FastRNA Pro Red Kit  (BIO 101 Systems) according to the manufacturers' instructions.

Labeling protocol
10 µg of total RNA was reverse transcribed using the SuperScript Choice system for cDNA synthesis (Life Technologies) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Genset Oligo).  Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf). In vitro transcription was performed on 1 µg of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

Hybridization protocol
10 µg of fragmented cRNA were hybridised (45°C, 16 hours). Hybridization was controled by use of the GeneChip™ Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 400 (Affymetrix) using the protocol EukGE-WS2v4.

Measurement data, specifications and data processing
Scanning was performed in an Affymetrix GeneChip scanner. Chip analysis was performed using the Affymetrix Microarray Suite v5.
Changes in gene expression were assessed by looking for concordant changes between all replicates using a signed Wilcoxon rank test. The “change” p-value threshold was       < 0.025 for increase and > 0.975 for decrease.

Array design
Microarray analysis was performed using YGS98 GeneChips™ oligonucleotide arrays (Affymetrix #900256) representing approximately 6000 ORFs. Sequences and GenBank accession numbers of all probe sets are available at the Affymetrix home page http://www.affymetrix.com/index.affx.

Keywords: ordered

first: Hisanori

last: Tamaki

first: Cheol-Won

last: Yun

first: Makiko

last: Shinozaki

first: Tonohiro

last: Mizutani

first: Takamichi

last: Tsuzuki

first: Yukinobu

last: Takagi

first: Yukiko

last: Kodama

first: Hidehiko

last: Kumagai


title: Epididymal fat tissues-DU6/DU6i-DUKs/DBA

status: Public on Nov 09 2004

city: Berlin

first: Soner

last: Aksu

institute: Humboldt-Universität zu Berlin

summary:
Pooled RNA samples were prepared for each of the four mouse strainsDU6, DU6i, DUKs, and DBA by epididymal fat tissues of 42 days old 20 male per lines. Pooling was used to reduce individual variability, which is high in outbred populations. For the hybridization of the tissue specific RNAs to the GeneChips, samples were prepared according to the recommendations of the Affymetrix user guide. First strand synthesis was carried out by a T7-(dT)24 primer and SuperScript II Reverse Transcriptase (Gibco BRL, Life Technologies GmbH, Eggenstein, Germany) using 10 mg whole RNA sample. Second strand synthesis was done according to the SuperScript Choice System (Gibco BRL, Life Technologies GmbH) by E. coli DNA-Polymerase I, E. coli Ligase and RNaseH. Fragment end-polishing was performed using T4-Polymerase. An in vitro transcription reaction was used to incorporate Biotin-11-CTP and Biotin-16-UTP to the cRNA probe (BioArray HighYield RNA Transcript Labeling Kit, Enzo). The fragmented cDNA was hybridized overnight at 45°C to ensure the quality of the probe. The expression levels were calculated with the GeneChip Expression Analysis softwares Data Mining Tool (Version 1.2.) and Microarray Suite (version 4.0.1.) provided by Affymetrix. Initially, hybridization signals on every GeneChip were scaled using all probe sets to minimize differences in overall signal intensities between two arrays allowing more reliable detection of biologically relevant changes in the sample. The Affymetrix decision matrix was used for the assessment of present, marginally present, and absent transcript amounts of a gene in a tested RNA.
Keywords = adiposity
Keywords = selected mouse lines
Keywords = diabetes
Keywords = insulin
Keywords = leptin
Keywords: parallel sample

first: Dirk

last: Koczan

first: Ulla

last: Renne

first: Hans

last: Thiesen

first: Gudrun

middle: A

last: Brockmann


title: Time series serum stimulation of ES cells of different Srf genotype

status: Public on Nov 15 2004

city: boston

first: Gerhard

last: Schratt

institute: Children's Hospital

summary:
Murine ES cells of different Srf genotype (E14wt, E100-/-, E100-/- rescue (Srf transgene)) were stimulated with FBS for 0-180 min. RNA was harvested and hybridized to Affymetrix MGU74A arrays.
Keywords: time-course

first: Ulrike

last: Philippar

first: Christoph

last: Dieterich

first: Judith

last: Mueller

first: Petra

last: Galgoczy

first: Felix

last: Engel

first: Mark

last: Keating

first: Frank

last: Gertler

first: Roland

last: Schuele

first: Martin

last: Vingron

first: Alfred

last: Nordheim


title: Phosphomannose isomerase gene (PMI40) deletion strain cultivated in varying initial mannose concentrations

status: Public on Nov 10 2004

city: Helsinki

first: Anssi

last: Torma

address: Haartmaninkatu 8

department: Department of Bacteriology and Immunology

country: Finland

institute: Haartman Institute

summary:
YEAST STRAIN:

A genetically modified Saccharomyces cerevisiae yeast strain with PMI40 knockout (MATa URA3 TRP1 LEU2 his3- 1 MAL2-8C SUC2 PMI40::HIS3). The parent strain was CEN.PK113-7A (MATa URA3 TRP1 LEU2 his3- 1 MAL2-8C SUC2) obtained from Euroscarf (9).

CULTIVATION MEDIUM:

The mineral medium used for the bioreactor cultivations was based on the composition described by Verduyn and co-workers (11). The medium consisted of 5 g/l (NH4)2SO4 (Sigma-Aldrich, USA), 3 g/l KH2PO4 (Fluka, Swizerland) and 0.5 g/l MgSO4 × 7 H2O (Sigma-Aldrich, USA), as well as 1 ml/l trace element and 1 ml/l vitamin solution. The composition of the trace element solution was 15 g/l EDTA, 4.5 g/l ZnSO4 × 7 H2O, 0.84 g/l MnCl2 × H2O, 0.3 g/l CuSO4 × 5 H2O, 3 g/l FeSO4 × 7 H2O (Riedel-de-Haën AG, Germany), 0.1 g/l KI, 0.3 g/l CoCl3 × 6 H2O, 1 g/l H3BO3, 4.5 g/l CaCl2 × 2 H2O (Merck, Germany), and 0.4 g/l Na2MoO4 × 2 H2O (BDH Laboratory Supplies, UK). The composition of the vitamin solution was 0.05 g/l D-Biotin, 1 g/l Ca-pantothenate, 1 g/l Nicotinic acid, 25 g/l myo-inositol, 1 g/l Thiamine-HCl, 1 g/l Pyridoxine HCl, and 0.2 g/l p-aminobenzoic acid (Sigma-Aldrich, USA).

The media in each cultivation contained initially 15 g/L D-glucose and a varying amount of D-mannose (0.75 g/L, 1.0 g/L, 1.5 g/L, 3.0 g/L, or 5.0 g/L).

CULTIVATIONS AND SAMPLING:

Bioreactor cultivations were performed in 3.2 l Braun Biostat CT2-DCU 3 instruments (B. Braun Biotech International GmbH, Germany). The cultivation temperature was +30 °C, agitation speed 1000 rpm, initial cultivation volume 2.0 l, airflow 1.0 l/min, and pH 5.0.

In each cultivation, samples for the measurement of gene expression levels were taken 6 hours after inoculation.

MEASUREMENT OF GENE EXPRESSION LEVELS:

0.9 mg CDW of cells were quenched in cold (-40 °C) methanol (45%) and centrifuged (1 min, +4 °C, 16100 G). The pellets were suspended in 400 µl of breaking buffer (20 mM Tris-HCl  pH 7.4, 100 mM KCl, 2 mM MgCl2, 2mM DTT), 400 µl 1:1 phenol-chloroform, and 5 µl 20% SDS. Equal volume of glass beads (diameter 0.40-0.60 mm, B.Braun Biotech International, Germany) were added and samples were shaken in a bead beater (Mini-BeadBeater-8, BioSpec Products, USA) three times 1 minute at +4 °C. The mixtures were centrifuged (15 min, +4 °C, 16100 G in 5415 R, Eppendorf AG, Germany) and supernatants were recovered. The total RNA was purified from the supernatants using the QIAGEN RNeasy Mini kit (Qiagen, USA) according to manufacturers instructions. After this step the double-stranded cDNA was synthesized from 15 µg of total RNA with SuperScript Double-Stranded cDNA synthesis kit (Invitrogen, USA) using a T7-oligo(dT) primer. Biotin-labeled cRNA was then synthesized employing an Enzo High Yield RNA Transcript Labeling Kit (Enzo Life Science, USA). The biotin-labeled cRNA was heat-fragmented and biotinylated cRNAs were hybridized to Affymetrix YG-S98 microarrays in Affymetrix Hybridization Oven 640. Washing and staining of arrays were performed using the GeneChip Fluidics Station 450 and scanning with the Affymetrix GeneChip Scanner 3000. Acquisition and quantification of array images were performed using the Affymetrix GeneChip Operating System 1.0. The signals were scaled into target intensity of 100. All samples were assayed in triplicates.

Keywords: dose response

first: Juha-Pekka

last: Pitkanen

first: Susanne

last: Alff

first: Laura

last: Huopaniemi

first: Pirkko

last: Mattila

first: Risto

last: Renkonen


title: Response of yeast to tomatidine treatment

status: Public on Nov 06 2004

city: Bracknell

first: Adam

middle: Alexander

last: Cleaver

institute: Syngenta

summary:
Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine.

Overnight  batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1.  After 1 hour of growth at 30°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM.

Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen.  Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA).  Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001).   Data were analyzed using Affymetrix® Microarray Suite version 5.0 software

Keywords: dose response

first: Veronika

last: Simons

first: John

last: Morrissey

first: Maita

last: Latijnhouwers

first: Michael

last: Csukai

first: Anne

last: Osbourn


title: SRF-VP16 overexpression in ES cells

first: Gerhard

last: Schratt

summary:
Empty vector, SRF-dM-VP16 (control construct lacking the SRF DNA binding domain), or SRF-VP16 were expressed in wild-type ES cells (E14wt), SRF heterozygotes (E99-/+) or two SRF ko cell lines (E81-/-,E100-/-). RNA was harvested 72h after transfection. Each condition was performed in duplicate, except E100-/- vector transfected.
Keywords: ordered

first: Ulrike

last: Philippar

first: Christoph

last: Dieterich

first: Judith

last: Mueller

first: Petra

last: Galgoczy

first: Felix

last: Engel

first: Mark

last: Keating


title: Ifh1 activates RP genes

city: Geneva

first: Stephan

middle: B.

last: Schawalder

address: Quai Ansermet 30

department: Departement of Molecular biology

country: Switzerland

institute: University of Geneva

summary:
Experiment Design:
•Type of experiment: time course after GAL (galactose) induction
•Experimental factor: time, genotype
•Number of hybridizations performed in the experiment: 24 (eight conditions with three biological replicates each)

Samples used, extract preparation and labeling:
•The origin of the biological sample:
Species: S. cerevisiae
Cell type:
wild-type (YSS37, IFH1-13myc-TRP1, MATa)
UASIFH1::HIS3-UASGAL1 (YSS89, UASGAL1-IFH1-13myc-TRP1, MATa)
•Growth conditions: log phase (2x107/mL) at 30°C in YPLG medium, then addition of Galactose to 2%
•Treatments: all cells were harvested by rapid centrifugation at 4°C then flash frozen in liquid nitrogen.
Keywords = IFH1
Keywords = Transcriptional control of RP genes
Keywords: time-course

middle: B

first: Mehdi

last: Kabani

first: Urmila

last: Choudhurry

first: Isabelle

last: Howald

first: Michel

last: Werner

first: David

last: Shore


title: A novel response to microtubule perturbation in meiosis

status: Public on Oct 18 2004

city: Basel

last: Primig

state: Basel Stadt

address: Klingelbergstr 50-70

department: Genome Bioinformatics

institute: Biozentrum and Swiss Institute of Bioinformatics

summary:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30C. Cells were washed with sterilized water the next day and re-suspended in SPII medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 to induce sporulation. Cells were sporulated at room temperature or 30C as indicated. Sporulation medium containing benomyl was always prepared freshly on the day of the experiment following the directions in {Shonn, 2000 #90}. Briefly, DMSO (dimethyl sulfoxide, Sigma-Aldrich) or benomyl [Methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, Sigma-Aldrich; 30 mg/ml stock in DMSO] was dissolved in near-boiling SPII medium to avoid precipitation. The medium was then allowed to slowly cool to 30C or room temperature. At the time of drug treatment, cells were filtered and immediately re-suspended in the medium containing benomyl or DMSO.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint
Keywords: ordered

first: Andreas

last: Hochwagen

first: Gunnar

last: Wrobel

first: Marie

last: Cartron

first: Philippe

last: Demougin

first: Christa

last: Wiederkehr

first: Monika

last: Boselli

first: Angelika

last: Amon


title: IL-2 transfection of A673-cells

status: Public on Oct 11 2004

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary: Response of A673-cells to transfection with interleukin 2 (IL-2). Ewing family tumor (EFT) cell line A673 was transfected with an expression vector for IL-2 (cell line SBVGA1) or empty control vector (cell line SBVGA3). Cells were harvested at 3 different time points and processed for DNA-microarray analysis using Affymetrix HG-U95A microarrays. Primary image analysis was performed using MAS 5.0. In addition, primary analysis was performed with MAS 4.0 and data were scaled to an target intesity of 200. These data have been analysed together with other published data that have been scaled to the same target intensity (see Staege et al. Pediatr Blood Cancer 2004 Jul;43(1):23-34. See also Staege et al. Cancer Res. 2004).

middle: S

first: Christoph

last: Hutter

first: Ingo

last: Neumann

first: Sabine

last: Foja

first: Uwe

middle: E

last: Hattenhorst

first: Gesine

last: Hansen

first: Danny

last: Afar

first: Stefan

last: Burdach


title: Rheumatoid arthritis

status: Public on Nov 04 2004

first: Ute

last: Ungethuem

department: Core Center for Functional Genome Research

institute: Charité University Hospital

summary:
Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from osteoarthritis patients and to normal donors.
Keywords: disease state analysis

overall_design: Two disease conditions (rheumatoid arthritis and osteoarthritis) in comparison to normal donors were investigated. For the two disease groups samples derived from three individual patients and two pools of patients were hybridised.

last: Blaess

first: Hans-Juergen

last: Thiesen

first: Dirk

last: Koczan

first: Thomas

last: Haeupl

first: Henning

last: Witt


title: Isolation of mRNA from fly photoreceptor cells by mRNA tagging

city: Houston

first: Zhiyong

last: Yang

state: TX

institute: Baylor College of Medicine

summary:
The method of mRNA tagging was recently developed to isolate mRNA population from muscle tissues in Caenohabditis elegans. This method utilizes a FLAG-tagged poly(A)-binding protein (PABP), which can bind to poly(A)-tail of eukaryotic mRNA. Thus, the mRNA population from specific tissue, in which FLAG- tagged PABP is expressed, can be co-immunoprecipitated with FLAG-tagged PABP using FLAG-specific antibody. To evaluate the applicability of this method to isolate mRNA from specific tissue in Drosophila, we generated Rh1-GLA4/P{UAS-dPABP-FLAG} flies which express a FLAG-tagged PABP in  photoreceptor cells R1-R6. We then prepared 4 individual mRNA samples (subset 1: GSM30900-30903)) presumably from photoreceptor cells of these flies by mRNA tagging method. We also prepared 4 individual mRNA samples (subset 2: GSM30832-30835) from whole heads of the Rh1-GAL4/P{UAS-dPABP-FLAG} flies, as well as 6 individual mRNA samples (subset 3: GSM30824-30828, GSM30830) from whole heads of wild type Canton-S flies. The total 14 mRNA samples were used to synthesize target separately and each of the resultant target was used to hybridize with 1 Drosophila Genome Array DrosGenome1 Affymetrix GeneChip. The raw data of the 14 microarray were imported to dChip program (version 1.3). The arrays were normalized to a common baseline array that has the median overall brightness. The expression value for each probe set on each chip was then calculated as model-based expression index (MBEI) by Perfect Match-only model. By comparing the results of subset 1 and subset 2, we found most known photoreceptor-specific genes were indeed enriched by mRNA tagging. Through the comparison of the results of subset 2 and subset 3, we found the mRNAs of most genes known to be involved in fly visual function were underrepresented in subset 2, which could be due to squelching effect of GAL4. By combining the data of subset 1, 2 and 3, we were able to identify 11 new photoreceptor cell-enriched genes.
Keywords: other

first: Howard

last: Edenberg

first: Ronald

last: Davis


title: Transcriptional effects of the TOR2-controlled signaling function

status: Public on Oct 15 2004

first: Dietmar

last: Martin

department: Division of Biochemistry

institute: Biozentrum University of Basel

summary:
We analysed the transcriptional effects of the TOR2-controlled signaling function using a genome-wide microarray approach in yeast. In S. cerevisiae, TOR2 has two essential signaling functions. One, shared with TOR1, is required for translation initiation, transcription, and cell growth in response to the presence of nutrients. The second is unique to TOR2, and functions in cell-cycle-dependent actin polarization and possibly in transcription. A previous genetic screen for mutants defective in the TOR-shared and the TOR2-unique functions identified several TOR2 temperature-sensitive alleles. In this study, we compared total transcription profiles for strain SH121, which is specifically defective in the TOR2-unique function, and its isogenic wild type counterpart SH100.
Keywords = TOR
Keywords: time-course

first: Philippe

last: Demougin

first: Michael

middle: N

last: Hall

first: Michel

last: Bellis


title: A549 parenchymal cell activation

status: Public on Oct 03 2004

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: Ontario

address: 200, Elizabeth Street

department: Critical Care

country: Canada

institute: Toronto General Research Institute

summary:
Alveolar epithalial cells (A549) were used as a model of pulmonary parenchymal cell activation to quiery gene expression profile of activation with either cyclic stretch (20% elongation), TNF (20 ng/ml), LPS (1 mcg/ml) or TNF+STRETCH at both 1 and 4 hrs.
Keywords: time-course

middle: C

first: Bing

last: Han

first: Xiao-hui

last: Bai

first: Monika

last: Lodyga

first: Melanie

last: Tsang

first: Cristiano

last: Andrade

last: Uhlig

first: Rolf

last: Hubmayr

first: Shaf

last: Keshavjee

first: Arthur

last: Slutsky

first: Mingyao

last: Liu